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-[{"content":"Welcome to my site! My name is Zachary Billman. I\u0026rsquo;m an MD-PhD student at UNC Chapel Hill in Ed Miao\u0026rsquo;s lab. The curious reader may be thinking: \u0026ldquo;But Zach, Ed Miao\u0026rsquo;s lab is at Duke now! What does that make you?\u0026rdquo; What an astute question! I am a card-carrying UNC Microbiology and Immunology student who happens to have all of their research take place at Duke. This move was quite a trial, especially when compounded with the onset of the pandemic. I suspect my research timeline suffered, though this is an extremely minor inconvenience compared to the tragedy the pandemic caused. This makes for very interesting basketball viewing parties with my Duke friends!\nMy research and scientific interests. I am broadly interested in innate immunology. I am in the 4th year of my PhD studying the host-pathogen interaction between the intracellular fungus Histoplasma capsulatum and macrophages. There are many unstudied curiosities regarding the innate immune response to Histoplasma spp. and other intracellular fungi that I think are quite interesting. Stay tuned, hopefully there is a major breakthrough to report here someday.\nHobbies I may write about. Besides my science, I am interested in birding, baking sourdough bread (I swear I began years before the pandemic, though hearing of people baking bread brings me joy no matter when they first began!), board games, roasting coffee, and self-hosting free and open source software. Over the course of the pandemic, I have learned how to maintain a basic suite of services on a server I rent that have replaced my need for Google Photos and Google Drive. I\u0026rsquo;m hoping to be able to move away from these platforms entirely soon. I think they provide a great service, but at a substantial cost to privacy. Hopefully more to be said about my thoughts on FOSS soon! I also transitioned my old, (and quite frankly, embarrassingly slow) managed WordPress site with this lean, static site made in Hugo that I host myself. Now that I have mangled together some CSS to get my precious sidenotes up and running again, I\u0026rsquo;m ready to begin putting some ideas to paper. I love marginalia. I\u0026rsquo;m not sure if this is unique to me, but I seem to get caught up in parenthetical / tangential thoughts very often, and I think using an Edward Tufte-esque sidenote is a great way for me to communicate in this way without distracting the reader too much. It seems marginalia such as this have been used throughout history, so perhaps it is normal, but most people can keep their thoughts focused better than me. The implementation I use is inspired by the Tufte CSS project and largely taken from this incredibly helpful post found at scripter.co. I\u0026rsquo;m quite proud of my progress in administering my server and self-hosting useful services.\nThe future of this site. On this site I plan to post updates about my journey through med school, grad school, and self-hosting I would like to share with the world. I have been helped immensely by many others\u0026rsquo; advice and I hope to impart similar tips to others someday. I suspect most posts will be about much lighter fare, like whatever hobbies tickle my fancy at the time.\n","permalink":"https://www.zacharybillman.com/posts/about-me/","summary":"\u003ch2 id=\"welcome-to-my-site\"\u003eWelcome to my site!\u003c/h2\u003e\n\u003cp\u003eMy name is Zachary Billman. I\u0026rsquo;m an MD-PhD student at UNC Chapel Hill in Ed Miao\u0026rsquo;s lab. The curious reader may be thinking: \u0026ldquo;But Zach, Ed Miao\u0026rsquo;s lab is at Duke now! What does that make you?\u0026rdquo; What an astute question! I am a card-carrying UNC Microbiology and Immunology student who happens to have all of their research take place at Duke.\n\u003cspan class=\"sidenote-number\"\u003e\u003csmall class=\"sidenote\"\u003e\nThis move was quite a trial, especially when compounded with the onset of the pandemic. I suspect my research timeline suffered, though this is an extremely minor inconvenience compared to the tragedy the pandemic caused.\n\u003c/small\u003e\u003c/span\u003e\nThis makes for very interesting basketball viewing parties with my Duke friends!\u003c/p\u003e","title":"About me. 👋"},{"content":"It\u0026rsquo;s over. My third year of medical school is officially behind me. I managed to get in a grand total of zero blog posts during grad school, so here\u0026rsquo;s to a new year with hopefully some more thoughts being shared. I have a lot to reflect on from the past year. It was wonderful. I wish everyone could experience what I did this past year. I think it goes without saying:\nI loved the third year of med school, but I do not want to do it again.\nA year of change. In the days leading up to my return to med school, I thought \u0026ldquo;Oh no, I really enjoy doing science, do I really have to go to med school?\u0026rdquo;. I also remember at the end of Step 1 and the first two years of med school thinking, \u0026ldquo;Oh no, I really enjoy med school, do I really have to do science again?\u0026rdquo;. I think I have a welcome problem of enjoying what I\u0026rsquo;m doing. The third year of med school is a shift. After years of memorizing and examinations, the doors to the promised land are finally opened. I have experienced nothing like it before It feels intentionally unsettling. You are thrown into the clinic with a modicum of guidance so you aren\u0026rsquo;t totally caught off guard, but you are thrown out to the wolves. I don\u0026rsquo;t mean this as a criticism of the system, it feels necessary. Third year medical students—commonly shorted to MS3s—have just one year to experience a broad swath of medicine and pick a specialty. So you had better be ready to dive in.\nTotal immersion I came to terms with my new reality quickly. Gone were the days of hitting the snooze button and going home when I pleased. I am now beholden to other people\u0026rsquo;s schedules. This came back relatively naturally. Maybe not hitting snooze. A regrettable personal failing of mine. I was, however, immediately faced with a new reality in the patient room. Patients come to the doctor for a number of reasons, but often seek relief. To get to the core of what ails them, they will tell you everything. I was not prepared for how vulnerable patients would be with me. I am not sure if this ever will feel natural. I hope it never does. I was told many stories of experiences living with scary diagnoses, and not knowing what to do with it. Family histories of all sorts. Personal details that were sometimes (oftentimes?) off the wall. I see all of these specifics as flailing, grasping at sand hoping that something could explain their pain. Sometimes it could. Usually it did not. But since I was in a white coat, I was privileged to hear it.\nI think my years spent in the lab have prepared me to face some of the challenges set before me. At the very least, having a few more years under my belt helped me approach the year with a bit of maturity. This seems to have paid off. I guess my recommendation is to simply get old before going to med school. Returning to studying The hospital is how I spent the majority of my time, but a new reality for me was also going back to daily studying. There is a strange dichotomy in medicine of \u0026ldquo;Oh, it doesn\u0026rsquo;t really matter\u0026rdquo; and \u0026ldquo;If you don\u0026rsquo;t get this class/score/grade then you won\u0026rsquo;t be able to be the kind of doctor you want to be, so you had better get your act together.\u0026rdquo; Simultaneously there are no expectations and immense responsibility for the looming specter of Step 2. I\u0026rsquo;m glad that studying regularly came back easily enough. I was concerned I would experience a studying whiplash. I\u0026rsquo;m glad it never came. I did UWorld and Anki nearly every day for a full year and felt alright.\nBecoming invisible I quickly learned I needed to change my understanding of my contribution to the team. Exiting grad school, people understood that they could come to me for help. I was a resource, a seasoned veteran of the lab. If someone needed an experiment done, I could do it, and be trusted to do it. In med school as a third year, I was nothing. A fly on the wall; a worm beneath the feet of the real doctors. In science, I felt like I was treated as a peer with even my committee members with multiple R01s. Even if I didn\u0026rsquo;t understand the science perfectly, I could contribute some different perspective. In medicine, sometimes not being recognized at all by my attendings was the best outcome. Which happened regularly. My role, was not as a contributor—as it was in science—it was simply to get in the reps. Once I understood that the expectations of me were below the ground, I understood that everything I did in third year was for myself. This is taken at face value by the team at times. I would spend 30 minutes working on a presentation, pre-rounding, the works, and at the end of my part, the intern would nod, then turn to the senior resident and say \u0026ldquo;I was thinking that we\u0026hellip;\u0026rdquo; without thinking of my work. This is perhaps a bit of cognitive restructuring, but recognizing this is what gave me the freedom to embed myself in the hospital flow, without a single worry about the outcome. Simply doing my best was the best thing I could do. Obviously. But this was not apparent to me at first. I needed more quality repetitions to develop good habits in the future. And also experience as much of medicine as possible to find what I want to do with my life. This permission allowed me to approach specialties I do not care about with the awe and respect they deserve.\nA year of wonder. Med school prepares you for the standardized tests. I think this is generally useful. The tests on aggregate are reasonable and evaluate your ability to think through common clinical scenarios. There will always be oddball questions that come out of left field, but I let these flow over me. No need to perseverate on the small stuff. The time for that can come later.\nWhat I didn\u0026rsquo;t realize is how much of the \u0026ldquo;classic\u0026rdquo; material we are fed in the first couple years of med school would come to the forefront. The \u0026ldquo;sandpaper rash\u0026rdquo; of scarlet fever really does feel like sandpaper. Nikolsky\u0026rsquo;s sign actually works. Tripoding for epiglottitis gets the physicians worked up. Don\u0026rsquo;t forget about von Willebrand\u0026rsquo;s disease when someone seems to be bleeding a bit too much. TB is out there, watch for hemoptosis. Night sweats, unintended weight loss, is cancer until proven otherwise. And yes, it really can be lupus.\nIn general, facing the unknown with a sense of earnestness was the way I felt best able to respect those who gathered and passed down the medical knowledge I am privileged to learn today. Sometimes, my excitement to see aspects of medicine would rouse a curious response from the residents. I project here, but I felt a sense of surprise, like that of a doting parent seeing their child experience something new, after forgetting the astonishment they once felt.\nEarnestness is next to med studentlyness.\nPerhaps what I\u0026rsquo;m getting at here is that I found it important to bask in the privilege of seeing the pathology I encountered in med school, and to remind the residents of this sensation. I felt childish at times—and perhaps overanimated—but I found this excitement was to my and my resident\u0026rsquo;s benefit.\nMy surgery rotation overflowed with examples of wonder of medicine. Partially because of the team I worked with, and the rest because of the undeniable coolness of surgery. The OR is a cool place. The orderliness and chaos ebb. The spans of steady, industrious work are interrupted with staccato notes of bedlam. The anatomy I learned in class was ever present, but the surgeons bemoaned \u0026ldquo;normal anatomic variation\u0026rdquo;.\nI was struck with wonder at the sight of human anatomy as it unfolded before me. What I was able to experience in the OR felt like the culmination of centuries of human curiosity. There is an ancientness to medicine that I catch flashes of—I could perform the physical exam on humans hundred of millions of years ago and interrogate the same pathologies as I do in the hospital today—and viewing the exposed anatomy is a pressure-bagged infusion of this collective wonder. To gaze upon the peristalsing of the small intestine, or steady beating of the heart is a sight to behold, indeed.\nA year of shame. It weighs upon me the circumstances that resulted in these transcendent experiences. Not one patient was in the hospital without reason. What to make of these patients with horrible pathology? I still feel unsettled about how the cause of their pain sparked wonder. How dare I gain, merely by the circumstance of having their care managed at UNC, Which, as a tertiary care center, layers on more complexity. Many patients end up at UNC because they have no where else they can go for help. And this signs them up for med students? For shame. from the very essence of their malady? I do not know what to do with my discomfort, but I think it is best that I dwell in it. With this, I respect the people before me in the hospital and recognize their humanity.\nBut I often complained of what I say here I was lucky to do. I find myself resentful of my future schedule; when was I supposed to learn that I will be working 13 hour days, 6 days a week for the rest of my life? And what of having a family? Medicine by necessity requires sacrifice. I happened to sign up for sacrifices years before I recognized how profound they were. How might I balance this dread and with the joy of practicing medicine? And why do I seem more concerned about this than others? Am I not grateful enough? Am I not capable of the sacrifices that others seem to offer so effortlessly? I don\u0026rsquo;t necessarily think this to be true, but these questions erode at my will to pursue medicine.\nPerhaps most shameful of all is how my understanding of the patient-provider interaction evolved over the year. It began as an exploration of an open book, a tabula rasa that held within it a diagnosis and how to best intervene. On my first day in the outpatient clinic, it was clear that this is not the case. My preceptor had only 20 minutes for me to ① interview the patient and perform the physical exam, ② present with a plan, ③ return to the room and do everything again, ④ write orders, educate, and get the patient out of the door. It simply is not amenable to the free form, personable, curious interview I hoped to perform. By the end of the year, I had optimized how I asked questions to keep patients from going off the rails. When prerounding in medicine, I was there to extract information and not much else. Small talk had to go, there was no time. I like to chat, so this came at a loss of who I think I am. I am not sure how to do this well, while still feeling like Zachary. And from what I gather from the interns, that may just come later in my career. I found myself questioning, \u0026ldquo;Is this the \u0026lsquo;patient interaction\u0026rsquo; that has been mythologized throughout my training?\u0026rdquo; The carrot at the end of the stick dangled before me with a \u0026ldquo;You are so lucky to be able to do this, so you had better not complain of any abuse that comes your way.\u0026rdquo; It wasn\u0026rsquo;t a genuine interaction as much as me leading the patient along to tell me what I wanted to know. Of course, I used open ended questions, but only open enough. Leave the door a bit too open and next thing you know, you are talking about their dog\u0026rsquo;s breeder while you constantly stare at your watch, imagining what your attending will say when you return. I feel like I am alone in missing the core human element that funnels sprightly youths into medicine. Or worse, finding it a façade.\nThe shame extends beyond the hospital. One aspect of my life that has changed most dramatically is the sheer amount of time I felt I needed to dedicate to medicine, whether at the hospital or at home. I spent all day basking in the wonder of medicine, then I would come home and study for hours. I relied on my partner for keeping our household together more than ever, because I spent all day—all year, rather—in a state of discovery. Her life was largely the same, with the normal challenges of being a scientist, with the added bonus of getting less help from me. The shame built over the year. Again, how dare I?\nA year of glad. This has been an undeniable year of growth and joy, with these quibbles. It is clear that I was happier than I was during grad school. I know this from within myself, and reinforced by my wife\u0026rsquo;s comments on my mood. The pace of the day, and immediacy of problem solving were a welcome change.\nI recall, during the very first days preparing for med school during xTAP, having to do a simulated patient encounter complete with patient presentation to an attending physician. We were told about this encounter days in advance. And yet, I dreaded it. And near the last day of my final rotation, I did 8 of these in a row without breaking a sweat. Progress!\nI think, in a word, what I\u0026rsquo;ve experienced in the third year of med school is gratitude. Gratitude to be privileged to learn what I am learning. Gratitude for the experiences in my life that brought me here. Gratitude for the support from my wife. Gratitude to be involved in people\u0026rsquo;s lives when they are fragile. Ever since reading Braiding Sweetgrass I think one could call me \u0026ldquo;gratitude-pilled\u0026rdquo;. I also selfishly enjoyed the gratitude from patients as I put on my best doctor performance. In reflection on the year, I have spent time thinking of a phrase that I heard a number of times throughout med school from residents, \u0026ldquo;The worst day of residency is better than the best day of med school.\u0026rdquo; I find this hard to believe. This year has been magical. It is hard to imagine a year filled with more wonder and joy of caring for those in need. I will have to rely on the experience of those who have walked this path and trust that the rest of my training has plenty of magic to spare.\n","permalink":"https://www.zacharybillman.com/posts/ms3-year-is-magical/","summary":"\u003ch2 id=\"it-s-over-dot\"\u003eIt\u0026rsquo;s over.\u003c/h2\u003e\n\u003cp\u003eMy third year of medical school is officially behind me. I managed to get in a grand total of \u003cem\u003ezero\u003c/em\u003e blog posts during grad school, so here\u0026rsquo;s to a new year with hopefully some more thoughts being shared. I have a lot to reflect on from the past year. It was wonderful. I wish everyone could experience what I did this past year. I think it goes without saying:\u003c/p\u003e","title":"The third year of medical school is magical."},{"content":"I, like many others, picked up a new hobby during the pandemic. Other people\u0026rsquo;s hobbies may bring them joy. This could be for many reasons. There is the joy of creating something from scratch. You can revel in your thriftiness. You can embrace the pride when you recognize that your creation is on par (or better!) than what you can buy. I feel like these are embodied in the sourdough craze that caught fire early on in COVID. Dare I say that I did this before it was cool? \u0026#x1f60e; I baked two loaves of bread almost every weekend through med school. Maybe I should bring that back, it\u0026rsquo;s been a while since I brought out the ole\u0026rsquo; starter. My pandemic hobby is similar, but different in that it often feels like a chore, costs more money, and often turns out worse than what I can buy. Of course, I am talking about how I\u0026rsquo;ve started roasting my own coffee at home.\nI\u0026rsquo;m not sure where this idea was planted into my brain. I don\u0026rsquo;t think I know anyone who roasts their own beans, and I certainly didn\u0026rsquo;t know how. I didn\u0026rsquo;t even drink coffee regularly until after college! I guess that extra time on the computer sent me down a rabbithole I have yet to emerge from.\nFirst, I want to preface the following with a disclaimer: This is not a detailed guide about how to roast your own coffee. If you are interested, I recommend checking out the How To Roast Your Own Coffee guide at Sweet Maria\u0026rsquo;s as a starting point. There is also the /r/roasting subreddit if that is your cup of tea. My only warning is there will be a lot of smoke. Roast your coffee outside, for Pete\u0026rsquo;s sake!\nIt all started with a trusty popcorn popper. There are a few things you want when you roast coffee:\nAir hot enough to roast coffee Remove the chaff from the beans Turns out that a classic popcorn popper fits the bill, as long as it has an upwards airflow and doesn\u0026rsquo;t let the chaff fall into the heating element. There is a bit of a cult following for the West Bend Poppery 2 model, but that one seemed a bit pricey, so I settled for a very capable popper from Nostalgia.\nFigure 1: I got a good bit of mileage out of my popcorn popper. If you are interested in roasting your own coffee I would give it a whirl.\nThings were simple back then. I still bought most of the coffee I drank, but I roasted enough to enjoy some freshly roasted coffee as an occasional treat. I ordered 10 pounds of green beans from Sweet Maria\u0026rsquo;s and life was good.\nThen I became a bit of a coffee snob.\nI could only roast 100 grams of coffee at a time in the popcorn popper, which is only enough for one pot of coffee in the morning for me. So it was time to upgrade.\nI bought the SR800 fluid bed roaster, which upped my roasting capacity and gave me finer control on temperature and airflow. Suffice to say my roasts improved a lot! At this point, I would consider my coffee good enough to sell at a farmer\u0026rsquo;s market to break even.\nIf you ever find yourself on a coffee roasting forum and bring up the SR800, someone is bound to bring up the famous RazzoRoasting extension tube. If you look for advice for how to use the SR800, I swear it\u0026rsquo;s assumed that you have this very specific accessory. \u0026hellip;And so I bought one.\nDon\u0026rsquo;t worry, that is the extent of all of my coffee spending (for now). I am a very satisfied coffee roaster now. Check out this quick series of images going from the green beans to a nearly finished product! I can spend about 45 minutes and go from nothing to nearly 2 pounds of roasted beans, enough for about a week and a half of coffee. Not bad! The only downside is that now I feel like I need to buy coffee from local roasters to get my fix. There are certainly crueler fates.\nAs a sign off, I will share something that surprised me about coffee roasting. When I roast coffee, the most important cue to determine if the coffee is roasted is the sound. That\u0026rsquo;s right, not the color, not the smell, but the sound. When heating up a coffee bean, the water trapped inside eventually bursts out of the bean in a rapid expansion. This is called \u0026ldquo;first crack\u0026rdquo;, and indicates that the coffee is roasted enough to be drinkable. The expansion also releases the chaff from the bean. If you continue heating up the bean, you will eventually reach \u0026ldquo;second crack\u0026rdquo;. I think a solid medium roast is taken out just before second crack, so I try to take my coffee out to this point and it hasn\u0026rsquo;t proved me wrong yet.\nHappy coffee-ing! \u0026#x2615;\n","permalink":"https://www.zacharybillman.com/posts/roasting-coffee-at-home/","summary":"\u003cp\u003eI, like many others, picked up a new hobby during the pandemic. Other people\u0026rsquo;s hobbies may bring them joy. This could be for many reasons. There is the joy of creating something from scratch. You can revel in your thriftiness. You can embrace the pride when you recognize that your creation is on par (or better!) than what you can buy. I feel like these are embodied in the sourdough craze that caught fire early on in COVID.\n\u003cspan class=\"sidenote-number\"\u003e\u003csmall class=\"sidenote\"\u003e\nDare I say that I did this before it was cool? \u0026#x1f60e; I baked two loaves of bread almost every weekend through med school. Maybe I should bring that back, it\u0026rsquo;s been a while since I brought out the ole\u0026rsquo; starter.\n\u003c/small\u003e\u003c/span\u003e\nMy pandemic hobby is similar, but different in that it often feels like a chore, costs more money, and often turns out worse than what I can buy. Of course, I am talking about how I\u0026rsquo;ve started roasting my own coffee at home.\u003c/p\u003e","title":"Roasting coffee at home. ☕"},{"content":"It is an age-old question: how can one keep up with the continuous output of science? I remember at the beginning of my PhD struggling to figure out how anyone found out when a new paper came out. \u0026#x1f635; Did they sit on nature.com and spam the refresh button? Did they know when each journal released their latest issue?\nBehold the power of RSS! Most websites have a page that contains information about each subpage in a computer-readable format called RSS (Really Simple Syndication). Mine has one right here! These pages can be parsed by a number of RSS feed aggregators. The way these pages are set up make it such that they add any new information hosted at that domain. This is useful in the science world because you can find the RSS feed of a given journal, subscribe to it, then have every new article published online be delivered right to you.\nThere are a plethora of RSS feed aggregators you can pick from manage your feeds. I have previously used Feedly and Inoreader, which are great free solutions, but have moved on to selfhosting my own instance of FreshRSS.\nAfter making an account at your friendly local RSS feed aggregator, you can add whatever feeds your heart desires. To find a journal\u0026rsquo;s rss feed, I often just search \u0026ldquo;$JOURNAL_NAME rss feed\u0026rdquo; and poke around until I find something that looks right. Most of the aggregators will test the feed out first to make sure that you are trying to add a legitimate one. Here are a few of the heavy hitters to get you started:\nhttp://feeds.nature.com/nature/rss/current https://www.science.org/rss/express.xml https://www.cell.com/cell/inpress.rss Nothing like a constant stream of Cell, Science, and Nature to make your project feel like a real winner, eh?\nHere is what my own site looks like.\nFigure 1: My current FreshRSS setup. On the left I have my feeds separated into folders. In the middle you can see the titles of papers that appear in my feed.\nAnd after I hit J to move to the first item in the feed.\nFigure 2: With a title selected, you can see the abstract and authors.\nAfter collecting all of your desired RSS feeds, you cannot forego your responsibility of actually reading them! Most RSS feed aggregators have shortcuts to move through titles quickly (Typically J to move on to the next one and K to move up.) They always seem to use vi keybindings. A bunch of computer nerds have really cornered the keybinding market. I have let them take over my computing life. Each morning when I get into the lab, I quickly set up something, then head to my desk to hit J until the counter reaches zero.\nBut what about my very specific field? You can subscribe to all of the journals you want, but that doesn\u0026rsquo;t make the papers with your specific interests pop out. Fortunately, the NIH has this exact circumstance in mind.\nWhen you make a new search on PubMed you might notice the \u0026ldquo;Create RSS\u0026rdquo; button. Give it a click, then you will have a personal link you can add to your favorite RSS feed aggregator.\nFigure 3: Somehow I never noticed this button until I needed it.\nThis changed the game for me for keeping up with papers. Unfortunately, it doesn\u0026rsquo;t solve the problem of library management, or actually getting around to reading the papers you care about. I will leave library management as an exercise for the interested reader. Here\u0026rsquo;s a tip, the best solution uses the Zotero citation manager. Bonus points for using Zotfile for renaming your PDFs and Better BibTex for Zotero. \u0026#x1f609; I hope this helps you get your eyeballs on that science you crave. If you have solved the problem of accruing papers to read faster than you read them, let me know.\n","permalink":"https://www.zacharybillman.com/posts/rss-feeds-to-find-science-papers/","summary":"\u003cp\u003eIt is an age-old question: how can one keep up with the continuous output of science? I remember at the beginning of my PhD struggling to figure out how anyone found out when a new paper came out. \u0026#x1f635; Did they sit on nature.com and spam the refresh button? Did they know when each journal released their latest issue?\u003c/p\u003e\n\u003ch2 id=\"behold-the-power-of-rss\"\u003eBehold the power of RSS!\u003c/h2\u003e\n\u003cp\u003eMost websites have a page that contains information about each subpage in a computer-readable format called RSS (Really Simple Syndication). \u003ca href=\"https://zacharybillman.com/index.xml\"\u003eMine has one right here!\u003c/a\u003e These pages can be parsed by a number of RSS feed aggregators. The way these pages are set up make it such that they add any new information hosted at that domain. This is useful in the science world because you can find the RSS feed of a given journal, subscribe to it, then have every new article published online be delivered right to you.\u003c/p\u003e","title":"Using RSS feeds to keep on top of science."},{"content":"My interest in self-hosting began in my with my interests in internet privacy. Plastered all over the internet are stories about how much Google, Facebook and Amazon know about you. I deleted my Facebook account years ago, and I\u0026rsquo;m too paranoid to go back to the site because there\u0026rsquo;s a real possibility that Facebook has cached my account, ready to spin it back up in case I try to login again. The ads served to me were too accurate for my liking. This is despite almost never clicking on them! I have become convinced of the idea that, if you are not paying for the product, you are the product. From this assumption, it follows that anywhere I trust with my data that I am not paying for (like Google Drive, Google Photos, Dropbox, Facebook, Twitter) is using my data to earn money. We know that Google uses the labels you add to Photos to train it\u0026rsquo;s AI, and Facebook uses (at least) Instagram photos to train it\u0026rsquo;s AI. For some, the value proposition of allowing a company to use your data for a useful service in return is an acceptable one. I find this to be a reasonable stance, but I took my growing interest in internet privacy as a chance to learn about how I can take control of my data.\nInitially, I lurked on forums like /r/privacy to learn what I could do to avoid big-tech\u0026rsquo;s watchful eye. There were numerous comments along the lines of: \u0026ldquo;The only way to be in control of your data is to self-host your services.\u0026rdquo; I had no idea what this meant! Hard to believe that less than a year later, I learned to use (and love) Linux as my primary OS, and have happily replaced Google Photos, Google Drive and other services with my own self-hosted alternatives. Self-hosting, I have since learned, is when you run useful programs from your own computer. By doing so, you have complete knowledge of where and how your data is stored and how it is being used. It has the additional effect of being a bottomless time sink.\nTo begin, I needed an always-on computer to run these useful programs. I began with a humble Raspberry Pi.\nFigure 1: My humble Raspberry Pi and its hard drive. This dude currently tirelessly runs the excellent Adguard Home and downloads a backup of my data every night.\nThese are tiny, but capable computers that are great for fiddling with. The projects people develop for these are amazing and diverse. With RPi in hand, I began with the ambitious project of replacing Google Drive with Nextcloud. After much frustration with a bare metal installation, I found the NextcloudPi project. Surprisingly, it went pretty okay! At first, I was intimidated by Linux defaults, but over time I grew to appreciate, and indeed, prefer Linux as an operating system. My decision to use Linux over Windows/MacOS is because it is free and open source software (FOSS). This is a topic for a different post, but I think using FOSS when possible is a moral imperative of sorts. I used Nextcloud strictly from my home for a few months, without the ability to connect to it from the internet, to test the self-hosting waters. My first true cloud replacement spun up once I decided to access this lil\u0026rsquo; guy from the internet. To do so, I purchased a domain (not the one this site is hosted on) and pointed it to the IP of my house. I forwarded the appropriate ports of my router to the RPi.\nThis is when the real exploration began. I was able to access my files and images using Nextcloud, but the photo viewing service left something to be desired. No problem, why not spin up an instance of Photoprism? I use RSS feeds to keep on top of the latest science in the journals relevant to my field using Feedly. Why not host my own RSS feed aggregator so I can subscribe to as many feeds as I desire?\nThis cycle continued, and I accrued many cool applications, but in the back of my mind I worried about opening up my home network to the internet. I also struggled to run some programs because the RPi uses the arm64 architecture, and most services are written with amd64 in mind. These two forces eventually convinced me to purchase a server where I could manage all of my services remotely. Some would say that not owning the hardware that is running your own services is not \u0026ldquo;true\u0026rdquo; self-hosting. I think this is needlessly exclusive. Let everyone self host, dangit! Someday, when I have more stable internet and a more permanent home, I hope to host everything from my own home, but until then, I\u0026rsquo;m extremely pleased with my current stack. And that is where I am now. I happily host numerous services on my virtual private server that entirely replace Google Photos, Google Drive and GitHub for me. Even better, there are specialized services that fill a need I never realized I had. What\u0026rsquo;s more, if I ever want to spin up a new service, all I have to do is add it to my to docker-compose file and it will be up within minutes. What a world!\nI thought about making this into a \u0026ldquo;guide\u0026rdquo; style post. I nixed that idea because, quite frankly, I feel like I don\u0026rsquo;t know what I\u0026rsquo;m doing. I am really happy with my setup, but I don\u0026rsquo;t feel like I have the authority to tell people how to administer their own services. If you are interested, allow me to point you toward the guide that really got me rolling: Ultimate Traefik Docker Compose Guide.\nFor those of you wondering what I am currently hosting, check out my current list at the link and let me know what you think!\n","permalink":"https://www.zacharybillman.com/posts/my-selfhosting-journey/","summary":"\u003cp\u003eMy interest in self-hosting began in my with my interests in internet privacy. Plastered all over the internet are stories about how much Google, Facebook and Amazon know about you. I deleted my Facebook account years ago, and I\u0026rsquo;m too paranoid to go back to the site because there\u0026rsquo;s \u003ca href=\"https://www.reddit.com/r/privacy/comments/6nmjfh/facebook_account_fully_recovered_3_years_after/\"\u003ea real possibility that Facebook has cached my account, ready to spin it back up\u003c/a\u003e in case I try to login again. The ads served to me were too accurate for my liking.\n\u003cspan class=\"sidenote-number\"\u003e\u003csmall class=\"sidenote\"\u003e\nThis is despite almost never clicking on them!\n\u003c/small\u003e\u003c/span\u003e\nI have become convinced of the idea that, if you are not paying for the product, you are the product. From this assumption, it follows that anywhere I trust with my data that I am not paying for (like Google Drive, Google Photos, Dropbox, Facebook, Twitter) is using my data to earn money. We know that \u003ca href=\"https://www.theverge.com/2020/11/11/21559930/google-train-ai-photos-image-labelling-app-android-update\"\u003eGoogle uses the labels you add to Photos to train it\u0026rsquo;s AI\u003c/a\u003e, and \u003ca href=\"https://ai.facebook.com/blog/seer-the-start-of-a-more-powerful-flexible-and-accessible-era-for-computer-vision/\"\u003eFacebook uses (at least) Instagram photos to train it\u0026rsquo;s AI\u003c/a\u003e. For some, the value proposition of allowing a company to use your data for a useful service in return is an acceptable one. I find this to be a reasonable stance, but I took my growing interest in internet privacy as a chance to learn about how I can take control of my data.\u003c/p\u003e","title":"My selfhosting journey."},{"content":"N.B.: I hope to add screenshots for each of these eventually. For now, I hope links to each services\u0026rsquo; website will suffice.\nSeafile\nThis is a great tool for managing files. I moved to this from Nextcloud because I am of the philosophy that I would prefer services that do one thing excellently instead of many things well. Nextcloud is an incredible Office365 replacement, but I found myself using a fraction of what it was capable of providing. Enter Seafile. It is cloud file syncing with a robust encryption implementation, just what the doctor ordered.\nPhotoprism\nNextcloud\u0026rsquo;s implementation of photo management was a bit clumsy for my tastes, so I began on a hunt for a more feature complete option. I was very lucky to stumble upon Photoprism early on in my self hosting journey. I am a proud supporter of this project. It brings a ton to the table, and doesn\u0026rsquo;t leave me missing Google Photos one bit. It is also actively developed. For instance, as of 2022-07-02, there was a recent update that improved scrolling a ton, which was one of my remaining quibbles with it\u0026rsquo;s functionality. Some people complain that it doesn\u0026rsquo;t scale up for libraries of 10,000+ photos, but my 2000 photo library works swimmingly. On my phone, I use the Folder Sync app to automatically send any pictures I take on my phone to the Photoprism imports folder. Within 15 minutes of snapping a photo, it is there on my Photoprism instance. I highly recommend giving it a go.\nMealie\nI have to admit that the name leaves something to be desired. Fortunately, the service itself doesn\u0026rsquo;t fall short. Mealie is a recipe management application. It is able to parse your favorite recipe websites to create immortalized versions of the recipe. This helps fight detestable link rot that plagues the internet. It allows you to edit ingredient amounts, make comments about what you would change next time, and plan out your weekly meals. It helps that it is beautiful and intuitive to use. If only I could get my partner to use it\u0026hellip; I want to go on the record here and say that I think it is sensible that she doesn\u0026rsquo;t trust my self hosted services that much. In the early days of my self hosting journey, let\u0026rsquo;s just say that the up-time of my services were extremely finicky. I like to think they are more permanent now, especially because I am hosting everything on a VPS, but I certainly cannot compete with the stability of Google and Amazon. (Or pretty much any other paid service for that matter.) \u0026#x1f609;\nGitea\nGitea is a community managed, lightweight code hosting solution written in Go. I use it to manage my data analysis (using Private repos) and even host the source code for this very website! Using Gitea has given me the surface level introduction to the behemoth that is git. Fortunately, that is all I need. Once I have removed any sensitive data (like passwords, etc.) I will make my docker-compose file public. The docker-compose file is where I determine which services I pick to host, and how to configure them to my liking. Hopefully someone will find this useful.\nSyncthing\nIf I could only tell someone to self host a single service, I would have to pick Syncthing. It is a continuous file synchronization program, which means it keeps a specific file or folder the same between any device running Syncthing. I use it to keep my password database and my org-mode notes Now org-mode might be the biggest rabbithole of them all, and definitely the topic for another blog post. I use it to manage my TODO list, my lab notebook, my shopping lists, write this blog, and maintain my Zettelkasten note database. It is an immensely powerful tool. up to date between all of my devices. With Syncthing, all of my data is stored on my own devices and encrypted in transit.\nFreshRSS\nI keep up to date on the science in my field by subscribing to relevant RSS feeds. Yet another topic to write a post about. This really changed the game for my ability to keep on top of the latest research. 2022-07-14 Update: post complete! Check it out here. FreshRSS replaced Feedly for me, as I ran up against the number of feeds I could subscribe to on a free account. Also, when self hosting, I can save as many articles as my heart desires (even if I will never look at them again \u0026#x1f635; ).\nWallabag\nRemember Pocket for Firefox? (Yes, I know it still exists, okay?) Give Wallabag a spin, it is great for storing articles you want to read later. I set up FreshRSS to save articles to my Wallabag instance to keep for later.\nChangeDetection\nNow this is a fun one! ChangeDetection.io is a service that loads a webpage and checks to see if something has changed since the last time. This might not sound useful at first, but I recently used this to check for when a hot item for my new coffee roasting hobby was back in stock. I got an email the other day to let me know it was in stock. Pretty cool!\nHugo\nHugo is the static site generator I use to make this here blog! I was amazed at how much more response my site was using Hugo compare to when I paid a company to host a WordPress site. I\u0026rsquo;m sure WordPress could be fast, but I just wanted a barebones, pure html experience, and Hugo made it easy.\nCommento++\nYou may have noticed that I have some pretty snazzy comments sections on my site. I initially used Disqus, which you may recognize from a ton of sites around the internet, but didn\u0026rsquo;t like how it would serve ads through my comments section, and provided sign-ins using Google/Facebook/Twitter. I wanted to serve the simplest comments section I could, that still gave me the ability to migrate the comments to wherever I decide to keep my server. Go ahead and use the anonymous comment button, fill in your name, and you are off to the races.\nAuthelia\nThere are a few services I host that I really want to lock down. For these services, Authelia is great. It puts up a \u0026ldquo;Enter the 6 digit code on your phone\u0026rdquo; style 2 factor authentication in front of the services I choose. Or, if you follow the guide here, you can have it send you a DUO push, just like you are one of the big hitters out there. I feel much more secure with Authelia in front of Adminer, Traefik, and Portainer.\nBoring stuff that allows everything else to work!\nPostgreSQL database MariaDB database Traefik reverse proxy Umami privacy respecting site analytics Portainer for docker container management Redis in-memory data store Adminer database management traefik-socket-proxy to prevent pesky backdoors to my server! ","permalink":"https://www.zacharybillman.com/posts/zpb-current-selfhosted/","summary":"\u003cp\u003e\u003cem\u003eN.B.: I hope to add screenshots for each of these eventually. For now, I hope links to each services\u0026rsquo; website will suffice.\u003c/em\u003e\u003c/p\u003e\n\u003col\u003e\n\u003cli\u003e\n\u003cp\u003e\u003ca href=\"https://www.seafile.com/en/home/\"\u003eSeafile\u003c/a\u003e\u003c/p\u003e\n\u003cp\u003eThis is a great tool for managing files. I moved to this from Nextcloud because I am of the philosophy that I would prefer services that do one thing excellently instead of many things well. Nextcloud is an incredible Office365 replacement, but I found myself using a fraction of what it was capable of providing. Enter Seafile. It is cloud file syncing with a robust encryption implementation, just what the doctor ordered.\u003c/p\u003e","title":"What I'm currently selfhosting."},{"content":"My partner and I took a trip to the Mason Farm Biological Reserve the other day, and what a glorious day it was. This year, I\u0026rsquo;ve been quite busy in the lab, and missed a lot of the early spring warbler season, so I was very excited by the opportunity to check out the old stomping grounds.\nI brought the camera with me despite the fact we were going to be there around midday when the birds are much less active. I\u0026rsquo;m glad I did, because I got the best look at a common yellowthroat I\u0026rsquo;ve ever had. Normally these guys are flighty, staying close to the ground in small brush or tall grasses, but this one was putting on a proper show for the mating season. Even when you get a glimpse of one, it is usually just that, as they have jumped away before you can pull out the camera, taunting you with their iconic call. I was very pleased to capture a few choice shots of the bird. Hopefully there are more to come. While we were out, I also got a nice picture of a hermit thrush and a king snake.\nThese images have been compressed quite a bit for a lighter internet footprint. These have all been resized to 25% of their original size. If you would like the full sized images, let me know and I will send you a link!\n","permalink":"https://www.zacharybillman.com/posts/the-uncommon-yellowthroat/","summary":"\u003cp\u003eMy partner and I took a trip to the \u003ca href=\"https://ncbg.unc.edu/visit/mason-farm-biological-reserve/\"\u003eMason Farm Biological Reserve\u003c/a\u003e the other day, and what a glorious day it was. This year, I\u0026rsquo;ve been quite busy in the lab, and missed a lot of the early spring warbler season, so I was very excited by the opportunity to check out the old stomping grounds.\u003c/p\u003e\n\u003cp\u003eI brought the camera with me despite the fact we were going to be there around midday when the birds are much less active. I\u0026rsquo;m glad I did, because I got the best look at a common yellowthroat I\u0026rsquo;ve ever had.\n\u003cspan class=\"sidenote-number\"\u003e\u003csmall class=\"sidenote\"\u003e\nNormally these guys are flighty, staying close to the ground in small brush or tall grasses, but this one was putting on a proper show for the mating season. Even when you get a glimpse of one, it is usually just that, as they have jumped away before you can pull out the camera, taunting you with their \u003ca href=\"https://ebird.org/species/comyel#Modal-playlist\"\u003eiconic call\u003c/a\u003e.\n\u003c/small\u003e\u003c/span\u003e\nI was very pleased to capture a few choice shots of the bird. Hopefully there are more to come. While we were out, I also got a nice picture of a hermit thrush and a king snake.\u003c/p\u003e","title":"The (un)common yellowthroat."},{"content":"Welcome to my site! ATTACH My name is Zachary Billman. I\u0026rsquo;m a UNC MD-PhD student in my 4th year of med school applying to pathology residency programs. I completed my PhD in Ed Miao\u0026rsquo;s lab. The curious reader may be thinking: \u0026ldquo;But Zach, Dr. Miao\u0026rsquo;s lab is at Duke, how did that come about?\u0026rdquo; What an astute question! Ed\u0026rsquo;s lab moved from UNC to Duke in early 2020, and I followed him down the street. My PhD was awarded by the UNC department of Microbiology and Immunology, but it just so happens that (nearly) all of my research took place at Duke. This move was quite a trial, especially when compounded with the onset of the pandemic. I suspect my research timeline suffered, though this is an extremely minor inconvenience compared to the tragedy the pandemic caused. This makes for very interesting basketball viewing parties with my Duke friends!\nMaybe having a diagram will make my training timeline make a bit more sense.\ntimeline.svg\nMy research and scientific interests. I am broadly interested in innate immunology. I spent most of my time in graduate school studying the host-pathogen interaction between the intracellular fungus Histoplasma capsulatum and macrophages. There are many unstudied curiosities regarding the innate immune response to Histoplasma spp. and other intracellular fungi that I think are quite interesting. I also spent a considerable time thinking about the evolution of proteins involved in the programmed cell death pathway called pyroptosis.\nHobbies I may write about. Besides my science, I am interested in birding, baking sourdough bread (I swear I began years before the pandemic, though hearing of people baking bread brings me joy no matter when they first began!), board games, roasting coffee, and self-hosting free and open source software. Over the course of the pandemic, I have learned how to maintain a basic suite of services spread between a server I rent and a computer at home that have replaced my need for Google Photos and Google Drive. I\u0026rsquo;m hoping to be able to move away from these platforms entirely soon. I think they provide a great service, but at a substantial cost to privacy. Hopefully more to be said about my thoughts on FOSS soon! I also transitioned my old, (and quite frankly, embarrassingly slow) managed WordPress site with this lean, static site made in Hugo that I host myself. Now that I have mangled together some CSS to get my precious sidenotes up and running again, I\u0026rsquo;m ready to begin putting some ideas to paper. I love marginalia (the word to describe these notes on the side of this webpage). I\u0026rsquo;m not sure if this is unique to me, but I seem to get caught up in parenthetical / tangential thoughts very often, and I think using an Edward Tufte-esque sidenote is a great way for me to communicate in this way without distracting the reader too much. It seems marginalia such as this have been used throughout history, so perhaps it is normal, but most people can keep their thoughts focused better than me. The implementation I use is inspired by the Tufte CSS project and largely taken from this incredibly helpful post found at scripter.co. I\u0026rsquo;m quite proud of my progress in administering my server and self-hosting useful services.\nThe future of this site. On this site I plan to post updates about my journey through med school, grad school, and self-hosting I would like to share with the world. I have been helped immensely by many others\u0026rsquo; advice and I hope to impart similar tips to others someday. I suspect most posts will be about much lighter fare, like whatever hobbies tickle my fancy at the time.\n","permalink":"https://www.zacharybillman.com/posts/about-me/about-me/","summary":"\u003ch2 id=\"welcome-to-my-site\"\u003eWelcome to my site! \u003cspan class=\"tag\"\u003e\u003cspan class=\"ATTACH\"\u003eATTACH\u003c/span\u003e\u003c/span\u003e\u003c/h2\u003e\n\u003cp\u003eMy name is Zachary Billman. I\u0026rsquo;m a UNC MD-PhD student in my 4th year of med school applying to pathology residency programs. I completed my PhD in Ed Miao\u0026rsquo;s lab. The curious reader may be thinking: \u0026ldquo;But Zach, Dr. Miao\u0026rsquo;s lab is at Duke, how did that come about?\u0026rdquo; What an astute question! Ed\u0026rsquo;s lab moved from UNC to Duke in early 2020, and I followed him down the street. My PhD was awarded by the UNC department of Microbiology and Immunology, but it just so happens that (nearly) all of my research took place at Duke.\n\u003cspan class=\"sidenote-number\"\u003e\u003csmall class=\"sidenote\"\u003e\nThis move was quite a trial, especially when compounded with the onset of the pandemic. I suspect my research timeline suffered, though this is an extremely minor inconvenience compared to the tragedy the pandemic caused.\n\u003c/small\u003e\u003c/span\u003e\nThis makes for very interesting basketball viewing parties with my Duke friends!\u003c/p\u003e","title":"About me. 👋"},{"content":"Welcome to my site! My name is Zachary Billman. I\u0026rsquo;m an MD-PhD student at UNC Chapel Hill in Ed Miao\u0026rsquo;s lab. The curious reader may be thinking: \u0026ldquo;But Zach, Ed Miao\u0026rsquo;s lab is at Duke now! What does that make you?\u0026rdquo; What an astute question! I am a card-carrying UNC Microbiology and Immunology student who happens to have all of their research take place at Duke. This move was quite a trial, especially when compounded with the onset of the pandemic. I suspect my research timeline suffered, though this is an extremely minor inconvenience compared to the tragedy the pandemic caused. This makes for very interesting basketball viewing parties with my Duke friends!\nMy research and scientific interests. I am broadly interested in innate immunology. I am in the 4th year of my PhD studying the host-pathogen interaction between the intracellular fungus Histoplasma capsulatum and macrophages. There are many unstudied curiosities regarding the innate immune response to Histoplasma spp. and other intracellular fungi that I think are quite interesting. Stay tuned, hopefully there is a major breakthrough to report here someday.\nHobbies I may write about. Besides my science, I am interested in birding, baking sourdough bread (I swear I began years before the pandemic, though hearing of people baking bread brings me joy no matter when they first began!), board games, roasting coffee, and self-hosting free and open source software. Over the course of the pandemic, I have learned how to maintain a basic suite of services on a server I rent that have replaced my need for Google Photos and Google Drive. I\u0026rsquo;m hoping to be able to move away from these platforms entirely soon. I think they provide a great service, but at a substantial cost to privacy. Hopefully more to be said about my thoughts on FOSS soon! I also transitioned my old, (and quite frankly, embarrassingly slow) managed WordPress site with this lean, static site made in Hugo that I host myself. Now that I have mangled together some CSS to get my precious sidenotes up and running again, I\u0026rsquo;m ready to begin putting some ideas to paper. I love marginalia. I\u0026rsquo;m not sure if this is unique to me, but I seem to get caught up in parenthetical / tangential thoughts very often, and I think using an Edward Tufte-esque sidenote is a great way for me to communicate in this way without distracting the reader too much. It seems marginalia such as this have been used throughout history, so perhaps it is normal, but most people can keep their thoughts focused better than me. The implementation I use is inspired by the Tufte CSS project and largely taken from this incredibly helpful post found at scripter.co. I\u0026rsquo;m quite proud of my progress in administering my server and self-hosting useful services.\nThe future of this site. On this site I plan to post updates about my journey through med school, grad school, and self-hosting I would like to share with the world. I have been helped immensely by many others\u0026rsquo; advice and I hope to impart similar tips to others someday. I suspect most posts will be about much lighter fare, like whatever hobbies tickle my fancy at the time.\n","permalink":"https://www.zacharybillman.com/posts/about-me/","summary":"\u003ch2 id=\"welcome-to-my-site\"\u003eWelcome to my site!\u003c/h2\u003e\n\u003cp\u003eMy name is Zachary Billman. I\u0026rsquo;m an MD-PhD student at UNC Chapel Hill in Ed Miao\u0026rsquo;s lab. The curious reader may be thinking: \u0026ldquo;But Zach, Ed Miao\u0026rsquo;s lab is at Duke now! What does that make you?\u0026rdquo; What an astute question! I am a card-carrying UNC Microbiology and Immunology student who happens to have all of their research take place at Duke.\n\u003cspan class=\"sidenote-number\"\u003e\u003csmall class=\"sidenote\"\u003e\nThis move was quite a trial, especially when compounded with the onset of the pandemic. I suspect my research timeline suffered, though this is an extremely minor inconvenience compared to the tragedy the pandemic caused.\n\u003c/small\u003e\u003c/span\u003e\nThis makes for very interesting basketball viewing parties with my Duke friends!\u003c/p\u003e","title":"About me. 👋"},{"content":"It\u0026rsquo;s over. My third year of medical school is officially behind me. I managed to get in a grand total of zero blog posts during grad school, so here\u0026rsquo;s to a new year with hopefully some more thoughts being shared. I have a lot to reflect on from the past year. It was wonderful. I wish everyone could experience what I did this past year. I think it goes without saying:\nI loved the third year of med school, but I do not want to do it again.\nA year of change. In the days leading up to my return to med school, I thought \u0026ldquo;Oh no, I really enjoy doing science, do I really have to go to med school?\u0026rdquo;. I also remember at the end of Step 1 and the first two years of med school thinking, \u0026ldquo;Oh no, I really enjoy med school, do I really have to do science again?\u0026rdquo;. I think I have a welcome problem of enjoying what I\u0026rsquo;m doing. The third year of med school is a shift. After years of memorizing and examinations, the doors to the promised land are finally opened. I have experienced nothing like it before It feels intentionally unsettling. You are thrown into the clinic with a modicum of guidance so you aren\u0026rsquo;t totally caught off guard, but you are thrown out to the wolves. I don\u0026rsquo;t mean this as a criticism of the system, it feels necessary. Third year medical students—commonly shorted to MS3s—have just one year to experience a broad swath of medicine and pick a specialty. So you had better be ready to dive in.\nTotal immersion I came to terms with my new reality quickly. Gone were the days of hitting the snooze button and going home when I pleased. I am now beholden to other people\u0026rsquo;s schedules. This came back relatively naturally. Maybe not hitting snooze. A regrettable personal failing of mine. I was, however, immediately faced with a new reality in the patient room. Patients come to the doctor for a number of reasons, but often seek relief. To get to the core of what ails them, they will tell you everything. I was not prepared for how vulnerable patients would be with me. I am not sure if this ever will feel natural. I hope it never does. I was told many stories of experiences living with scary diagnoses, and not knowing what to do with it. Family histories of all sorts. Personal details that were sometimes (oftentimes?) off the wall. I see all of these specifics as flailing, grasping at sand hoping that something could explain their pain. Sometimes it could. Usually it did not. But since I was in a white coat, I was privileged to hear it.\nI think my years spent in the lab have prepared me to face some of the challenges set before me. At the very least, having a few more years under my belt helped me approach the year with a bit of maturity. This seems to have paid off. I guess my recommendation is to simply get old before going to med school. Returning to studying The hospital is how I spent the majority of my time, but a new reality for me was also going back to daily studying. There is a strange dichotomy in medicine of \u0026ldquo;Oh, it doesn\u0026rsquo;t really matter\u0026rdquo; and \u0026ldquo;If you don\u0026rsquo;t get this class/score/grade then you won\u0026rsquo;t be able to be the kind of doctor you want to be, so you had better get your act together.\u0026rdquo; Simultaneously there are no expectations and immense responsibility for the looming specter of Step 2. I\u0026rsquo;m glad that studying regularly came back easily enough. I was concerned I would experience a studying whiplash. I\u0026rsquo;m glad it never came. I did UWorld and Anki nearly every day for a full year and felt alright.\nBecoming invisible I quickly learned I needed to change my understanding of my contribution to the team. Exiting grad school, people understood that they could come to me for help. I was a resource, a seasoned veteran of the lab. If someone needed an experiment done, I could do it, and be trusted to do it. In med school as a third year, I was nothing. A fly on the wall; a worm beneath the feet of the real doctors. In science, I felt like I was treated as a peer with even my committee members with multiple R01s. Even if I didn\u0026rsquo;t understand the science perfectly, I could contribute some different perspective. In medicine, sometimes not being recognized at all by my attendings was the best outcome. Which happened regularly. My role, was not as a contributor—as it was in science—it was simply to get in the reps. Once I understood that the expectations of me were below the ground, I understood that everything I did in third year was for myself. This is taken at face value by the team at times. I would spend 30 minutes working on a presentation, pre-rounding, the works, and at the end of my part, the intern would nod, then turn to the senior resident and say \u0026ldquo;I was thinking that we\u0026hellip;\u0026rdquo; without thinking of my work. This is perhaps a bit of cognitive restructuring, but recognizing this is what gave me the freedom to embed myself in the hospital flow, without a single worry about the outcome. Simply doing my best was the best thing I could do. Obviously. But this was not apparent to me at first. I needed more quality repetitions to develop good habits in the future. And also experience as much of medicine as possible to find what I want to do with my life. This permission allowed me to approach specialties I do not care about with the awe and respect they deserve.\nA year of wonder. Med school prepares you for the standardized tests. I think this is generally useful. The tests on aggregate are reasonable and evaluate your ability to think through common clinical scenarios. There will always be oddball questions that come out of left field, but I let these flow over me. No need to perseverate on the small stuff. The time for that can come later.\nWhat I didn\u0026rsquo;t realize is how much of the \u0026ldquo;classic\u0026rdquo; material we are fed in the first couple years of med school would come to the forefront. The \u0026ldquo;sandpaper rash\u0026rdquo; of scarlet fever really does feel like sandpaper. Nikolsky\u0026rsquo;s sign actually works. Tripoding for epiglottitis gets the physicians worked up. Don\u0026rsquo;t forget about von Willebrand\u0026rsquo;s disease when someone seems to be bleeding a bit too much. TB is out there, watch for hemoptosis. Night sweats, unintended weight loss, is cancer until proven otherwise. And yes, it really can be lupus.\nIn general, facing the unknown with a sense of earnestness was the way I felt best able to respect those who gathered and passed down the medical knowledge I am privileged to learn today. Sometimes, my excitement to see aspects of medicine would rouse a curious response from the residents. I project here, but I felt a sense of surprise, like that of a doting parent seeing their child experience something new, after forgetting the astonishment they once felt.\nEarnestness is next to med studentlyness.\nPerhaps what I\u0026rsquo;m getting at here is that I found it important to bask in the privilege of seeing the pathology I encountered in med school, and to remind the residents of this sensation. I felt childish at times—and perhaps overanimated—but I found this excitement was to my and my resident\u0026rsquo;s benefit.\nMy surgery rotation overflowed with examples of wonder of medicine. Partially because of the team I worked with, and the rest because of the undeniable coolness of surgery. The OR is a cool place. The orderliness and chaos ebb. The spans of steady, industrious work are interrupted with staccato notes of bedlam. The anatomy I learned in class was ever present, but the surgeons bemoaned \u0026ldquo;normal anatomic variation\u0026rdquo;.\nI was struck with wonder at the sight of human anatomy as it unfolded before me. What I was able to experience in the OR felt like the culmination of centuries of human curiosity. There is an ancientness to medicine that I catch flashes of—I could perform the physical exam on humans hundred of millions of years ago and interrogate the same pathologies as I do in the hospital today—and viewing the exposed anatomy is a pressure-bagged infusion of this collective wonder. To gaze upon the peristalsing of the small intestine, or steady beating of the heart is a sight to behold, indeed.\nA year of shame. It weighs upon me the circumstances that resulted in these transcendent experiences. Not one patient was in the hospital without reason. What to make of these patients with horrible pathology? I still feel unsettled about how the cause of their pain sparked wonder. How dare I gain, merely by the circumstance of having their care managed at UNC, Which, as a tertiary care center, layers on more complexity. Many patients end up at UNC because they have no where else they can go for help. And this signs them up for med students? For shame. from the very essence of their malady? I do not know what to do with my discomfort, but I think it is best that I dwell in it. With this, I respect the people before me in the hospital and recognize their humanity.\nBut I often complained of what I say here I was lucky to do. I find myself resentful of my future schedule; when was I supposed to learn that I will be working 13 hour days, 6 days a week for the rest of my life? And what of having a family? Medicine by necessity requires sacrifice. I happened to sign up for sacrifices years before I recognized how profound they were. How might I balance this dread and with the joy of practicing medicine? And why do I seem more concerned about this than others? Am I not grateful enough? Am I not capable of the sacrifices that others seem to offer so effortlessly? I don\u0026rsquo;t necessarily think this to be true, but these questions erode at my will to pursue medicine.\nPerhaps most shameful of all is how my understanding of the patient-provider interaction evolved over the year. It began as an exploration of an open book, a tabula rasa that held within it a diagnosis and how to best intervene. On my first day in the outpatient clinic, it was clear that this is not the case. My preceptor had only 20 minutes for me to ① interview the patient and perform the physical exam, ② present with a plan, ③ return to the room and do everything again, ④ write orders, educate, and get the patient out of the door. It simply is not amenable to the free form, personable, curious interview I hoped to perform. By the end of the year, I had optimized how I asked questions to keep patients from going off the rails. When prerounding in medicine, I was there to extract information and not much else. Small talk had to go, there was no time. I like to chat, so this came at a loss of who I think I am. I am not sure how to do this well, while still feeling like Zachary. And from what I gather from the interns, that may just come later in my career. I found myself questioning, \u0026ldquo;Is this the \u0026lsquo;patient interaction\u0026rsquo; that has been mythologized throughout my training?\u0026rdquo; The carrot at the end of the stick dangled before me with a \u0026ldquo;You are so lucky to be able to do this, so you had better not complain of any abuse that comes your way.\u0026rdquo; It wasn\u0026rsquo;t a genuine interaction as much as me leading the patient along to tell me what I wanted to know. Of course, I used open ended questions, but only open enough. Leave the door a bit too open and next thing you know, you are talking about their dog\u0026rsquo;s breeder while you constantly stare at your watch, imagining what your attending will say when you return. I feel like I am alone in missing the core human element that funnels sprightly youths into medicine. Or worse, finding it a façade.\nThe shame extends beyond the hospital. One aspect of my life that has changed most dramatically is the sheer amount of time I felt I needed to dedicate to medicine, whether at the hospital or at home. I spent all day basking in the wonder of medicine, then I would come home and study for hours. I relied on my partner for keeping our household together more than ever, because I spent all day—all year, rather—in a state of discovery. Her life was largely the same, with the normal challenges of being a scientist, with the added bonus of getting less help from me. The shame built over the year. Again, how dare I?\nA year of glad. This has been an undeniable year of growth and joy, with these quibbles. It is clear that I was happier than I was during grad school. I know this from within myself, and reinforced by my wife\u0026rsquo;s comments on my mood. The pace of the day, and immediacy of problem solving were a welcome change.\nI recall, during the very first days preparing for med school during xTAP, having to do a simulated patient encounter complete with patient presentation to an attending physician. We were told about this encounter days in advance. And yet, I dreaded it. And near the last day of my final rotation, I did 8 of these in a row without breaking a sweat. Progress!\nI think, in a word, what I\u0026rsquo;ve experienced in the third year of med school is gratitude. Gratitude to be privileged to learn what I am learning. Gratitude for the experiences in my life that brought me here. Gratitude for the support from my wife. Gratitude to be involved in people\u0026rsquo;s lives when they are fragile. Ever since reading Braiding Sweetgrass I think one could call me \u0026ldquo;gratitude-pilled\u0026rdquo;. I also selfishly enjoyed the gratitude from patients as I put on my best doctor performance. In reflection on the year, I have spent time thinking of a phrase that I heard a number of times throughout med school from residents, \u0026ldquo;The worst day of residency is better than the best day of med school.\u0026rdquo; I find this hard to believe. This year has been magical. It is hard to imagine a year filled with more wonder and joy of caring for those in need. I will have to rely on the experience of those who have walked this path and trust that the rest of my training has plenty of magic to spare.\n","permalink":"https://www.zacharybillman.com/posts/ms3-year-is-magical/","summary":"\u003ch2 id=\"it-s-over-dot\"\u003eIt\u0026rsquo;s over.\u003c/h2\u003e\n\u003cp\u003eMy third year of medical school is officially behind me. I managed to get in a grand total of \u003cem\u003ezero\u003c/em\u003e blog posts during grad school, so here\u0026rsquo;s to a new year with hopefully some more thoughts being shared. I have a lot to reflect on from the past year. It was wonderful. I wish everyone could experience what I did this past year. I think it goes without saying:\u003c/p\u003e","title":"The third year of medical school is magical."},{"content":"I, like many others, picked up a new hobby during the pandemic. Other people\u0026rsquo;s hobbies may bring them joy. This could be for many reasons. There is the joy of creating something from scratch. You can revel in your thriftiness. You can embrace the pride when you recognize that your creation is on par (or better!) than what you can buy. I feel like these are embodied in the sourdough craze that caught fire early on in COVID. Dare I say that I did this before it was cool? \u0026#x1f60e; I baked two loaves of bread almost every weekend through med school. Maybe I should bring that back, it\u0026rsquo;s been a while since I brought out the ole\u0026rsquo; starter. My pandemic hobby is similar, but different in that it often feels like a chore, costs more money, and often turns out worse than what I can buy. Of course, I am talking about how I\u0026rsquo;ve started roasting my own coffee at home.\nI\u0026rsquo;m not sure where this idea was planted into my brain. I don\u0026rsquo;t think I know anyone who roasts their own beans, and I certainly didn\u0026rsquo;t know how. I didn\u0026rsquo;t even drink coffee regularly until after college! I guess that extra time on the computer sent me down a rabbithole I have yet to emerge from.\nFirst, I want to preface the following with a disclaimer: This is not a detailed guide about how to roast your own coffee. If you are interested, I recommend checking out the How To Roast Your Own Coffee guide at Sweet Maria\u0026rsquo;s as a starting point. There is also the /r/roasting subreddit if that is your cup of tea. My only warning is there will be a lot of smoke. Roast your coffee outside, for Pete\u0026rsquo;s sake!\nIt all started with a trusty popcorn popper. There are a few things you want when you roast coffee:\nAir hot enough to roast coffee Remove the chaff from the beans Turns out that a classic popcorn popper fits the bill, as long as it has an upwards airflow and doesn\u0026rsquo;t let the chaff fall into the heating element. There is a bit of a cult following for the West Bend Poppery 2 model, but that one seemed a bit pricey, so I settled for a very capable popper from Nostalgia.\nFigure 1: I got a good bit of mileage out of my popcorn popper. If you are interested in roasting your own coffee I would give it a whirl.\nThings were simple back then. I still bought most of the coffee I drank, but I roasted enough to enjoy some freshly roasted coffee as an occasional treat. I ordered 10 pounds of green beans from Sweet Maria\u0026rsquo;s and life was good.\nThen I became a bit of a coffee snob.\nI could only roast 100 grams of coffee at a time in the popcorn popper, which is only enough for one pot of coffee in the morning for me. So it was time to upgrade.\nI bought the SR800 fluid bed roaster, which upped my roasting capacity and gave me finer control on temperature and airflow. Suffice to say my roasts improved a lot! At this point, I would consider my coffee good enough to sell at a farmer\u0026rsquo;s market to break even.\nIf you ever find yourself on a coffee roasting forum and bring up the SR800, someone is bound to bring up the famous RazzoRoasting extension tube. If you look for advice for how to use the SR800, I swear it\u0026rsquo;s assumed that you have this very specific accessory. \u0026hellip;And so I bought one.\nDon\u0026rsquo;t worry, that is the extent of all of my coffee spending (for now). I am a very satisfied coffee roaster now. Check out this quick series of images going from the green beans to a nearly finished product! I can spend about 45 minutes and go from nothing to nearly 2 pounds of roasted beans, enough for about a week and a half of coffee. Not bad! The only downside is that now I feel like I need to buy coffee from local roasters to get my fix. There are certainly crueler fates.\nAs a sign off, I will share something that surprised me about coffee roasting. When I roast coffee, the most important cue to determine if the coffee is roasted is the sound. That\u0026rsquo;s right, not the color, not the smell, but the sound. When heating up a coffee bean, the water trapped inside eventually bursts out of the bean in a rapid expansion. This is called \u0026ldquo;first crack\u0026rdquo;, and indicates that the coffee is roasted enough to be drinkable. The expansion also releases the chaff from the bean. If you continue heating up the bean, you will eventually reach \u0026ldquo;second crack\u0026rdquo;. I think a solid medium roast is taken out just before second crack, so I try to take my coffee out to this point and it hasn\u0026rsquo;t proved me wrong yet.\nHappy coffee-ing! \u0026#x2615;\n","permalink":"https://www.zacharybillman.com/posts/roasting-coffee-at-home/","summary":"\u003cp\u003eI, like many others, picked up a new hobby during the pandemic. Other people\u0026rsquo;s hobbies may bring them joy. This could be for many reasons. There is the joy of creating something from scratch. You can revel in your thriftiness. You can embrace the pride when you recognize that your creation is on par (or better!) than what you can buy. I feel like these are embodied in the sourdough craze that caught fire early on in COVID.\n\u003cspan class=\"sidenote-number\"\u003e\u003csmall class=\"sidenote\"\u003e\nDare I say that I did this before it was cool? \u0026#x1f60e; I baked two loaves of bread almost every weekend through med school. Maybe I should bring that back, it\u0026rsquo;s been a while since I brought out the ole\u0026rsquo; starter.\n\u003c/small\u003e\u003c/span\u003e\nMy pandemic hobby is similar, but different in that it often feels like a chore, costs more money, and often turns out worse than what I can buy. Of course, I am talking about how I\u0026rsquo;ve started roasting my own coffee at home.\u003c/p\u003e","title":"Roasting coffee at home. ☕"},{"content":"It is an age-old question: how can one keep up with the continuous output of science? I remember at the beginning of my PhD struggling to figure out how anyone found out when a new paper came out. \u0026#x1f635; Did they sit on nature.com and spam the refresh button? Did they know when each journal released their latest issue?\nBehold the power of RSS! Most websites have a page that contains information about each subpage in a computer-readable format called RSS (Really Simple Syndication). Mine has one right here! These pages can be parsed by a number of RSS feed aggregators. The way these pages are set up make it such that they add any new information hosted at that domain. This is useful in the science world because you can find the RSS feed of a given journal, subscribe to it, then have every new article published online be delivered right to you.\nThere are a plethora of RSS feed aggregators you can pick from manage your feeds. I have previously used Feedly and Inoreader, which are great free solutions, but have moved on to selfhosting my own instance of FreshRSS.\nAfter making an account at your friendly local RSS feed aggregator, you can add whatever feeds your heart desires. To find a journal\u0026rsquo;s rss feed, I often just search \u0026ldquo;$JOURNAL_NAME rss feed\u0026rdquo; and poke around until I find something that looks right. Most of the aggregators will test the feed out first to make sure that you are trying to add a legitimate one. Here are a few of the heavy hitters to get you started:\nhttp://feeds.nature.com/nature/rss/current https://www.science.org/rss/express.xml https://www.cell.com/cell/inpress.rss Nothing like a constant stream of Cell, Science, and Nature to make your project feel like a real winner, eh?\nHere is what my own site looks like.\nFigure 1: My current FreshRSS setup. On the left I have my feeds separated into folders. In the middle you can see the titles of papers that appear in my feed.\nAnd after I hit J to move to the first item in the feed.\nFigure 2: With a title selected, you can see the abstract and authors.\nAfter collecting all of your desired RSS feeds, you cannot forego your responsibility of actually reading them! Most RSS feed aggregators have shortcuts to move through titles quickly (Typically J to move on to the next one and K to move up.) They always seem to use vi keybindings. A bunch of computer nerds have really cornered the keybinding market. I have let them take over my computing life. Each morning when I get into the lab, I quickly set up something, then head to my desk to hit J until the counter reaches zero.\nBut what about my very specific field? You can subscribe to all of the journals you want, but that doesn\u0026rsquo;t make the papers with your specific interests pop out. Fortunately, the NIH has this exact circumstance in mind.\nWhen you make a new search on PubMed you might notice the \u0026ldquo;Create RSS\u0026rdquo; button. Give it a click, then you will have a personal link you can add to your favorite RSS feed aggregator.\nFigure 3: Somehow I never noticed this button until I needed it.\nThis changed the game for me for keeping up with papers. Unfortunately, it doesn\u0026rsquo;t solve the problem of library management, or actually getting around to reading the papers you care about. I will leave library management as an exercise for the interested reader. Here\u0026rsquo;s a tip, the best solution uses the Zotero citation manager. Bonus points for using Zotfile for renaming your PDFs and Better BibTex for Zotero. \u0026#x1f609; I hope this helps you get your eyeballs on that science you crave. If you have solved the problem of accruing papers to read faster than you read them, let me know.\n","permalink":"https://www.zacharybillman.com/posts/rss-feeds-to-find-science-papers/","summary":"\u003cp\u003eIt is an age-old question: how can one keep up with the continuous output of science? I remember at the beginning of my PhD struggling to figure out how anyone found out when a new paper came out. \u0026#x1f635; Did they sit on nature.com and spam the refresh button? Did they know when each journal released their latest issue?\u003c/p\u003e\n\u003ch2 id=\"behold-the-power-of-rss\"\u003eBehold the power of RSS!\u003c/h2\u003e\n\u003cp\u003eMost websites have a page that contains information about each subpage in a computer-readable format called RSS (Really Simple Syndication). \u003ca href=\"https://zacharybillman.com/index.xml\"\u003eMine has one right here!\u003c/a\u003e These pages can be parsed by a number of RSS feed aggregators. The way these pages are set up make it such that they add any new information hosted at that domain. This is useful in the science world because you can find the RSS feed of a given journal, subscribe to it, then have every new article published online be delivered right to you.\u003c/p\u003e","title":"Using RSS feeds to keep on top of science."},{"content":"My interest in self-hosting began in my with my interests in internet privacy. Plastered all over the internet are stories about how much Google, Facebook and Amazon know about you. I deleted my Facebook account years ago, and I\u0026rsquo;m too paranoid to go back to the site because there\u0026rsquo;s a real possibility that Facebook has cached my account, ready to spin it back up in case I try to login again. The ads served to me were too accurate for my liking. This is despite almost never clicking on them! I have become convinced of the idea that, if you are not paying for the product, you are the product. From this assumption, it follows that anywhere I trust with my data that I am not paying for (like Google Drive, Google Photos, Dropbox, Facebook, Twitter) is using my data to earn money. We know that Google uses the labels you add to Photos to train it\u0026rsquo;s AI, and Facebook uses (at least) Instagram photos to train it\u0026rsquo;s AI. For some, the value proposition of allowing a company to use your data for a useful service in return is an acceptable one. I find this to be a reasonable stance, but I took my growing interest in internet privacy as a chance to learn about how I can take control of my data.\nInitially, I lurked on forums like /r/privacy to learn what I could do to avoid big-tech\u0026rsquo;s watchful eye. There were numerous comments along the lines of: \u0026ldquo;The only way to be in control of your data is to self-host your services.\u0026rdquo; I had no idea what this meant! Hard to believe that less than a year later, I learned to use (and love) Linux as my primary OS, and have happily replaced Google Photos, Google Drive and other services with my own self-hosted alternatives. Self-hosting, I have since learned, is when you run useful programs from your own computer. By doing so, you have complete knowledge of where and how your data is stored and how it is being used. It has the additional effect of being a bottomless time sink.\nTo begin, I needed an always-on computer to run these useful programs. I began with a humble Raspberry Pi.\nFigure 1: My humble Raspberry Pi and its hard drive. This dude currently tirelessly runs the excellent Adguard Home and downloads a backup of my data every night.\nThese are tiny, but capable computers that are great for fiddling with. The projects people develop for these are amazing and diverse. With RPi in hand, I began with the ambitious project of replacing Google Drive with Nextcloud. After much frustration with a bare metal installation, I found the NextcloudPi project. Surprisingly, it went pretty okay! At first, I was intimidated by Linux defaults, but over time I grew to appreciate, and indeed, prefer Linux as an operating system. My decision to use Linux over Windows/MacOS is because it is free and open source software (FOSS). This is a topic for a different post, but I think using FOSS when possible is a moral imperative of sorts. I used Nextcloud strictly from my home for a few months, without the ability to connect to it from the internet, to test the self-hosting waters. My first true cloud replacement spun up once I decided to access this lil\u0026rsquo; guy from the internet. To do so, I purchased a domain (not the one this site is hosted on) and pointed it to the IP of my house. I forwarded the appropriate ports of my router to the RPi.\nThis is when the real exploration began. I was able to access my files and images using Nextcloud, but the photo viewing service left something to be desired. No problem, why not spin up an instance of Photoprism? I use RSS feeds to keep on top of the latest science in the journals relevant to my field using Feedly. Why not host my own RSS feed aggregator so I can subscribe to as many feeds as I desire?\nThis cycle continued, and I accrued many cool applications, but in the back of my mind I worried about opening up my home network to the internet. I also struggled to run some programs because the RPi uses the arm64 architecture, and most services are written with amd64 in mind. These two forces eventually convinced me to purchase a server where I could manage all of my services remotely. Some would say that not owning the hardware that is running your own services is not \u0026ldquo;true\u0026rdquo; self-hosting. I think this is needlessly exclusive. Let everyone self host, dangit! Someday, when I have more stable internet and a more permanent home, I hope to host everything from my own home, but until then, I\u0026rsquo;m extremely pleased with my current stack. And that is where I am now. I happily host numerous services on my virtual private server that entirely replace Google Photos, Google Drive and GitHub for me. Even better, there are specialized services that fill a need I never realized I had. What\u0026rsquo;s more, if I ever want to spin up a new service, all I have to do is add it to my to docker-compose file and it will be up within minutes. What a world!\nI thought about making this into a \u0026ldquo;guide\u0026rdquo; style post. I nixed that idea because, quite frankly, I feel like I don\u0026rsquo;t know what I\u0026rsquo;m doing. I am really happy with my setup, but I don\u0026rsquo;t feel like I have the authority to tell people how to administer their own services. If you are interested, allow me to point you toward the guide that really got me rolling: Ultimate Traefik Docker Compose Guide.\nFor those of you wondering what I am currently hosting, check out my current list at the link and let me know what you think!\n","permalink":"https://www.zacharybillman.com/posts/my-selfhosting-journey/","summary":"\u003cp\u003eMy interest in self-hosting began in my with my interests in internet privacy. Plastered all over the internet are stories about how much Google, Facebook and Amazon know about you. I deleted my Facebook account years ago, and I\u0026rsquo;m too paranoid to go back to the site because there\u0026rsquo;s \u003ca href=\"https://www.reddit.com/r/privacy/comments/6nmjfh/facebook_account_fully_recovered_3_years_after/\"\u003ea real possibility that Facebook has cached my account, ready to spin it back up\u003c/a\u003e in case I try to login again. The ads served to me were too accurate for my liking.\n\u003cspan class=\"sidenote-number\"\u003e\u003csmall class=\"sidenote\"\u003e\nThis is despite almost never clicking on them!\n\u003c/small\u003e\u003c/span\u003e\nI have become convinced of the idea that, if you are not paying for the product, you are the product. From this assumption, it follows that anywhere I trust with my data that I am not paying for (like Google Drive, Google Photos, Dropbox, Facebook, Twitter) is using my data to earn money. We know that \u003ca href=\"https://www.theverge.com/2020/11/11/21559930/google-train-ai-photos-image-labelling-app-android-update\"\u003eGoogle uses the labels you add to Photos to train it\u0026rsquo;s AI\u003c/a\u003e, and \u003ca href=\"https://ai.facebook.com/blog/seer-the-start-of-a-more-powerful-flexible-and-accessible-era-for-computer-vision/\"\u003eFacebook uses (at least) Instagram photos to train it\u0026rsquo;s AI\u003c/a\u003e. For some, the value proposition of allowing a company to use your data for a useful service in return is an acceptable one. I find this to be a reasonable stance, but I took my growing interest in internet privacy as a chance to learn about how I can take control of my data.\u003c/p\u003e","title":"My selfhosting journey."},{"content":"N.B.: I hope to add screenshots for each of these eventually. For now, I hope links to each services\u0026rsquo; website will suffice.\nSeafile\nThis is a great tool for managing files. I moved to this from Nextcloud because I am of the philosophy that I would prefer services that do one thing excellently instead of many things well. Nextcloud is an incredible Office365 replacement, but I found myself using a fraction of what it was capable of providing. Enter Seafile. It is cloud file syncing with a robust encryption implementation, just what the doctor ordered.\nPhotoprism\nNextcloud\u0026rsquo;s implementation of photo management was a bit clumsy for my tastes, so I began on a hunt for a more feature complete option. I was very lucky to stumble upon Photoprism early on in my self hosting journey. I am a proud supporter of this project. It brings a ton to the table, and doesn\u0026rsquo;t leave me missing Google Photos one bit. It is also actively developed. For instance, as of 2022-07-02, there was a recent update that improved scrolling a ton, which was one of my remaining quibbles with it\u0026rsquo;s functionality. Some people complain that it doesn\u0026rsquo;t scale up for libraries of 10,000+ photos, but my 2000 photo library works swimmingly. On my phone, I use the Folder Sync app to automatically send any pictures I take on my phone to the Photoprism imports folder. Within 15 minutes of snapping a photo, it is there on my Photoprism instance. I highly recommend giving it a go.\nMealie\nI have to admit that the name leaves something to be desired. Fortunately, the service itself doesn\u0026rsquo;t fall short. Mealie is a recipe management application. It is able to parse your favorite recipe websites to create immortalized versions of the recipe. This helps fight detestable link rot that plagues the internet. It allows you to edit ingredient amounts, make comments about what you would change next time, and plan out your weekly meals. It helps that it is beautiful and intuitive to use. If only I could get my partner to use it\u0026hellip; I want to go on the record here and say that I think it is sensible that she doesn\u0026rsquo;t trust my self hosted services that much. In the early days of my self hosting journey, let\u0026rsquo;s just say that the up-time of my services were extremely finicky. I like to think they are more permanent now, especially because I am hosting everything on a VPS, but I certainly cannot compete with the stability of Google and Amazon. (Or pretty much any other paid service for that matter.) \u0026#x1f609;\nGitea\nGitea is a community managed, lightweight code hosting solution written in Go. I use it to manage my data analysis (using Private repos) and even host the source code for this very website! Using Gitea has given me the surface level introduction to the behemoth that is git. Fortunately, that is all I need. Once I have removed any sensitive data (like passwords, etc.) I will make my docker-compose file public. The docker-compose file is where I determine which services I pick to host, and how to configure them to my liking. Hopefully someone will find this useful.\nSyncthing\nIf I could only tell someone to self host a single service, I would have to pick Syncthing. It is a continuous file synchronization program, which means it keeps a specific file or folder the same between any device running Syncthing. I use it to keep my password database and my org-mode notes Now org-mode might be the biggest rabbithole of them all, and definitely the topic for another blog post. I use it to manage my TODO list, my lab notebook, my shopping lists, write this blog, and maintain my Zettelkasten note database. It is an immensely powerful tool. up to date between all of my devices. With Syncthing, all of my data is stored on my own devices and encrypted in transit.\nFreshRSS\nI keep up to date on the science in my field by subscribing to relevant RSS feeds. Yet another topic to write a post about. This really changed the game for my ability to keep on top of the latest research. 2022-07-14 Update: post complete! Check it out here. FreshRSS replaced Feedly for me, as I ran up against the number of feeds I could subscribe to on a free account. Also, when self hosting, I can save as many articles as my heart desires (even if I will never look at them again \u0026#x1f635; ).\nWallabag\nRemember Pocket for Firefox? (Yes, I know it still exists, okay?) Give Wallabag a spin, it is great for storing articles you want to read later. I set up FreshRSS to save articles to my Wallabag instance to keep for later.\nChangeDetection\nNow this is a fun one! ChangeDetection.io is a service that loads a webpage and checks to see if something has changed since the last time. This might not sound useful at first, but I recently used this to check for when a hot item for my new coffee roasting hobby was back in stock. I got an email the other day to let me know it was in stock. Pretty cool!\nHugo\nHugo is the static site generator I use to make this here blog! I was amazed at how much more response my site was using Hugo compare to when I paid a company to host a WordPress site. I\u0026rsquo;m sure WordPress could be fast, but I just wanted a barebones, pure html experience, and Hugo made it easy.\nCommento++\nYou may have noticed that I have some pretty snazzy comments sections on my site. I initially used Disqus, which you may recognize from a ton of sites around the internet, but didn\u0026rsquo;t like how it would serve ads through my comments section, and provided sign-ins using Google/Facebook/Twitter. I wanted to serve the simplest comments section I could, that still gave me the ability to migrate the comments to wherever I decide to keep my server. Go ahead and use the anonymous comment button, fill in your name, and you are off to the races.\nAuthelia\nThere are a few services I host that I really want to lock down. For these services, Authelia is great. It puts up a \u0026ldquo;Enter the 6 digit code on your phone\u0026rdquo; style 2 factor authentication in front of the services I choose. Or, if you follow the guide here, you can have it send you a DUO push, just like you are one of the big hitters out there. I feel much more secure with Authelia in front of Adminer, Traefik, and Portainer.\nBoring stuff that allows everything else to work!\nPostgreSQL database MariaDB database Traefik reverse proxy Umami privacy respecting site analytics Portainer for docker container management Redis in-memory data store Adminer database management traefik-socket-proxy to prevent pesky backdoors to my server! ","permalink":"https://www.zacharybillman.com/posts/zpb-current-selfhosted/","summary":"\u003cp\u003e\u003cem\u003eN.B.: I hope to add screenshots for each of these eventually. For now, I hope links to each services\u0026rsquo; website will suffice.\u003c/em\u003e\u003c/p\u003e\n\u003col\u003e\n\u003cli\u003e\n\u003cp\u003e\u003ca href=\"https://www.seafile.com/en/home/\"\u003eSeafile\u003c/a\u003e\u003c/p\u003e\n\u003cp\u003eThis is a great tool for managing files. I moved to this from Nextcloud because I am of the philosophy that I would prefer services that do one thing excellently instead of many things well. Nextcloud is an incredible Office365 replacement, but I found myself using a fraction of what it was capable of providing. Enter Seafile. It is cloud file syncing with a robust encryption implementation, just what the doctor ordered.\u003c/p\u003e","title":"What I'm currently selfhosting."},{"content":"My partner and I took a trip to the Mason Farm Biological Reserve the other day, and what a glorious day it was. This year, I\u0026rsquo;ve been quite busy in the lab, and missed a lot of the early spring warbler season, so I was very excited by the opportunity to check out the old stomping grounds.\nI brought the camera with me despite the fact we were going to be there around midday when the birds are much less active. I\u0026rsquo;m glad I did, because I got the best look at a common yellowthroat I\u0026rsquo;ve ever had. Normally these guys are flighty, staying close to the ground in small brush or tall grasses, but this one was putting on a proper show for the mating season. Even when you get a glimpse of one, it is usually just that, as they have jumped away before you can pull out the camera, taunting you with their iconic call. I was very pleased to capture a few choice shots of the bird. Hopefully there are more to come. While we were out, I also got a nice picture of a hermit thrush and a king snake.\nThese images have been compressed quite a bit for a lighter internet footprint. These have all been resized to 25% of their original size. If you would like the full sized images, let me know and I will send you a link!\n","permalink":"https://www.zacharybillman.com/posts/the-uncommon-yellowthroat/","summary":"\u003cp\u003eMy partner and I took a trip to the \u003ca href=\"https://ncbg.unc.edu/visit/mason-farm-biological-reserve/\"\u003eMason Farm Biological Reserve\u003c/a\u003e the other day, and what a glorious day it was. This year, I\u0026rsquo;ve been quite busy in the lab, and missed a lot of the early spring warbler season, so I was very excited by the opportunity to check out the old stomping grounds.\u003c/p\u003e\n\u003cp\u003eI brought the camera with me despite the fact we were going to be there around midday when the birds are much less active. I\u0026rsquo;m glad I did, because I got the best look at a common yellowthroat I\u0026rsquo;ve ever had.\n\u003cspan class=\"sidenote-number\"\u003e\u003csmall class=\"sidenote\"\u003e\nNormally these guys are flighty, staying close to the ground in small brush or tall grasses, but this one was putting on a proper show for the mating season. Even when you get a glimpse of one, it is usually just that, as they have jumped away before you can pull out the camera, taunting you with their \u003ca href=\"https://ebird.org/species/comyel#Modal-playlist\"\u003eiconic call\u003c/a\u003e.\n\u003c/small\u003e\u003c/span\u003e\nI was very pleased to capture a few choice shots of the bird. Hopefully there are more to come. While we were out, I also got a nice picture of a hermit thrush and a king snake.\u003c/p\u003e","title":"The (un)common yellowthroat."},{"content":"It\u0026rsquo;s over. My third year of medical school is officially behind me. I managed to get in a grand total of zero blog posts during grad school, so here\u0026rsquo;s to a new year with hopefully some more thoughts being shared. I have a lot to reflect on from the past year. It was wonderful. I wish everyone could experience what I did this past year. I think it goes without saying:\nI loved the third year of med school, but I do not want to do it again.\nA year of change. In the days leading up to my return to med school, I thought \u0026ldquo;Oh no, I really enjoy doing science, do I really have to go to med school?\u0026rdquo;. I also remember at the end of Step 1 and the first two years of med school thinking, \u0026ldquo;Oh no, I really enjoy med school, do I really have to do science again?\u0026rdquo;. I think I have a welcome problem of enjoying what I\u0026rsquo;m doing. The third year of med school is a shift. After years of memorizing and examinations, the doors to the promised land are finally opened. I have experienced nothing like it before It feels intentionally unsettling. You are thrown into the clinic with a modicum of guidance so you aren\u0026rsquo;t totally caught off guard, but you are thrown out to the wolves. I don\u0026rsquo;t mean this as a criticism of the system, it feels necessary. Third year medical students—commonly shorted to MS3s—have just one year to experience a broad swath of medicine and pick a specialty. So you had better be ready to dive in.\nTotal immersion I came to terms with my new reality quickly. Gone were the days of hitting the snooze button and going home when I pleased. I am now beholden to other people\u0026rsquo;s schedules. This came back relatively naturally. Maybe not hitting snooze. A regrettable personal failing of mine. I was, however, immediately faced with a new reality in the patient room. Patients come to the doctor for a number of reasons, but often seek relief. To get to the core of what ails them, they will tell you everything. I was not prepared for how vulnerable patients would be with me. I am not sure if this ever will feel natural. I hope it never does. I was told many stories of experiences living with scary diagnoses, and not knowing what to do with it. Family histories of all sorts. Personal details that were sometimes (oftentimes?) off the wall. I see all of these specifics as flailing, grasping at sand hoping that something could explain their pain. Sometimes it could. Usually it did not. But since I was in a white coat, I was privileged to hear it.\nI think my years spent in the lab have prepared me to face some of the challenges set before me. At the very least, having a few more years under my belt helped me approach the year with a bit of maturity. This seems to have paid off. I guess my recommendation is to simply get old before going to med school. Returning to studying The hospital is how I spent the majority of my time, but a new reality for me was also going back to daily studying. There is a strange dichotomy in medicine of \u0026ldquo;Oh, it doesn\u0026rsquo;t really matter\u0026rdquo; and \u0026ldquo;If you don\u0026rsquo;t get this class/score/grade then you won\u0026rsquo;t be able to be the kind of doctor you want to be, so you had better get your act together.\u0026rdquo; Simultaneously there are no expectations and immense responsibility for the looming specter of Step 2. I\u0026rsquo;m glad that studying regularly came back easily enough. I was concerned I would experience a studying whiplash. I\u0026rsquo;m glad it never came. I did UWorld and Anki nearly every day for a full year and felt alright.\nBecoming invisible I quickly learned I needed to change my understanding of my contribution to the team. Exiting grad school, people understood that they could come to me for help. I was a resource, a seasoned veteran of the lab. If someone needed an experiment done, I could do it, and be trusted to do it. In med school as a third year, I was nothing. A fly on the wall; a worm beneath the feet of the real doctors. In science, I felt like I was treated as a peer with even my committee members with multiple R01s. Even if I didn\u0026rsquo;t understand the science perfectly, I could contribute some different perspective. In medicine, sometimes not being recognized at all by my attendings was the best outcome. Which happened regularly. My role, was not as a contributor—as it was in science—it was simply to get in the reps. Once I understood that the expectations of me were below the ground, I understood that everything I did in third year was for myself. This is taken at face value by the team at times. I would spend 30 minutes working on a presentation, pre-rounding, the works, and at the end of my part, the intern would nod, then turn to the senior resident and say \u0026ldquo;I was thinking that we\u0026hellip;\u0026rdquo; without thinking of my work. This is perhaps a bit of cognitive restructuring, but recognizing this is what gave me the freedom to embed myself in the hospital flow, without a single worry about the outcome. Simply doing my best was the best thing I could do. Obviously. But this was not apparent to me at first. I needed more quality repetitions to develop good habits in the future. And also experience as much of medicine as possible to find what I want to do with my life. This permission allowed me to approach specialties I do not care about with the awe and respect they deserve.\nA year of wonder. Med school prepares you for the standardized tests. I think this is generally useful. The tests on aggregate are reasonable and evaluate your ability to think through common clinical scenarios. There will always be oddball questions that come out of left field, but I let these flow over me. No need to perseverate on the small stuff. The time for that can come later.\nWhat I didn\u0026rsquo;t realize is how much of the \u0026ldquo;classic\u0026rdquo; material we are fed in the first couple years of med school would come to the forefront. The \u0026ldquo;sandpaper rash\u0026rdquo; of scarlet fever really does feel like sandpaper. Nikolsky\u0026rsquo;s sign actually works. Tripoding for epiglottitis gets the physicians worked up. Don\u0026rsquo;t forget about von Willebrand\u0026rsquo;s disease when someone seems to be bleeding a bit too much. TB is out there, watch for hemoptosis. Night sweats, unintended weight loss, is cancer until proven otherwise. And yes, it really can be lupus.\nIn general, facing the unknown with a sense of earnestness was the way I felt best able to respect those who gathered and passed down the medical knowledge I am privileged to learn today. Sometimes, my excitement to see aspects of medicine would rouse a curious response from the residents. I project here, but I felt a sense of surprise, like that of a doting parent seeing their child experience something new, after forgetting the astonishment they once felt.\nEarnestness is next to med studentlyness.\nPerhaps what I\u0026rsquo;m getting at here is that I found it important to bask in the privilege of seeing the pathology I encountered in med school, and to remind the residents of this sensation. I felt childish at times—and perhaps overanimated—but I found this excitement was to my and my resident\u0026rsquo;s benefit.\nMy surgery rotation overflowed with examples of wonder of medicine. Partially because of the team I worked with, and the rest because of the undeniable coolness of surgery. The OR is a cool place. The orderliness and chaos ebb. The spans of steady, industrious work are interrupted with staccato notes of bedlam. The anatomy I learned in class was ever present, but the surgeons bemoaned \u0026ldquo;normal anatomic variation\u0026rdquo;.\nI was struck with wonder at the sight of human anatomy as it unfolded before me. What I was able to experience in the OR felt like the culmination of centuries of human curiosity. There is an ancientness to medicine that I catch flashes of—I could perform the physical exam on humans hundred of millions of years ago and interrogate the same pathologies as I do in the hospital today—and viewing the exposed anatomy is a pressure-bagged infusion of this collective wonder. To gaze upon the peristalsing of the small intestine, or steady beating of the heart is a sight to behold, indeed.\nA year of shame. It weighs upon me the circumstances that resulted in these transcendent experiences. Not one patient was in the hospital without reason. What to make of these patients with horrible pathology? I still feel unsettled about how the cause of their pain sparked wonder. How dare I gain, merely by the circumstance of having their care managed at UNC, Which, as a tertiary care center, layers on more complexity. Many patients end up at UNC because they have no where else they can go for help. And this signs them up for med students? For shame. from the very essence of their malady? I do not know what to do with my discomfort, but I think it is best that I dwell in it. With this, I respect the people before me in the hospital and recognize their humanity.\nBut I often complained of what I say here I was lucky to do. I find myself resentful of my future schedule; when was I supposed to learn that I will be working 13 hour days, 6 days a week for the rest of my life? And what of having a family? Medicine by necessity requires sacrifice. I happened to sign up for sacrifices years before I recognized how profound they were. How might I balance this dread and with the joy of practicing medicine? And why do I seem more concerned about this than others? Am I not grateful enough? Am I not capable of the sacrifices that others seem to offer so effortlessly? I don\u0026rsquo;t necessarily think this to be true, but these questions erode at my will to pursue medicine.\nPerhaps most shameful of all is how my understanding of the patient-provider interaction evolved over the year. It began as an exploration of an open book, a tabula rasa that held within it a diagnosis and how to best intervene. On my first day in the outpatient clinic, it was clear that this is not the case. My preceptor had only 20 minutes for me to ① interview the patient and perform the physical exam, ② present with a plan, ③ return to the room and do everything again, ④ write orders, educate, and get the patient out of the door. It simply is not amenable to the free form, personable, curious interview I hoped to perform. By the end of the year, I had optimized how I asked questions to keep patients from going off the rails. When prerounding in medicine, I was there to extract information and not much else. Small talk had to go, there was no time. I like to chat, so this came at a loss of who I think I am. I am not sure how to do this well, while still feeling like Zachary. And from what I gather from the interns, that may just come later in my career. I found myself questioning, \u0026ldquo;Is this the \u0026lsquo;patient interaction\u0026rsquo; that has been mythologized throughout my training?\u0026rdquo; The carrot at the end of the stick dangled before me with a \u0026ldquo;You are so lucky to be able to do this, so you had better not complain of any abuse that comes your way.\u0026rdquo; It wasn\u0026rsquo;t a genuine interaction as much as me leading the patient along to tell me what I wanted to know. Of course, I used open ended questions, but only open enough. Leave the door a bit too open and next thing you know, you are talking about their dog\u0026rsquo;s breeder while you constantly stare at your watch, imagining what your attending will say when you return. I feel like I am alone in missing the core human element that funnels sprightly youths into medicine. Or worse, finding it a façade.\nThe shame extends beyond the hospital. One aspect of my life that has changed most dramatically is the sheer amount of time I felt I needed to dedicate to medicine, whether at the hospital or at home. I spent all day basking in the wonder of medicine, then I would come home and study for hours. I relied on my partner for keeping our household together more than ever, because I spent all day—all year, rather—in a state of discovery. Her life was largely the same, with the normal challenges of being a scientist, with the added bonus of getting less help from me. The shame built over the year. Again, how dare I?\nA year of glad. This has been an undeniable year of growth and joy, with these quibbles. It is clear that I was happier than I was during grad school. I know this from within myself, and reinforced by my wife\u0026rsquo;s comments on my mood. The pace of the day, and immediacy of problem solving were a welcome change.\nI recall, during the very first days preparing for med school during xTAP, having to do a simulated patient encounter complete with patient presentation to an attending physician. We were told about this encounter days in advance. And yet, I dreaded it. And near the last day of my final rotation, I did 8 of these in a row without breaking a sweat. Progress!\nI think, in a word, what I\u0026rsquo;ve experienced in the third year of med school is gratitude. Gratitude to be privileged to learn what I am learning. Gratitude for the experiences in my life that brought me here. Gratitude for the support from my wife. Gratitude to be involved in people\u0026rsquo;s lives when they are fragile. Ever since reading Braiding Sweetgrass I think one could call me \u0026ldquo;gratitude-pilled\u0026rdquo;. I also selfishly enjoyed the gratitude from patients as I put on my best doctor performance. In reflection on the year, I have spent time thinking of a phrase that I heard a number of times throughout med school from residents, \u0026ldquo;The worst day of residency is better than the best day of med school.\u0026rdquo; I find this hard to believe. This year has been magical. It is hard to imagine a year filled with more wonder and joy of caring for those in need. I will have to rely on the experience of those who have walked this path and trust that the rest of my training has plenty of magic to spare.\n","permalink":"https://www.zacharybillman.com/posts/ms3-year-is-magical/","summary":"\u003ch2 id=\"it-s-over-dot\"\u003eIt\u0026rsquo;s over.\u003c/h2\u003e\n\u003cp\u003eMy third year of medical school is officially behind me. I managed to get in a grand total of \u003cem\u003ezero\u003c/em\u003e blog posts during grad school, so here\u0026rsquo;s to a new year with hopefully some more thoughts being shared. I have a lot to reflect on from the past year. It was wonderful. I wish everyone could experience what I did this past year. I think it goes without saying:\u003c/p\u003e","title":"The third year of medical school is magical."},{"content":"I, like many others, picked up a new hobby during the pandemic. Other people\u0026rsquo;s hobbies may bring them joy. This could be for many reasons. There is the joy of creating something from scratch. You can revel in your thriftiness. You can embrace the pride when you recognize that your creation is on par (or better!) than what you can buy. I feel like these are embodied in the sourdough craze that caught fire early on in COVID. Dare I say that I did this before it was cool? \u0026#x1f60e; I baked two loaves of bread almost every weekend through med school. Maybe I should bring that back, it\u0026rsquo;s been a while since I brought out the ole\u0026rsquo; starter. My pandemic hobby is similar, but different in that it often feels like a chore, costs more money, and often turns out worse than what I can buy. Of course, I am talking about how I\u0026rsquo;ve started roasting my own coffee at home.\nI\u0026rsquo;m not sure where this idea was planted into my brain. I don\u0026rsquo;t think I know anyone who roasts their own beans, and I certainly didn\u0026rsquo;t know how. I didn\u0026rsquo;t even drink coffee regularly until after college! I guess that extra time on the computer sent me down a rabbithole I have yet to emerge from.\nFirst, I want to preface the following with a disclaimer: This is not a detailed guide about how to roast your own coffee. If you are interested, I recommend checking out the How To Roast Your Own Coffee guide at Sweet Maria\u0026rsquo;s as a starting point. There is also the /r/roasting subreddit if that is your cup of tea. My only warning is there will be a lot of smoke. Roast your coffee outside, for Pete\u0026rsquo;s sake!\nIt all started with a trusty popcorn popper. There are a few things you want when you roast coffee:\nAir hot enough to roast coffee Remove the chaff from the beans Turns out that a classic popcorn popper fits the bill, as long as it has an upwards airflow and doesn\u0026rsquo;t let the chaff fall into the heating element. There is a bit of a cult following for the West Bend Poppery 2 model, but that one seemed a bit pricey, so I settled for a very capable popper from Nostalgia.\nFigure 1: I got a good bit of mileage out of my popcorn popper. If you are interested in roasting your own coffee I would give it a whirl.\nThings were simple back then. I still bought most of the coffee I drank, but I roasted enough to enjoy some freshly roasted coffee as an occasional treat. I ordered 10 pounds of green beans from Sweet Maria\u0026rsquo;s and life was good.\nThen I became a bit of a coffee snob.\nI could only roast 100 grams of coffee at a time in the popcorn popper, which is only enough for one pot of coffee in the morning for me. So it was time to upgrade.\nI bought the SR800 fluid bed roaster, which upped my roasting capacity and gave me finer control on temperature and airflow. Suffice to say my roasts improved a lot! At this point, I would consider my coffee good enough to sell at a farmer\u0026rsquo;s market to break even.\nIf you ever find yourself on a coffee roasting forum and bring up the SR800, someone is bound to bring up the famous RazzoRoasting extension tube. If you look for advice for how to use the SR800, I swear it\u0026rsquo;s assumed that you have this very specific accessory. \u0026hellip;And so I bought one.\nDon\u0026rsquo;t worry, that is the extent of all of my coffee spending (for now). I am a very satisfied coffee roaster now. Check out this quick series of images going from the green beans to a nearly finished product! I can spend about 45 minutes and go from nothing to nearly 2 pounds of roasted beans, enough for about a week and a half of coffee. Not bad! The only downside is that now I feel like I need to buy coffee from local roasters to get my fix. There are certainly crueler fates.\nAs a sign off, I will share something that surprised me about coffee roasting. When I roast coffee, the most important cue to determine if the coffee is roasted is the sound. That\u0026rsquo;s right, not the color, not the smell, but the sound. When heating up a coffee bean, the water trapped inside eventually bursts out of the bean in a rapid expansion. This is called \u0026ldquo;first crack\u0026rdquo;, and indicates that the coffee is roasted enough to be drinkable. The expansion also releases the chaff from the bean. If you continue heating up the bean, you will eventually reach \u0026ldquo;second crack\u0026rdquo;. I think a solid medium roast is taken out just before second crack, so I try to take my coffee out to this point and it hasn\u0026rsquo;t proved me wrong yet.\nHappy coffee-ing! \u0026#x2615;\n","permalink":"https://www.zacharybillman.com/posts/roasting-coffee-at-home/","summary":"\u003cp\u003eI, like many others, picked up a new hobby during the pandemic. Other people\u0026rsquo;s hobbies may bring them joy. This could be for many reasons. There is the joy of creating something from scratch. You can revel in your thriftiness. You can embrace the pride when you recognize that your creation is on par (or better!) than what you can buy. I feel like these are embodied in the sourdough craze that caught fire early on in COVID.\n\u003cspan class=\"sidenote-number\"\u003e\u003csmall class=\"sidenote\"\u003e\nDare I say that I did this before it was cool? \u0026#x1f60e; I baked two loaves of bread almost every weekend through med school. Maybe I should bring that back, it\u0026rsquo;s been a while since I brought out the ole\u0026rsquo; starter.\n\u003c/small\u003e\u003c/span\u003e\nMy pandemic hobby is similar, but different in that it often feels like a chore, costs more money, and often turns out worse than what I can buy. Of course, I am talking about how I\u0026rsquo;ve started roasting my own coffee at home.\u003c/p\u003e","title":"Roasting coffee at home. ☕"},{"content":"It is an age-old question: how can one keep up with the continuous output of science? I remember at the beginning of my PhD struggling to figure out how anyone found out when a new paper came out. \u0026#x1f635; Did they sit on nature.com and spam the refresh button? Did they know when each journal released their latest issue?\nBehold the power of RSS! Most websites have a page that contains information about each subpage in a computer-readable format called RSS (Really Simple Syndication). Mine has one right here! These pages can be parsed by a number of RSS feed aggregators. The way these pages are set up make it such that they add any new information hosted at that domain. This is useful in the science world because you can find the RSS feed of a given journal, subscribe to it, then have every new article published online be delivered right to you.\nThere are a plethora of RSS feed aggregators you can pick from manage your feeds. I have previously used Feedly and Inoreader, which are great free solutions, but have moved on to selfhosting my own instance of FreshRSS.\nAfter making an account at your friendly local RSS feed aggregator, you can add whatever feeds your heart desires. To find a journal\u0026rsquo;s rss feed, I often just search \u0026ldquo;$JOURNAL_NAME rss feed\u0026rdquo; and poke around until I find something that looks right. Most of the aggregators will test the feed out first to make sure that you are trying to add a legitimate one. Here are a few of the heavy hitters to get you started:\nhttp://feeds.nature.com/nature/rss/current https://www.science.org/rss/express.xml https://www.cell.com/cell/inpress.rss Nothing like a constant stream of Cell, Science, and Nature to make your project feel like a real winner, eh?\nHere is what my own site looks like.\nFigure 1: My current FreshRSS setup. On the left I have my feeds separated into folders. In the middle you can see the titles of papers that appear in my feed.\nAnd after I hit J to move to the first item in the feed.\nFigure 2: With a title selected, you can see the abstract and authors.\nAfter collecting all of your desired RSS feeds, you cannot forego your responsibility of actually reading them! Most RSS feed aggregators have shortcuts to move through titles quickly (Typically J to move on to the next one and K to move up.) They always seem to use vi keybindings. A bunch of computer nerds have really cornered the keybinding market. I have let them take over my computing life. Each morning when I get into the lab, I quickly set up something, then head to my desk to hit J until the counter reaches zero.\nBut what about my very specific field? You can subscribe to all of the journals you want, but that doesn\u0026rsquo;t make the papers with your specific interests pop out. Fortunately, the NIH has this exact circumstance in mind.\nWhen you make a new search on PubMed you might notice the \u0026ldquo;Create RSS\u0026rdquo; button. Give it a click, then you will have a personal link you can add to your favorite RSS feed aggregator.\nFigure 3: Somehow I never noticed this button until I needed it.\nThis changed the game for me for keeping up with papers. Unfortunately, it doesn\u0026rsquo;t solve the problem of library management, or actually getting around to reading the papers you care about. I will leave library management as an exercise for the interested reader. Here\u0026rsquo;s a tip, the best solution uses the Zotero citation manager. Bonus points for using Zotfile for renaming your PDFs and Better BibTex for Zotero. \u0026#x1f609; I hope this helps you get your eyeballs on that science you crave. If you have solved the problem of accruing papers to read faster than you read them, let me know.\n","permalink":"https://www.zacharybillman.com/posts/rss-feeds-to-find-science-papers/","summary":"\u003cp\u003eIt is an age-old question: how can one keep up with the continuous output of science? I remember at the beginning of my PhD struggling to figure out how anyone found out when a new paper came out. \u0026#x1f635; Did they sit on nature.com and spam the refresh button? Did they know when each journal released their latest issue?\u003c/p\u003e\n\u003ch2 id=\"behold-the-power-of-rss\"\u003eBehold the power of RSS!\u003c/h2\u003e\n\u003cp\u003eMost websites have a page that contains information about each subpage in a computer-readable format called RSS (Really Simple Syndication). \u003ca href=\"https://zacharybillman.com/index.xml\"\u003eMine has one right here!\u003c/a\u003e These pages can be parsed by a number of RSS feed aggregators. The way these pages are set up make it such that they add any new information hosted at that domain. This is useful in the science world because you can find the RSS feed of a given journal, subscribe to it, then have every new article published online be delivered right to you.\u003c/p\u003e","title":"Using RSS feeds to keep on top of science."},{"content":"My interest in self-hosting began in my with my interests in internet privacy. Plastered all over the internet are stories about how much Google, Facebook and Amazon know about you. I deleted my Facebook account years ago, and I\u0026rsquo;m too paranoid to go back to the site because there\u0026rsquo;s a real possibility that Facebook has cached my account, ready to spin it back up in case I try to login again. The ads served to me were too accurate for my liking. This is despite almost never clicking on them! I have become convinced of the idea that, if you are not paying for the product, you are the product. From this assumption, it follows that anywhere I trust with my data that I am not paying for (like Google Drive, Google Photos, Dropbox, Facebook, Twitter) is using my data to earn money. We know that Google uses the labels you add to Photos to train it\u0026rsquo;s AI, and Facebook uses (at least) Instagram photos to train it\u0026rsquo;s AI. For some, the value proposition of allowing a company to use your data for a useful service in return is an acceptable one. I find this to be a reasonable stance, but I took my growing interest in internet privacy as a chance to learn about how I can take control of my data.\nInitially, I lurked on forums like /r/privacy to learn what I could do to avoid big-tech\u0026rsquo;s watchful eye. There were numerous comments along the lines of: \u0026ldquo;The only way to be in control of your data is to self-host your services.\u0026rdquo; I had no idea what this meant! Hard to believe that less than a year later, I learned to use (and love) Linux as my primary OS, and have happily replaced Google Photos, Google Drive and other services with my own self-hosted alternatives. Self-hosting, I have since learned, is when you run useful programs from your own computer. By doing so, you have complete knowledge of where and how your data is stored and how it is being used. It has the additional effect of being a bottomless time sink.\nTo begin, I needed an always-on computer to run these useful programs. I began with a humble Raspberry Pi.\nFigure 1: My humble Raspberry Pi and its hard drive. This dude currently tirelessly runs the excellent Adguard Home and downloads a backup of my data every night.\nThese are tiny, but capable computers that are great for fiddling with. The projects people develop for these are amazing and diverse. With RPi in hand, I began with the ambitious project of replacing Google Drive with Nextcloud. After much frustration with a bare metal installation, I found the NextcloudPi project. Surprisingly, it went pretty okay! At first, I was intimidated by Linux defaults, but over time I grew to appreciate, and indeed, prefer Linux as an operating system. My decision to use Linux over Windows/MacOS is because it is free and open source software (FOSS). This is a topic for a different post, but I think using FOSS when possible is a moral imperative of sorts. I used Nextcloud strictly from my home for a few months, without the ability to connect to it from the internet, to test the self-hosting waters. My first true cloud replacement spun up once I decided to access this lil\u0026rsquo; guy from the internet. To do so, I purchased a domain (not the one this site is hosted on) and pointed it to the IP of my house. I forwarded the appropriate ports of my router to the RPi.\nThis is when the real exploration began. I was able to access my files and images using Nextcloud, but the photo viewing service left something to be desired. No problem, why not spin up an instance of Photoprism? I use RSS feeds to keep on top of the latest science in the journals relevant to my field using Feedly. Why not host my own RSS feed aggregator so I can subscribe to as many feeds as I desire?\nThis cycle continued, and I accrued many cool applications, but in the back of my mind I worried about opening up my home network to the internet. I also struggled to run some programs because the RPi uses the arm64 architecture, and most services are written with amd64 in mind. These two forces eventually convinced me to purchase a server where I could manage all of my services remotely. Some would say that not owning the hardware that is running your own services is not \u0026ldquo;true\u0026rdquo; self-hosting. I think this is needlessly exclusive. Let everyone self host, dangit! Someday, when I have more stable internet and a more permanent home, I hope to host everything from my own home, but until then, I\u0026rsquo;m extremely pleased with my current stack. And that is where I am now. I happily host numerous services on my virtual private server that entirely replace Google Photos, Google Drive and GitHub for me. Even better, there are specialized services that fill a need I never realized I had. What\u0026rsquo;s more, if I ever want to spin up a new service, all I have to do is add it to my to docker-compose file and it will be up within minutes. What a world!\nI thought about making this into a \u0026ldquo;guide\u0026rdquo; style post. I nixed that idea because, quite frankly, I feel like I don\u0026rsquo;t know what I\u0026rsquo;m doing. I am really happy with my setup, but I don\u0026rsquo;t feel like I have the authority to tell people how to administer their own services. If you are interested, allow me to point you toward the guide that really got me rolling: Ultimate Traefik Docker Compose Guide.\nFor those of you wondering what I am currently hosting, check out my current list at the link and let me know what you think!\n","permalink":"https://www.zacharybillman.com/posts/my-selfhosting-journey/","summary":"\u003cp\u003eMy interest in self-hosting began in my with my interests in internet privacy. Plastered all over the internet are stories about how much Google, Facebook and Amazon know about you. I deleted my Facebook account years ago, and I\u0026rsquo;m too paranoid to go back to the site because there\u0026rsquo;s \u003ca href=\"https://www.reddit.com/r/privacy/comments/6nmjfh/facebook_account_fully_recovered_3_years_after/\"\u003ea real possibility that Facebook has cached my account, ready to spin it back up\u003c/a\u003e in case I try to login again. The ads served to me were too accurate for my liking.\n\u003cspan class=\"sidenote-number\"\u003e\u003csmall class=\"sidenote\"\u003e\nThis is despite almost never clicking on them!\n\u003c/small\u003e\u003c/span\u003e\nI have become convinced of the idea that, if you are not paying for the product, you are the product. From this assumption, it follows that anywhere I trust with my data that I am not paying for (like Google Drive, Google Photos, Dropbox, Facebook, Twitter) is using my data to earn money. We know that \u003ca href=\"https://www.theverge.com/2020/11/11/21559930/google-train-ai-photos-image-labelling-app-android-update\"\u003eGoogle uses the labels you add to Photos to train it\u0026rsquo;s AI\u003c/a\u003e, and \u003ca href=\"https://ai.facebook.com/blog/seer-the-start-of-a-more-powerful-flexible-and-accessible-era-for-computer-vision/\"\u003eFacebook uses (at least) Instagram photos to train it\u0026rsquo;s AI\u003c/a\u003e. For some, the value proposition of allowing a company to use your data for a useful service in return is an acceptable one. I find this to be a reasonable stance, but I took my growing interest in internet privacy as a chance to learn about how I can take control of my data.\u003c/p\u003e","title":"My selfhosting journey."},{"content":"N.B.: I hope to add screenshots for each of these eventually. For now, I hope links to each services\u0026rsquo; website will suffice.\nSeafile\nThis is a great tool for managing files. I moved to this from Nextcloud because I am of the philosophy that I would prefer services that do one thing excellently instead of many things well. Nextcloud is an incredible Office365 replacement, but I found myself using a fraction of what it was capable of providing. Enter Seafile. It is cloud file syncing with a robust encryption implementation, just what the doctor ordered.\nPhotoprism\nNextcloud\u0026rsquo;s implementation of photo management was a bit clumsy for my tastes, so I began on a hunt for a more feature complete option. I was very lucky to stumble upon Photoprism early on in my self hosting journey. I am a proud supporter of this project. It brings a ton to the table, and doesn\u0026rsquo;t leave me missing Google Photos one bit. It is also actively developed. For instance, as of 2022-07-02, there was a recent update that improved scrolling a ton, which was one of my remaining quibbles with it\u0026rsquo;s functionality. Some people complain that it doesn\u0026rsquo;t scale up for libraries of 10,000+ photos, but my 2000 photo library works swimmingly. On my phone, I use the Folder Sync app to automatically send any pictures I take on my phone to the Photoprism imports folder. Within 15 minutes of snapping a photo, it is there on my Photoprism instance. I highly recommend giving it a go.\nMealie\nI have to admit that the name leaves something to be desired. Fortunately, the service itself doesn\u0026rsquo;t fall short. Mealie is a recipe management application. It is able to parse your favorite recipe websites to create immortalized versions of the recipe. This helps fight detestable link rot that plagues the internet. It allows you to edit ingredient amounts, make comments about what you would change next time, and plan out your weekly meals. It helps that it is beautiful and intuitive to use. If only I could get my partner to use it\u0026hellip; I want to go on the record here and say that I think it is sensible that she doesn\u0026rsquo;t trust my self hosted services that much. In the early days of my self hosting journey, let\u0026rsquo;s just say that the up-time of my services were extremely finicky. I like to think they are more permanent now, especially because I am hosting everything on a VPS, but I certainly cannot compete with the stability of Google and Amazon. (Or pretty much any other paid service for that matter.) \u0026#x1f609;\nGitea\nGitea is a community managed, lightweight code hosting solution written in Go. I use it to manage my data analysis (using Private repos) and even host the source code for this very website! Using Gitea has given me the surface level introduction to the behemoth that is git. Fortunately, that is all I need. Once I have removed any sensitive data (like passwords, etc.) I will make my docker-compose file public. The docker-compose file is where I determine which services I pick to host, and how to configure them to my liking. Hopefully someone will find this useful.\nSyncthing\nIf I could only tell someone to self host a single service, I would have to pick Syncthing. It is a continuous file synchronization program, which means it keeps a specific file or folder the same between any device running Syncthing. I use it to keep my password database and my org-mode notes Now org-mode might be the biggest rabbithole of them all, and definitely the topic for another blog post. I use it to manage my TODO list, my lab notebook, my shopping lists, write this blog, and maintain my Zettelkasten note database. It is an immensely powerful tool. up to date between all of my devices. With Syncthing, all of my data is stored on my own devices and encrypted in transit.\nFreshRSS\nI keep up to date on the science in my field by subscribing to relevant RSS feeds. Yet another topic to write a post about. This really changed the game for my ability to keep on top of the latest research. 2022-07-14 Update: post complete! Check it out here. FreshRSS replaced Feedly for me, as I ran up against the number of feeds I could subscribe to on a free account. Also, when self hosting, I can save as many articles as my heart desires (even if I will never look at them again \u0026#x1f635; ).\nWallabag\nRemember Pocket for Firefox? (Yes, I know it still exists, okay?) Give Wallabag a spin, it is great for storing articles you want to read later. I set up FreshRSS to save articles to my Wallabag instance to keep for later.\nChangeDetection\nNow this is a fun one! ChangeDetection.io is a service that loads a webpage and checks to see if something has changed since the last time. This might not sound useful at first, but I recently used this to check for when a hot item for my new coffee roasting hobby was back in stock. I got an email the other day to let me know it was in stock. Pretty cool!\nHugo\nHugo is the static site generator I use to make this here blog! I was amazed at how much more response my site was using Hugo compare to when I paid a company to host a WordPress site. I\u0026rsquo;m sure WordPress could be fast, but I just wanted a barebones, pure html experience, and Hugo made it easy.\nCommento++\nYou may have noticed that I have some pretty snazzy comments sections on my site. I initially used Disqus, which you may recognize from a ton of sites around the internet, but didn\u0026rsquo;t like how it would serve ads through my comments section, and provided sign-ins using Google/Facebook/Twitter. I wanted to serve the simplest comments section I could, that still gave me the ability to migrate the comments to wherever I decide to keep my server. Go ahead and use the anonymous comment button, fill in your name, and you are off to the races.\nAuthelia\nThere are a few services I host that I really want to lock down. For these services, Authelia is great. It puts up a \u0026ldquo;Enter the 6 digit code on your phone\u0026rdquo; style 2 factor authentication in front of the services I choose. Or, if you follow the guide here, you can have it send you a DUO push, just like you are one of the big hitters out there. I feel much more secure with Authelia in front of Adminer, Traefik, and Portainer.\nBoring stuff that allows everything else to work!\nPostgreSQL database MariaDB database Traefik reverse proxy Umami privacy respecting site analytics Portainer for docker container management Redis in-memory data store Adminer database management traefik-socket-proxy to prevent pesky backdoors to my server! ","permalink":"https://www.zacharybillman.com/posts/zpb-current-selfhosted/","summary":"\u003cp\u003e\u003cem\u003eN.B.: I hope to add screenshots for each of these eventually. For now, I hope links to each services\u0026rsquo; website will suffice.\u003c/em\u003e\u003c/p\u003e\n\u003col\u003e\n\u003cli\u003e\n\u003cp\u003e\u003ca href=\"https://www.seafile.com/en/home/\"\u003eSeafile\u003c/a\u003e\u003c/p\u003e\n\u003cp\u003eThis is a great tool for managing files. I moved to this from Nextcloud because I am of the philosophy that I would prefer services that do one thing excellently instead of many things well. Nextcloud is an incredible Office365 replacement, but I found myself using a fraction of what it was capable of providing. Enter Seafile. It is cloud file syncing with a robust encryption implementation, just what the doctor ordered.\u003c/p\u003e","title":"What I'm currently selfhosting."},{"content":"My partner and I took a trip to the Mason Farm Biological Reserve the other day, and what a glorious day it was. This year, I\u0026rsquo;ve been quite busy in the lab, and missed a lot of the early spring warbler season, so I was very excited by the opportunity to check out the old stomping grounds.\nI brought the camera with me despite the fact we were going to be there around midday when the birds are much less active. I\u0026rsquo;m glad I did, because I got the best look at a common yellowthroat I\u0026rsquo;ve ever had. Normally these guys are flighty, staying close to the ground in small brush or tall grasses, but this one was putting on a proper show for the mating season. Even when you get a glimpse of one, it is usually just that, as they have jumped away before you can pull out the camera, taunting you with their iconic call. I was very pleased to capture a few choice shots of the bird. Hopefully there are more to come. While we were out, I also got a nice picture of a hermit thrush and a king snake.\nThese images have been compressed quite a bit for a lighter internet footprint. These have all been resized to 25% of their original size. If you would like the full sized images, let me know and I will send you a link!\n","permalink":"https://www.zacharybillman.com/posts/the-uncommon-yellowthroat/","summary":"\u003cp\u003eMy partner and I took a trip to the \u003ca href=\"https://ncbg.unc.edu/visit/mason-farm-biological-reserve/\"\u003eMason Farm Biological Reserve\u003c/a\u003e the other day, and what a glorious day it was. This year, I\u0026rsquo;ve been quite busy in the lab, and missed a lot of the early spring warbler season, so I was very excited by the opportunity to check out the old stomping grounds.\u003c/p\u003e\n\u003cp\u003eI brought the camera with me despite the fact we were going to be there around midday when the birds are much less active. I\u0026rsquo;m glad I did, because I got the best look at a common yellowthroat I\u0026rsquo;ve ever had.\n\u003cspan class=\"sidenote-number\"\u003e\u003csmall class=\"sidenote\"\u003e\nNormally these guys are flighty, staying close to the ground in small brush or tall grasses, but this one was putting on a proper show for the mating season. Even when you get a glimpse of one, it is usually just that, as they have jumped away before you can pull out the camera, taunting you with their \u003ca href=\"https://ebird.org/species/comyel#Modal-playlist\"\u003eiconic call\u003c/a\u003e.\n\u003c/small\u003e\u003c/span\u003e\nI was very pleased to capture a few choice shots of the bird. Hopefully there are more to come. While we were out, I also got a nice picture of a hermit thrush and a king snake.\u003c/p\u003e","title":"The (un)common yellowthroat."},{"content":"Welcome to my site! My name is Zachary Billman. I\u0026rsquo;m a UNC MD-PhD student in my 4th year of med school applying to pathology residency programs. I completed my PhD in Ed Miao\u0026rsquo;s lab. The curious reader may be thinking: \u0026ldquo;But Zach, Dr. Miao\u0026rsquo;s lab is at Duke, how did that come about?\u0026rdquo; What an astute question! Ed\u0026rsquo;s lab moved from UNC to Duke in early 2020, and I followed him down the street. My PhD was awarded by the UNC department of Microbiology and Immunology, but it just so happens that (nearly) all of my research took place at Duke. This move was quite a trial, especially when compounded with the onset of the pandemic. I suspect my research timeline suffered, though this is an extremely minor inconvenience compared to the tragedy the pandemic caused. This makes for very interesting basketball viewing parties with my Duke friends!\nMaybe having a diagram will make my training timeline make a bit more sense.\ntimeline.png\nMy research and scientific interests. I am broadly interested in innate immunology. I spent most of my time in graduate school studying the host-pathogen interaction between the intracellular fungus Histoplasma capsulatum and macrophages. There are many unstudied curiosities regarding the innate immune response to Histoplasma spp. and other intracellular fungi that I think are quite interesting. I also spent a considerable time thinking about the evolution of proteins involved in the programmed cell death pathway called pyroptosis.\nHobbies I may write about. Besides my science, I am interested in birding, baking sourdough bread (I swear I began years before the pandemic, though hearing of people baking bread brings me joy no matter when they first began!), board games, roasting coffee, and self-hosting free and open source software. Over the course of the pandemic, I have learned how to maintain a basic suite of services spread between a server I rent and a computer at home that have replaced my need for Google Photos and Google Drive. I\u0026rsquo;m hoping to be able to move away from these platforms entirely soon. I think they provide a great service, but at a substantial cost to privacy. Hopefully more to be said about my thoughts on FOSS soon! I also transitioned my old, (and quite frankly, embarrassingly slow) managed WordPress site with this lean, static site made in Hugo that I host myself. Now that I have mangled together some CSS to get my precious sidenotes up and running again, I\u0026rsquo;m ready to begin putting some ideas to paper. I love marginalia (the word to describe these notes on the side of this webpage). I\u0026rsquo;m not sure if this is unique to me, but I seem to get caught up in parenthetical / tangential thoughts very often, and I think using an Edward Tufte-esque sidenote is a great way for me to communicate in this way without distracting the reader too much. It seems marginalia such as this have been used throughout history, so perhaps it is normal, but most people can keep their thoughts focused better than me. The implementation I use is inspired by the Tufte CSS project and largely taken from this incredibly helpful post found at scripter.co. I\u0026rsquo;m quite proud of my progress in administering my server and self-hosting useful services.\nThe future of this site. On this site I plan to post updates about my journey through med school, grad school, and self-hosting I would like to share with the world. I have been helped immensely by many others\u0026rsquo; advice and I hope to impart similar tips to others someday. I suspect most posts will be about much lighter fare, like whatever hobbies tickle my fancy at the time.\n","permalink":"https://www.zacharybillman.com/posts/about-me/","summary":"\u003ch2 id=\"welcome-to-my-site\"\u003eWelcome to my site!\u003c/h2\u003e\n\u003cp\u003eMy name is Zachary Billman. I\u0026rsquo;m a UNC MD-PhD student in my 4th year of med school applying to pathology residency programs. I completed my PhD in Ed Miao\u0026rsquo;s lab. The curious reader may be thinking: \u0026ldquo;But Zach, Dr. Miao\u0026rsquo;s lab is at Duke, how did that come about?\u0026rdquo; What an astute question! Ed\u0026rsquo;s lab moved from UNC to Duke in early 2020, and I followed him down the street. My PhD was awarded by the UNC department of Microbiology and Immunology, but it just so happens that (nearly) all of my research took place at Duke.\n\u003cspan class=\"sidenote-number\"\u003e\u003csmall class=\"sidenote\"\u003e\nThis move was quite a trial, especially when compounded with the onset of the pandemic. I suspect my research timeline suffered, though this is an extremely minor inconvenience compared to the tragedy the pandemic caused.\n\u003c/small\u003e\u003c/span\u003e\nThis makes for very interesting basketball viewing parties with my Duke friends!\u003c/p\u003e","title":"About me. 👋"},{"content":"It\u0026rsquo;s over. My third year of medical school is officially behind me. I managed to get in a grand total of zero blog posts during grad school, so here\u0026rsquo;s to a new year with hopefully some more thoughts being shared. I have a lot to reflect on from the past year. It was wonderful. I wish everyone could experience what I did this past year. I think it goes without saying:\nI loved the third year of med school, but I do not want to do it again.\nA year of change. In the days leading up to my return to med school, I thought \u0026ldquo;Oh no, I really enjoy doing science, do I really have to go to med school?\u0026rdquo;. I also remember at the end of Step 1 and the first two years of med school thinking, \u0026ldquo;Oh no, I really enjoy med school, do I really have to do science again?\u0026rdquo;. I think I have a welcome problem of enjoying what I\u0026rsquo;m doing. The third year of med school is a shift. After years of memorizing and examinations, the doors to the promised land are finally opened. I have experienced nothing like it before It feels intentionally unsettling. You are thrown into the clinic with a modicum of guidance so you aren\u0026rsquo;t totally caught off guard, but you are thrown out to the wolves. I don\u0026rsquo;t mean this as a criticism of the system, it feels necessary. Third year medical students—commonly shorted to MS3s—have just one year to experience a broad swath of medicine and pick a specialty. So you had better be ready to dive in.\nTotal immersion I came to terms with my new reality quickly. Gone were the days of hitting the snooze button and going home when I pleased. I am now beholden to other people\u0026rsquo;s schedules. This came back relatively naturally. Maybe not hitting snooze. A regrettable personal failing of mine. I was, however, immediately faced with a new reality in the patient room. Patients come to the doctor for a number of reasons, but often seek relief. To get to the core of what ails them, they will tell you everything. I was not prepared for how vulnerable patients would be with me. I am not sure if this ever will feel natural. I hope it never does. I was told many stories of experiences living with scary diagnoses, and not knowing what to do with it. Family histories of all sorts. Personal details that were sometimes (oftentimes?) off the wall. I see all of these specifics as flailing, grasping at sand hoping that something could explain their pain. Sometimes it could. Usually it did not. But since I was in a white coat, I was privileged to hear it.\nI think my years spent in the lab have prepared me to face some of the challenges set before me. At the very least, having a few more years under my belt helped me approach the year with a bit of maturity. This seems to have paid off. I guess my recommendation is to simply get old before going to med school. Returning to studying The hospital is how I spent the majority of my time, but a new reality for me was also going back to daily studying. There is a strange dichotomy in medicine of \u0026ldquo;Oh, it doesn\u0026rsquo;t really matter\u0026rdquo; and \u0026ldquo;If you don\u0026rsquo;t get this class/score/grade then you won\u0026rsquo;t be able to be the kind of doctor you want to be, so you had better get your act together.\u0026rdquo; Simultaneously there are no expectations and immense responsibility for the looming specter of Step 2. I\u0026rsquo;m glad that studying regularly came back easily enough. I was concerned I would experience a studying whiplash. I\u0026rsquo;m glad it never came. I did UWorld and Anki nearly every day for a full year and felt alright.\nBecoming invisible I quickly learned I needed to change my understanding of my contribution to the team. Exiting grad school, people understood that they could come to me for help. I was a resource, a seasoned veteran of the lab. If someone needed an experiment done, I could do it, and be trusted to do it. In med school as a third year, I was nothing. A fly on the wall; a worm beneath the feet of the real doctors. In science, I felt like I was treated as a peer with even my committee members with multiple R01s. Even if I didn\u0026rsquo;t understand the science perfectly, I could contribute some different perspective. In medicine, sometimes not being recognized at all by my attendings was the best outcome. Which happened regularly. My role, was not as a contributor—as it was in science—it was simply to get in the reps. Once I understood that the expectations of me were below the ground, I understood that everything I did in third year was for myself. This is taken at face value by the team at times. I would spend 30 minutes working on a presentation, pre-rounding, the works, and at the end of my part, the intern would nod, then turn to the senior resident and say \u0026ldquo;I was thinking that we\u0026hellip;\u0026rdquo; without thinking of my work. This is perhaps a bit of cognitive restructuring, but recognizing this is what gave me the freedom to embed myself in the hospital flow, without a single worry about the outcome. Simply doing my best was the best thing I could do. Obviously. But this was not apparent to me at first. I needed more quality repetitions to develop good habits in the future. And also experience as much of medicine as possible to find what I want to do with my life. This permission allowed me to approach specialties I do not care about with the awe and respect they deserve.\nA year of wonder. Med school prepares you for the standardized tests. I think this is generally useful. The tests on aggregate are reasonable and evaluate your ability to think through common clinical scenarios. There will always be oddball questions that come out of left field, but I let these flow over me. No need to perseverate on the small stuff. The time for that can come later.\nWhat I didn\u0026rsquo;t realize is how much of the \u0026ldquo;classic\u0026rdquo; material we are fed in the first couple years of med school would come to the forefront. The \u0026ldquo;sandpaper rash\u0026rdquo; of scarlet fever really does feel like sandpaper. Nikolsky\u0026rsquo;s sign actually works. Tripoding for epiglottitis gets the physicians worked up. Don\u0026rsquo;t forget about von Willebrand\u0026rsquo;s disease when someone seems to be bleeding a bit too much. TB is out there, watch for hemoptosis. Night sweats, unintended weight loss, is cancer until proven otherwise. And yes, it really can be lupus.\nIn general, facing the unknown with a sense of earnestness was the way I felt best able to respect those who gathered and passed down the medical knowledge I am privileged to learn today. Sometimes, my excitement to see aspects of medicine would rouse a curious response from the residents. I project here, but I felt a sense of surprise, like that of a doting parent seeing their child experience something new, after forgetting the astonishment they once felt.\nEarnestness is next to med studentlyness.\nPerhaps what I\u0026rsquo;m getting at here is that I found it important to bask in the privilege of seeing the pathology I encountered in med school, and to remind the residents of this sensation. I felt childish at times—and perhaps overanimated—but I found this excitement was to my and my resident\u0026rsquo;s benefit.\nMy surgery rotation overflowed with examples of wonder of medicine. Partially because of the team I worked with, and the rest because of the undeniable coolness of surgery. The OR is a cool place. The orderliness and chaos ebb. The spans of steady, industrious work are interrupted with staccato notes of bedlam. The anatomy I learned in class was ever present, but the surgeons bemoaned \u0026ldquo;normal anatomic variation\u0026rdquo;.\nI was struck with wonder at the sight of human anatomy as it unfolded before me. What I was able to experience in the OR felt like the culmination of centuries of human curiosity. There is an ancientness to medicine that I catch flashes of—I could perform the physical exam on humans hundred of millions of years ago and interrogate the same pathologies as I do in the hospital today—and viewing the exposed anatomy is a pressure-bagged infusion of this collective wonder. To gaze upon the peristalsing of the small intestine, or steady beating of the heart is a sight to behold, indeed.\nA year of shame. It weighs upon me the circumstances that resulted in these transcendent experiences. Not one patient was in the hospital without reason. What to make of these patients with horrible pathology? I still feel unsettled about how the cause of their pain sparked wonder. How dare I gain, merely by the circumstance of having their care managed at UNC, Which, as a tertiary care center, layers on more complexity. Many patients end up at UNC because they have no where else they can go for help. And this signs them up for med students? For shame. from the very essence of their malady? I do not know what to do with my discomfort, but I think it is best that I dwell in it. With this, I respect the people before me in the hospital and recognize their humanity.\nBut I often complained of what I say here I was lucky to do. I find myself resentful of my future schedule; when was I supposed to learn that I will be working 13 hour days, 6 days a week for the rest of my life? And what of having a family? Medicine by necessity requires sacrifice. I happened to sign up for sacrifices years before I recognized how profound they were. How might I balance this dread and with the joy of practicing medicine? And why do I seem more concerned about this than others? Am I not grateful enough? Am I not capable of the sacrifices that others seem to offer so effortlessly? I don\u0026rsquo;t necessarily think this to be true, but these questions erode at my will to pursue medicine.\nPerhaps most shameful of all is how my understanding of the patient-provider interaction evolved over the year. It began as an exploration of an open book, a tabula rasa that held within it a diagnosis and how to best intervene. On my first day in the outpatient clinic, it was clear that this is not the case. My preceptor had only 20 minutes for me to ① interview the patient and perform the physical exam, ② present with a plan, ③ return to the room and do everything again, ④ write orders, educate, and get the patient out of the door. It simply is not amenable to the free form, personable, curious interview I hoped to perform. By the end of the year, I had optimized how I asked questions to keep patients from going off the rails. When prerounding in medicine, I was there to extract information and not much else. Small talk had to go, there was no time. I like to chat, so this came at a loss of who I think I am. I am not sure how to do this well, while still feeling like Zachary. And from what I gather from the interns, that may just come later in my career. I found myself questioning, \u0026ldquo;Is this the \u0026lsquo;patient interaction\u0026rsquo; that has been mythologized throughout my training?\u0026rdquo; The carrot at the end of the stick dangled before me with a \u0026ldquo;You are so lucky to be able to do this, so you had better not complain of any abuse that comes your way.\u0026rdquo; It wasn\u0026rsquo;t a genuine interaction as much as me leading the patient along to tell me what I wanted to know. Of course, I used open ended questions, but only open enough. Leave the door a bit too open and next thing you know, you are talking about their dog\u0026rsquo;s breeder while you constantly stare at your watch, imagining what your attending will say when you return. I feel like I am alone in missing the core human element that funnels sprightly youths into medicine. Or worse, finding it a façade.\nThe shame extends beyond the hospital. One aspect of my life that has changed most dramatically is the sheer amount of time I felt I needed to dedicate to medicine, whether at the hospital or at home. I spent all day basking in the wonder of medicine, then I would come home and study for hours. I relied on my partner for keeping our household together more than ever, because I spent all day—all year, rather—in a state of discovery. Her life was largely the same, with the normal challenges of being a scientist, with the added bonus of getting less help from me. The shame built over the year. Again, how dare I?\nA year of glad. This has been an undeniable year of growth and joy, with these quibbles. It is clear that I was happier than I was during grad school. I know this from within myself, and reinforced by my wife\u0026rsquo;s comments on my mood. The pace of the day, and immediacy of problem solving were a welcome change.\nI recall, during the very first days preparing for med school during xTAP, having to do a simulated patient encounter complete with patient presentation to an attending physician. We were told about this encounter days in advance. And yet, I dreaded it. And near the last day of my final rotation, I did 8 of these in a row without breaking a sweat. Progress!\nI think, in a word, what I\u0026rsquo;ve experienced in the third year of med school is gratitude. Gratitude to be privileged to learn what I am learning. Gratitude for the experiences in my life that brought me here. Gratitude for the support from my wife. Gratitude to be involved in people\u0026rsquo;s lives when they are fragile. Ever since reading Braiding Sweetgrass I think one could call me \u0026ldquo;gratitude-pilled\u0026rdquo;. I also selfishly enjoyed the gratitude from patients as I put on my best doctor performance. In reflection on the year, I have spent time thinking of a phrase that I heard a number of times throughout med school from residents, \u0026ldquo;The worst day of residency is better than the best day of med school.\u0026rdquo; I find this hard to believe. This year has been magical. It is hard to imagine a year filled with more wonder and joy of caring for those in need. I will have to rely on the experience of those who have walked this path and trust that the rest of my training has plenty of magic to spare.\n","permalink":"https://www.zacharybillman.com/posts/ms3-year-is-magical/","summary":"\u003ch2 id=\"it-s-over-dot\"\u003eIt\u0026rsquo;s over.\u003c/h2\u003e\n\u003cp\u003eMy third year of medical school is officially behind me. I managed to get in a grand total of \u003cem\u003ezero\u003c/em\u003e blog posts during grad school, so here\u0026rsquo;s to a new year with hopefully some more thoughts being shared. I have a lot to reflect on from the past year. It was wonderful. I wish everyone could experience what I did this past year. I think it goes without saying:\u003c/p\u003e","title":"The third year of medical school is magical."},{"content":"I, like many others, picked up a new hobby during the pandemic. Other people\u0026rsquo;s hobbies may bring them joy. This could be for many reasons. There is the joy of creating something from scratch. You can revel in your thriftiness. You can embrace the pride when you recognize that your creation is on par (or better!) than what you can buy. I feel like these are embodied in the sourdough craze that caught fire early on in COVID. Dare I say that I did this before it was cool? \u0026#x1f60e; I baked two loaves of bread almost every weekend through med school. Maybe I should bring that back, it\u0026rsquo;s been a while since I brought out the ole\u0026rsquo; starter. My pandemic hobby is similar, but different in that it often feels like a chore, costs more money, and often turns out worse than what I can buy. Of course, I am talking about how I\u0026rsquo;ve started roasting my own coffee at home.\nI\u0026rsquo;m not sure where this idea was planted into my brain. I don\u0026rsquo;t think I know anyone who roasts their own beans, and I certainly didn\u0026rsquo;t know how. I didn\u0026rsquo;t even drink coffee regularly until after college! I guess that extra time on the computer sent me down a rabbithole I have yet to emerge from.\nFirst, I want to preface the following with a disclaimer: This is not a detailed guide about how to roast your own coffee. If you are interested, I recommend checking out the How To Roast Your Own Coffee guide at Sweet Maria\u0026rsquo;s as a starting point. There is also the /r/roasting subreddit if that is your cup of tea. My only warning is there will be a lot of smoke. Roast your coffee outside, for Pete\u0026rsquo;s sake!\nIt all started with a trusty popcorn popper. There are a few things you want when you roast coffee:\nAir hot enough to roast coffee Remove the chaff from the beans Turns out that a classic popcorn popper fits the bill, as long as it has an upwards airflow and doesn\u0026rsquo;t let the chaff fall into the heating element. There is a bit of a cult following for the West Bend Poppery 2 model, but that one seemed a bit pricey, so I settled for a very capable popper from Nostalgia.\nFigure 1: I got a good bit of mileage out of my popcorn popper. If you are interested in roasting your own coffee I would give it a whirl.\nThings were simple back then. I still bought most of the coffee I drank, but I roasted enough to enjoy some freshly roasted coffee as an occasional treat. I ordered 10 pounds of green beans from Sweet Maria\u0026rsquo;s and life was good.\nThen I became a bit of a coffee snob.\nI could only roast 100 grams of coffee at a time in the popcorn popper, which is only enough for one pot of coffee in the morning for me. So it was time to upgrade.\nI bought the SR800 fluid bed roaster, which upped my roasting capacity and gave me finer control on temperature and airflow. Suffice to say my roasts improved a lot! At this point, I would consider my coffee good enough to sell at a farmer\u0026rsquo;s market to break even.\nIf you ever find yourself on a coffee roasting forum and bring up the SR800, someone is bound to bring up the famous RazzoRoasting extension tube. If you look for advice for how to use the SR800, I swear it\u0026rsquo;s assumed that you have this very specific accessory. \u0026hellip;And so I bought one.\nDon\u0026rsquo;t worry, that is the extent of all of my coffee spending (for now). I am a very satisfied coffee roaster now. Check out this quick series of images going from the green beans to a nearly finished product! I can spend about 45 minutes and go from nothing to nearly 2 pounds of roasted beans, enough for about a week and a half of coffee. Not bad! The only downside is that now I feel like I need to buy coffee from local roasters to get my fix. There are certainly crueler fates.\nAs a sign off, I will share something that surprised me about coffee roasting. When I roast coffee, the most important cue to determine if the coffee is roasted is the sound. That\u0026rsquo;s right, not the color, not the smell, but the sound. When heating up a coffee bean, the water trapped inside eventually bursts out of the bean in a rapid expansion. This is called \u0026ldquo;first crack\u0026rdquo;, and indicates that the coffee is roasted enough to be drinkable. The expansion also releases the chaff from the bean. If you continue heating up the bean, you will eventually reach \u0026ldquo;second crack\u0026rdquo;. I think a solid medium roast is taken out just before second crack, so I try to take my coffee out to this point and it hasn\u0026rsquo;t proved me wrong yet.\nHappy coffee-ing! \u0026#x2615;\n","permalink":"https://www.zacharybillman.com/posts/roasting-coffee-at-home/","summary":"\u003cp\u003eI, like many others, picked up a new hobby during the pandemic. Other people\u0026rsquo;s hobbies may bring them joy. This could be for many reasons. There is the joy of creating something from scratch. You can revel in your thriftiness. You can embrace the pride when you recognize that your creation is on par (or better!) than what you can buy. I feel like these are embodied in the sourdough craze that caught fire early on in COVID.\n\u003cspan class=\"sidenote-number\"\u003e\u003csmall class=\"sidenote\"\u003e\nDare I say that I did this before it was cool? \u0026#x1f60e; I baked two loaves of bread almost every weekend through med school. Maybe I should bring that back, it\u0026rsquo;s been a while since I brought out the ole\u0026rsquo; starter.\n\u003c/small\u003e\u003c/span\u003e\nMy pandemic hobby is similar, but different in that it often feels like a chore, costs more money, and often turns out worse than what I can buy. Of course, I am talking about how I\u0026rsquo;ve started roasting my own coffee at home.\u003c/p\u003e","title":"Roasting coffee at home. ☕"},{"content":"It is an age-old question: how can one keep up with the continuous output of science? I remember at the beginning of my PhD struggling to figure out how anyone found out when a new paper came out. \u0026#x1f635; Did they sit on nature.com and spam the refresh button? Did they know when each journal released their latest issue?\nBehold the power of RSS! Most websites have a page that contains information about each subpage in a computer-readable format called RSS (Really Simple Syndication). Mine has one right here! These pages can be parsed by a number of RSS feed aggregators. The way these pages are set up make it such that they add any new information hosted at that domain. This is useful in the science world because you can find the RSS feed of a given journal, subscribe to it, then have every new article published online be delivered right to you.\nThere are a plethora of RSS feed aggregators you can pick from manage your feeds. I have previously used Feedly and Inoreader, which are great free solutions, but have moved on to selfhosting my own instance of FreshRSS.\nAfter making an account at your friendly local RSS feed aggregator, you can add whatever feeds your heart desires. To find a journal\u0026rsquo;s rss feed, I often just search \u0026ldquo;$JOURNAL_NAME rss feed\u0026rdquo; and poke around until I find something that looks right. Most of the aggregators will test the feed out first to make sure that you are trying to add a legitimate one. Here are a few of the heavy hitters to get you started:\nhttp://feeds.nature.com/nature/rss/current https://www.science.org/rss/express.xml https://www.cell.com/cell/inpress.rss Nothing like a constant stream of Cell, Science, and Nature to make your project feel like a real winner, eh?\nHere is what my own site looks like.\nFigure 1: My current FreshRSS setup. On the left I have my feeds separated into folders. In the middle you can see the titles of papers that appear in my feed.\nAnd after I hit J to move to the first item in the feed.\nFigure 2: With a title selected, you can see the abstract and authors.\nAfter collecting all of your desired RSS feeds, you cannot forego your responsibility of actually reading them! Most RSS feed aggregators have shortcuts to move through titles quickly (Typically J to move on to the next one and K to move up.) They always seem to use vi keybindings. A bunch of computer nerds have really cornered the keybinding market. I have let them take over my computing life. Each morning when I get into the lab, I quickly set up something, then head to my desk to hit J until the counter reaches zero.\nBut what about my very specific field? You can subscribe to all of the journals you want, but that doesn\u0026rsquo;t make the papers with your specific interests pop out. Fortunately, the NIH has this exact circumstance in mind.\nWhen you make a new search on PubMed you might notice the \u0026ldquo;Create RSS\u0026rdquo; button. Give it a click, then you will have a personal link you can add to your favorite RSS feed aggregator.\nFigure 3: Somehow I never noticed this button until I needed it.\nThis changed the game for me for keeping up with papers. Unfortunately, it doesn\u0026rsquo;t solve the problem of library management, or actually getting around to reading the papers you care about. I will leave library management as an exercise for the interested reader. Here\u0026rsquo;s a tip, the best solution uses the Zotero citation manager. Bonus points for using Zotfile for renaming your PDFs and Better BibTex for Zotero. \u0026#x1f609; I hope this helps you get your eyeballs on that science you crave. If you have solved the problem of accruing papers to read faster than you read them, let me know.\n","permalink":"https://www.zacharybillman.com/posts/rss-feeds-to-find-science-papers/","summary":"\u003cp\u003eIt is an age-old question: how can one keep up with the continuous output of science? I remember at the beginning of my PhD struggling to figure out how anyone found out when a new paper came out. \u0026#x1f635; Did they sit on nature.com and spam the refresh button? Did they know when each journal released their latest issue?\u003c/p\u003e\n\u003ch2 id=\"behold-the-power-of-rss\"\u003eBehold the power of RSS!\u003c/h2\u003e\n\u003cp\u003eMost websites have a page that contains information about each subpage in a computer-readable format called RSS (Really Simple Syndication). \u003ca href=\"https://zacharybillman.com/index.xml\"\u003eMine has one right here!\u003c/a\u003e These pages can be parsed by a number of RSS feed aggregators. The way these pages are set up make it such that they add any new information hosted at that domain. This is useful in the science world because you can find the RSS feed of a given journal, subscribe to it, then have every new article published online be delivered right to you.\u003c/p\u003e","title":"Using RSS feeds to keep on top of science."},{"content":"My interest in self-hosting began in my with my interests in internet privacy. Plastered all over the internet are stories about how much Google, Facebook and Amazon know about you. I deleted my Facebook account years ago, and I\u0026rsquo;m too paranoid to go back to the site because there\u0026rsquo;s a real possibility that Facebook has cached my account, ready to spin it back up in case I try to login again. The ads served to me were too accurate for my liking. This is despite almost never clicking on them! I have become convinced of the idea that, if you are not paying for the product, you are the product. From this assumption, it follows that anywhere I trust with my data that I am not paying for (like Google Drive, Google Photos, Dropbox, Facebook, Twitter) is using my data to earn money. We know that Google uses the labels you add to Photos to train it\u0026rsquo;s AI, and Facebook uses (at least) Instagram photos to train it\u0026rsquo;s AI. For some, the value proposition of allowing a company to use your data for a useful service in return is an acceptable one. I find this to be a reasonable stance, but I took my growing interest in internet privacy as a chance to learn about how I can take control of my data.\nInitially, I lurked on forums like /r/privacy to learn what I could do to avoid big-tech\u0026rsquo;s watchful eye. There were numerous comments along the lines of: \u0026ldquo;The only way to be in control of your data is to self-host your services.\u0026rdquo; I had no idea what this meant! Hard to believe that less than a year later, I learned to use (and love) Linux as my primary OS, and have happily replaced Google Photos, Google Drive and other services with my own self-hosted alternatives. Self-hosting, I have since learned, is when you run useful programs from your own computer. By doing so, you have complete knowledge of where and how your data is stored and how it is being used. It has the additional effect of being a bottomless time sink.\nTo begin, I needed an always-on computer to run these useful programs. I began with a humble Raspberry Pi.\nFigure 1: My humble Raspberry Pi and its hard drive. This dude currently tirelessly runs the excellent Adguard Home and downloads a backup of my data every night.\nThese are tiny, but capable computers that are great for fiddling with. The projects people develop for these are amazing and diverse. With RPi in hand, I began with the ambitious project of replacing Google Drive with Nextcloud. After much frustration with a bare metal installation, I found the NextcloudPi project. Surprisingly, it went pretty okay! At first, I was intimidated by Linux defaults, but over time I grew to appreciate, and indeed, prefer Linux as an operating system. My decision to use Linux over Windows/MacOS is because it is free and open source software (FOSS). This is a topic for a different post, but I think using FOSS when possible is a moral imperative of sorts. I used Nextcloud strictly from my home for a few months, without the ability to connect to it from the internet, to test the self-hosting waters. My first true cloud replacement spun up once I decided to access this lil\u0026rsquo; guy from the internet. To do so, I purchased a domain (not the one this site is hosted on) and pointed it to the IP of my house. I forwarded the appropriate ports of my router to the RPi.\nThis is when the real exploration began. I was able to access my files and images using Nextcloud, but the photo viewing service left something to be desired. No problem, why not spin up an instance of Photoprism? I use RSS feeds to keep on top of the latest science in the journals relevant to my field using Feedly. Why not host my own RSS feed aggregator so I can subscribe to as many feeds as I desire?\nThis cycle continued, and I accrued many cool applications, but in the back of my mind I worried about opening up my home network to the internet. I also struggled to run some programs because the RPi uses the arm64 architecture, and most services are written with amd64 in mind. These two forces eventually convinced me to purchase a server where I could manage all of my services remotely. Some would say that not owning the hardware that is running your own services is not \u0026ldquo;true\u0026rdquo; self-hosting. I think this is needlessly exclusive. Let everyone self host, dangit! Someday, when I have more stable internet and a more permanent home, I hope to host everything from my own home, but until then, I\u0026rsquo;m extremely pleased with my current stack. And that is where I am now. I happily host numerous services on my virtual private server that entirely replace Google Photos, Google Drive and GitHub for me. Even better, there are specialized services that fill a need I never realized I had. What\u0026rsquo;s more, if I ever want to spin up a new service, all I have to do is add it to my to docker-compose file and it will be up within minutes. What a world!\nI thought about making this into a \u0026ldquo;guide\u0026rdquo; style post. I nixed that idea because, quite frankly, I feel like I don\u0026rsquo;t know what I\u0026rsquo;m doing. I am really happy with my setup, but I don\u0026rsquo;t feel like I have the authority to tell people how to administer their own services. If you are interested, allow me to point you toward the guide that really got me rolling: Ultimate Traefik Docker Compose Guide.\nFor those of you wondering what I am currently hosting, check out my current list at the link and let me know what you think!\n","permalink":"https://www.zacharybillman.com/posts/my-selfhosting-journey/","summary":"\u003cp\u003eMy interest in self-hosting began in my with my interests in internet privacy. Plastered all over the internet are stories about how much Google, Facebook and Amazon know about you. I deleted my Facebook account years ago, and I\u0026rsquo;m too paranoid to go back to the site because there\u0026rsquo;s \u003ca href=\"https://www.reddit.com/r/privacy/comments/6nmjfh/facebook_account_fully_recovered_3_years_after/\"\u003ea real possibility that Facebook has cached my account, ready to spin it back up\u003c/a\u003e in case I try to login again. The ads served to me were too accurate for my liking.\n\u003cspan class=\"sidenote-number\"\u003e\u003csmall class=\"sidenote\"\u003e\nThis is despite almost never clicking on them!\n\u003c/small\u003e\u003c/span\u003e\nI have become convinced of the idea that, if you are not paying for the product, you are the product. From this assumption, it follows that anywhere I trust with my data that I am not paying for (like Google Drive, Google Photos, Dropbox, Facebook, Twitter) is using my data to earn money. We know that \u003ca href=\"https://www.theverge.com/2020/11/11/21559930/google-train-ai-photos-image-labelling-app-android-update\"\u003eGoogle uses the labels you add to Photos to train it\u0026rsquo;s AI\u003c/a\u003e, and \u003ca href=\"https://ai.facebook.com/blog/seer-the-start-of-a-more-powerful-flexible-and-accessible-era-for-computer-vision/\"\u003eFacebook uses (at least) Instagram photos to train it\u0026rsquo;s AI\u003c/a\u003e. For some, the value proposition of allowing a company to use your data for a useful service in return is an acceptable one. I find this to be a reasonable stance, but I took my growing interest in internet privacy as a chance to learn about how I can take control of my data.\u003c/p\u003e","title":"My selfhosting journey."},{"content":"N.B.: I hope to add screenshots for each of these eventually. For now, I hope links to each services\u0026rsquo; website will suffice.\nSeafile\nThis is a great tool for managing files. I moved to this from Nextcloud because I am of the philosophy that I would prefer services that do one thing excellently instead of many things well. Nextcloud is an incredible Office365 replacement, but I found myself using a fraction of what it was capable of providing. Enter Seafile. It is cloud file syncing with a robust encryption implementation, just what the doctor ordered.\nPhotoprism\nNextcloud\u0026rsquo;s implementation of photo management was a bit clumsy for my tastes, so I began on a hunt for a more feature complete option. I was very lucky to stumble upon Photoprism early on in my self hosting journey. I am a proud supporter of this project. It brings a ton to the table, and doesn\u0026rsquo;t leave me missing Google Photos one bit. It is also actively developed. For instance, as of 2022-07-02, there was a recent update that improved scrolling a ton, which was one of my remaining quibbles with it\u0026rsquo;s functionality. Some people complain that it doesn\u0026rsquo;t scale up for libraries of 10,000+ photos, but my 2000 photo library works swimmingly. On my phone, I use the Folder Sync app to automatically send any pictures I take on my phone to the Photoprism imports folder. Within 15 minutes of snapping a photo, it is there on my Photoprism instance. I highly recommend giving it a go.\nMealie\nI have to admit that the name leaves something to be desired. Fortunately, the service itself doesn\u0026rsquo;t fall short. Mealie is a recipe management application. It is able to parse your favorite recipe websites to create immortalized versions of the recipe. This helps fight detestable link rot that plagues the internet. It allows you to edit ingredient amounts, make comments about what you would change next time, and plan out your weekly meals. It helps that it is beautiful and intuitive to use. If only I could get my partner to use it\u0026hellip; I want to go on the record here and say that I think it is sensible that she doesn\u0026rsquo;t trust my self hosted services that much. In the early days of my self hosting journey, let\u0026rsquo;s just say that the up-time of my services were extremely finicky. I like to think they are more permanent now, especially because I am hosting everything on a VPS, but I certainly cannot compete with the stability of Google and Amazon. (Or pretty much any other paid service for that matter.) \u0026#x1f609;\nGitea\nGitea is a community managed, lightweight code hosting solution written in Go. I use it to manage my data analysis (using Private repos) and even host the source code for this very website! Using Gitea has given me the surface level introduction to the behemoth that is git. Fortunately, that is all I need. Once I have removed any sensitive data (like passwords, etc.) I will make my docker-compose file public. The docker-compose file is where I determine which services I pick to host, and how to configure them to my liking. Hopefully someone will find this useful.\nSyncthing\nIf I could only tell someone to self host a single service, I would have to pick Syncthing. It is a continuous file synchronization program, which means it keeps a specific file or folder the same between any device running Syncthing. I use it to keep my password database and my org-mode notes Now org-mode might be the biggest rabbithole of them all, and definitely the topic for another blog post. I use it to manage my TODO list, my lab notebook, my shopping lists, write this blog, and maintain my Zettelkasten note database. It is an immensely powerful tool. up to date between all of my devices. With Syncthing, all of my data is stored on my own devices and encrypted in transit.\nFreshRSS\nI keep up to date on the science in my field by subscribing to relevant RSS feeds. Yet another topic to write a post about. This really changed the game for my ability to keep on top of the latest research. 2022-07-14 Update: post complete! Check it out here. FreshRSS replaced Feedly for me, as I ran up against the number of feeds I could subscribe to on a free account. Also, when self hosting, I can save as many articles as my heart desires (even if I will never look at them again \u0026#x1f635; ).\nWallabag\nRemember Pocket for Firefox? (Yes, I know it still exists, okay?) Give Wallabag a spin, it is great for storing articles you want to read later. I set up FreshRSS to save articles to my Wallabag instance to keep for later.\nChangeDetection\nNow this is a fun one! ChangeDetection.io is a service that loads a webpage and checks to see if something has changed since the last time. This might not sound useful at first, but I recently used this to check for when a hot item for my new coffee roasting hobby was back in stock. I got an email the other day to let me know it was in stock. Pretty cool!\nHugo\nHugo is the static site generator I use to make this here blog! I was amazed at how much more response my site was using Hugo compare to when I paid a company to host a WordPress site. I\u0026rsquo;m sure WordPress could be fast, but I just wanted a barebones, pure html experience, and Hugo made it easy.\nCommento++\nYou may have noticed that I have some pretty snazzy comments sections on my site. I initially used Disqus, which you may recognize from a ton of sites around the internet, but didn\u0026rsquo;t like how it would serve ads through my comments section, and provided sign-ins using Google/Facebook/Twitter. I wanted to serve the simplest comments section I could, that still gave me the ability to migrate the comments to wherever I decide to keep my server. Go ahead and use the anonymous comment button, fill in your name, and you are off to the races.\nAuthelia\nThere are a few services I host that I really want to lock down. For these services, Authelia is great. It puts up a \u0026ldquo;Enter the 6 digit code on your phone\u0026rdquo; style 2 factor authentication in front of the services I choose. Or, if you follow the guide here, you can have it send you a DUO push, just like you are one of the big hitters out there. I feel much more secure with Authelia in front of Adminer, Traefik, and Portainer.\nBoring stuff that allows everything else to work!\nPostgreSQL database MariaDB database Traefik reverse proxy Umami privacy respecting site analytics Portainer for docker container management Redis in-memory data store Adminer database management traefik-socket-proxy to prevent pesky backdoors to my server! ","permalink":"https://www.zacharybillman.com/posts/zpb-current-selfhosted/","summary":"\u003cp\u003e\u003cem\u003eN.B.: I hope to add screenshots for each of these eventually. For now, I hope links to each services\u0026rsquo; website will suffice.\u003c/em\u003e\u003c/p\u003e\n\u003col\u003e\n\u003cli\u003e\n\u003cp\u003e\u003ca href=\"https://www.seafile.com/en/home/\"\u003eSeafile\u003c/a\u003e\u003c/p\u003e\n\u003cp\u003eThis is a great tool for managing files. I moved to this from Nextcloud because I am of the philosophy that I would prefer services that do one thing excellently instead of many things well. Nextcloud is an incredible Office365 replacement, but I found myself using a fraction of what it was capable of providing. Enter Seafile. It is cloud file syncing with a robust encryption implementation, just what the doctor ordered.\u003c/p\u003e","title":"What I'm currently selfhosting."},{"content":"My partner and I took a trip to the Mason Farm Biological Reserve the other day, and what a glorious day it was. This year, I\u0026rsquo;ve been quite busy in the lab, and missed a lot of the early spring warbler season, so I was very excited by the opportunity to check out the old stomping grounds.\nI brought the camera with me despite the fact we were going to be there around midday when the birds are much less active. I\u0026rsquo;m glad I did, because I got the best look at a common yellowthroat I\u0026rsquo;ve ever had. Normally these guys are flighty, staying close to the ground in small brush or tall grasses, but this one was putting on a proper show for the mating season. Even when you get a glimpse of one, it is usually just that, as they have jumped away before you can pull out the camera, taunting you with their iconic call. I was very pleased to capture a few choice shots of the bird. Hopefully there are more to come. While we were out, I also got a nice picture of a hermit thrush and a king snake.\nThese images have been compressed quite a bit for a lighter internet footprint. These have all been resized to 25% of their original size. If you would like the full sized images, let me know and I will send you a link!\n","permalink":"https://www.zacharybillman.com/posts/the-uncommon-yellowthroat/","summary":"\u003cp\u003eMy partner and I took a trip to the \u003ca href=\"https://ncbg.unc.edu/visit/mason-farm-biological-reserve/\"\u003eMason Farm Biological Reserve\u003c/a\u003e the other day, and what a glorious day it was. This year, I\u0026rsquo;ve been quite busy in the lab, and missed a lot of the early spring warbler season, so I was very excited by the opportunity to check out the old stomping grounds.\u003c/p\u003e\n\u003cp\u003eI brought the camera with me despite the fact we were going to be there around midday when the birds are much less active. I\u0026rsquo;m glad I did, because I got the best look at a common yellowthroat I\u0026rsquo;ve ever had.\n\u003cspan class=\"sidenote-number\"\u003e\u003csmall class=\"sidenote\"\u003e\nNormally these guys are flighty, staying close to the ground in small brush or tall grasses, but this one was putting on a proper show for the mating season. Even when you get a glimpse of one, it is usually just that, as they have jumped away before you can pull out the camera, taunting you with their \u003ca href=\"https://ebird.org/species/comyel#Modal-playlist\"\u003eiconic call\u003c/a\u003e.\n\u003c/small\u003e\u003c/span\u003e\nI was very pleased to capture a few choice shots of the bird. Hopefully there are more to come. While we were out, I also got a nice picture of a hermit thrush and a king snake.\u003c/p\u003e","title":"The (un)common yellowthroat."},{"content":"Welcome to my site! My name is Zachary Billman. I\u0026rsquo;m a UNC MD-PhD student in my 4th year of med school applying to pathology residency programs. I completed my PhD in Ed Miao\u0026rsquo;s lab. The curious reader may be thinking: \u0026ldquo;But Zach, Dr. Miao\u0026rsquo;s lab is at Duke, how did that come about?\u0026rdquo; What an astute question! Ed\u0026rsquo;s lab moved from UNC to Duke in early 2020, and I followed him down the street. My PhD was awarded by the UNC department of Microbiology and Immunology, but it just so happens that (nearly) all of my research took place at Duke. This move was quite a trial, especially when compounded with the onset of the pandemic. I suspect my research timeline suffered, though this is an extremely minor inconvenience compared to the tragedy the pandemic caused. This makes for very interesting basketball viewing parties with my Duke friends!\nMaybe having a diagram will make my training timeline make a bit more sense.\nMy research and scientific interests. I am broadly interested in innate immunology. I spent most of my time in graduate school studying the host-pathogen interaction between the intracellular fungus Histoplasma capsulatum and macrophages. There are many unstudied curiosities regarding the innate immune response to Histoplasma spp. and other intracellular fungi that I think are quite interesting. I also spent a considerable time thinking about the evolution of proteins involved in the programmed cell death pathway called pyroptosis.\nHobbies I may write about. Besides my science, I am interested in birding, baking sourdough bread (I swear I began years before the pandemic, though hearing of people baking bread brings me joy no matter when they first began!), board games, roasting coffee, and self-hosting free and open source software. Over the course of the pandemic, I have learned how to maintain a basic suite of services spread between a server I rent and a computer at home that have replaced my need for Google Photos and Google Drive. I\u0026rsquo;m hoping to be able to move away from these platforms entirely soon. I think they provide a great service, but at a substantial cost to privacy. Hopefully more to be said about my thoughts on FOSS soon! I also transitioned my old, (and quite frankly, embarrassingly slow) managed WordPress site with this lean, static site made in Hugo that I host myself. Now that I have mangled together some CSS to get my precious sidenotes up and running again, I\u0026rsquo;m ready to begin putting some ideas to paper. I love marginalia (the word to describe these notes on the side of this webpage). I\u0026rsquo;m not sure if this is unique to me, but I seem to get caught up in parenthetical / tangential thoughts very often, and I think using an Edward Tufte-esque sidenote is a great way for me to communicate in this way without distracting the reader too much. It seems marginalia such as this have been used throughout history, so perhaps it is normal, but most people can keep their thoughts focused better than me. The implementation I use is inspired by the Tufte CSS project and largely taken from this incredibly helpful post found at scripter.co. I\u0026rsquo;m quite proud of my progress in administering my server and self-hosting useful services.\nThe future of this site. On this site I plan to post updates about my journey through med school, grad school, and self-hosting I would like to share with the world. I have been helped immensely by many others\u0026rsquo; advice and I hope to impart similar tips to others someday. I suspect most posts will be about much lighter fare, like whatever hobbies tickle my fancy at the time.\n","permalink":"https://www.zacharybillman.com/posts/about-me/","summary":"\u003ch2 id=\"welcome-to-my-site\"\u003eWelcome to my site!\u003c/h2\u003e\n\u003cp\u003eMy name is Zachary Billman. I\u0026rsquo;m a UNC MD-PhD student in my 4th year of med school applying to pathology residency programs. I completed my PhD in Ed Miao\u0026rsquo;s lab. The curious reader may be thinking: \u0026ldquo;But Zach, Dr. Miao\u0026rsquo;s lab is at Duke, how did that come about?\u0026rdquo; What an astute question! Ed\u0026rsquo;s lab moved from UNC to Duke in early 2020, and I followed him down the street. My PhD was awarded by the UNC department of Microbiology and Immunology, but it just so happens that (nearly) all of my research took place at Duke.\n\u003cspan class=\"sidenote-number\"\u003e\u003csmall class=\"sidenote\"\u003e\nThis move was quite a trial, especially when compounded with the onset of the pandemic. I suspect my research timeline suffered, though this is an extremely minor inconvenience compared to the tragedy the pandemic caused.\n\u003c/small\u003e\u003c/span\u003e\nThis makes for very interesting basketball viewing parties with my Duke friends!\u003c/p\u003e","title":"About me. 👋"},{"content":"It\u0026rsquo;s over. My third year of medical school is officially behind me. I managed to get in a grand total of zero blog posts during grad school, so here\u0026rsquo;s to a new year with hopefully some more thoughts being shared. I have a lot to reflect on from the past year. It was wonderful. I wish everyone could experience what I did this past year. I think it goes without saying:\nI loved the third year of med school, but I do not want to do it again.\nA year of change. In the days leading up to my return to med school, I thought \u0026ldquo;Oh no, I really enjoy doing science, do I really have to go to med school?\u0026rdquo;. I also remember at the end of Step 1 and the first two years of med school thinking, \u0026ldquo;Oh no, I really enjoy med school, do I really have to do science again?\u0026rdquo;. I think I have a welcome problem of enjoying what I\u0026rsquo;m doing. The third year of med school is a shift. After years of memorizing and examinations, the doors to the promised land are finally opened. I have experienced nothing like it before It feels intentionally unsettling. You are thrown into the clinic with a modicum of guidance so you aren\u0026rsquo;t totally caught off guard, but you are thrown out to the wolves. I don\u0026rsquo;t mean this as a criticism of the system, it feels necessary. Third year medical students—commonly shorted to MS3s—have just one year to experience a broad swath of medicine and pick a specialty. So you had better be ready to dive in.\nTotal immersion I came to terms with my new reality quickly. Gone were the days of hitting the snooze button and going home when I pleased. I am now beholden to other people\u0026rsquo;s schedules. This came back relatively naturally. Maybe not hitting snooze. A regrettable personal failing of mine. I was, however, immediately faced with a new reality in the patient room. Patients come to the doctor for a number of reasons, but often seek relief. To get to the core of what ails them, they will tell you everything. I was not prepared for how vulnerable patients would be with me. I am not sure if this ever will feel natural. I hope it never does. I was told many stories of experiences living with scary diagnoses, and not knowing what to do with it. Family histories of all sorts. Personal details that were sometimes (oftentimes?) off the wall. I see all of these specifics as flailing, grasping at sand hoping that something could explain their pain. Sometimes it could. Usually it did not. But since I was in a white coat, I was privileged to hear it.\nI think my years spent in the lab have prepared me to face some of the challenges set before me. At the very least, having a few more years under my belt helped me approach the year with a bit of maturity. This seems to have paid off. I guess my recommendation is to simply get old before going to med school. Returning to studying The hospital is how I spent the majority of my time, but a new reality for me was also going back to daily studying. There is a strange dichotomy in medicine of \u0026ldquo;Oh, it doesn\u0026rsquo;t really matter\u0026rdquo; and \u0026ldquo;If you don\u0026rsquo;t get this class/score/grade then you won\u0026rsquo;t be able to be the kind of doctor you want to be, so you had better get your act together.\u0026rdquo; Simultaneously there are no expectations and immense responsibility for the looming specter of Step 2. I\u0026rsquo;m glad that studying regularly came back easily enough. I was concerned I would experience a studying whiplash. I\u0026rsquo;m glad it never came. I did UWorld and Anki nearly every day for a full year and felt alright.\nBecoming invisible I quickly learned I needed to change my understanding of my contribution to the team. Exiting grad school, people understood that they could come to me for help. I was a resource, a seasoned veteran of the lab. If someone needed an experiment done, I could do it, and be trusted to do it. In med school as a third year, I was nothing. A fly on the wall; a worm beneath the feet of the real doctors. In science, I felt like I was treated as a peer with even my committee members with multiple R01s. Even if I didn\u0026rsquo;t understand the science perfectly, I could contribute some different perspective. In medicine, sometimes not being recognized at all by my attendings was the best outcome. Which happened regularly. My role, was not as a contributor—as it was in science—it was simply to get in the reps. Once I understood that the expectations of me were below the ground, I understood that everything I did in third year was for myself. This is taken at face value by the team at times. I would spend 30 minutes working on a presentation, pre-rounding, the works, and at the end of my part, the intern would nod, then turn to the senior resident and say \u0026ldquo;I was thinking that we\u0026hellip;\u0026rdquo; without thinking of my work. This is perhaps a bit of cognitive restructuring, but recognizing this is what gave me the freedom to embed myself in the hospital flow, without a single worry about the outcome. Simply doing my best was the best thing I could do. Obviously. But this was not apparent to me at first. I needed more quality repetitions to develop good habits in the future. And also experience as much of medicine as possible to find what I want to do with my life. This permission allowed me to approach specialties I do not care about with the awe and respect they deserve.\nA year of wonder. Med school prepares you for the standardized tests. I think this is generally useful. The tests on aggregate are reasonable and evaluate your ability to think through common clinical scenarios. There will always be oddball questions that come out of left field, but I let these flow over me. No need to perseverate on the small stuff. The time for that can come later.\nWhat I didn\u0026rsquo;t realize is how much of the \u0026ldquo;classic\u0026rdquo; material we are fed in the first couple years of med school would come to the forefront. The \u0026ldquo;sandpaper rash\u0026rdquo; of scarlet fever really does feel like sandpaper. Nikolsky\u0026rsquo;s sign actually works. Tripoding for epiglottitis gets the physicians worked up. Don\u0026rsquo;t forget about von Willebrand\u0026rsquo;s disease when someone seems to be bleeding a bit too much. TB is out there, watch for hemoptosis. Night sweats, unintended weight loss, is cancer until proven otherwise. And yes, it really can be lupus.\nIn general, facing the unknown with a sense of earnestness was the way I felt best able to respect those who gathered and passed down the medical knowledge I am privileged to learn today. Sometimes, my excitement to see aspects of medicine would rouse a curious response from the residents. I project here, but I felt a sense of surprise, like that of a doting parent seeing their child experience something new, after forgetting the astonishment they once felt.\nEarnestness is next to med studentlyness.\nPerhaps what I\u0026rsquo;m getting at here is that I found it important to bask in the privilege of seeing the pathology I encountered in med school, and to remind the residents of this sensation. I felt childish at times—and perhaps overanimated—but I found this excitement was to my and my resident\u0026rsquo;s benefit.\nMy surgery rotation overflowed with examples of wonder of medicine. Partially because of the team I worked with, and the rest because of the undeniable coolness of surgery. The OR is a cool place. The orderliness and chaos ebb. The spans of steady, industrious work are interrupted with staccato notes of bedlam. The anatomy I learned in class was ever present, but the surgeons bemoaned \u0026ldquo;normal anatomic variation\u0026rdquo;.\nI was struck with wonder at the sight of human anatomy as it unfolded before me. What I was able to experience in the OR felt like the culmination of centuries of human curiosity. There is an ancientness to medicine that I catch flashes of—I could perform the physical exam on humans hundred of millions of years ago and interrogate the same pathologies as I do in the hospital today—and viewing the exposed anatomy is a pressure-bagged infusion of this collective wonder. To gaze upon the peristalsing of the small intestine, or steady beating of the heart is a sight to behold, indeed.\nA year of shame. It weighs upon me the circumstances that resulted in these transcendent experiences. Not one patient was in the hospital without reason. What to make of these patients with horrible pathology? I still feel unsettled about how the cause of their pain sparked wonder. How dare I gain, merely by the circumstance of having their care managed at UNC, Which, as a tertiary care center, layers on more complexity. Many patients end up at UNC because they have no where else they can go for help. And this signs them up for med students? For shame. from the very essence of their malady? I do not know what to do with my discomfort, but I think it is best that I dwell in it. With this, I respect the people before me in the hospital and recognize their humanity.\nBut I often complained of what I say here I was lucky to do. I find myself resentful of my future schedule; when was I supposed to learn that I will be working 13 hour days, 6 days a week for the rest of my life? And what of having a family? Medicine by necessity requires sacrifice. I happened to sign up for sacrifices years before I recognized how profound they were. How might I balance this dread and with the joy of practicing medicine? And why do I seem more concerned about this than others? Am I not grateful enough? Am I not capable of the sacrifices that others seem to offer so effortlessly? I don\u0026rsquo;t necessarily think this to be true, but these questions erode at my will to pursue medicine.\nPerhaps most shameful of all is how my understanding of the patient-provider interaction evolved over the year. It began as an exploration of an open book, a tabula rasa that held within it a diagnosis and how to best intervene. On my first day in the outpatient clinic, it was clear that this is not the case. My preceptor had only 20 minutes for me to ① interview the patient and perform the physical exam, ② present with a plan, ③ return to the room and do everything again, ④ write orders, educate, and get the patient out of the door. It simply is not amenable to the free form, personable, curious interview I hoped to perform. By the end of the year, I had optimized how I asked questions to keep patients from going off the rails. When prerounding in medicine, I was there to extract information and not much else. Small talk had to go, there was no time. I like to chat, so this came at a loss of who I think I am. I am not sure how to do this well, while still feeling like Zachary. And from what I gather from the interns, that may just come later in my career. I found myself questioning, \u0026ldquo;Is this the \u0026lsquo;patient interaction\u0026rsquo; that has been mythologized throughout my training?\u0026rdquo; The carrot at the end of the stick dangled before me with a \u0026ldquo;You are so lucky to be able to do this, so you had better not complain of any abuse that comes your way.\u0026rdquo; It wasn\u0026rsquo;t a genuine interaction as much as me leading the patient along to tell me what I wanted to know. Of course, I used open ended questions, but only open enough. Leave the door a bit too open and next thing you know, you are talking about their dog\u0026rsquo;s breeder while you constantly stare at your watch, imagining what your attending will say when you return. I feel like I am alone in missing the core human element that funnels sprightly youths into medicine. Or worse, finding it a façade.\nThe shame extends beyond the hospital. One aspect of my life that has changed most dramatically is the sheer amount of time I felt I needed to dedicate to medicine, whether at the hospital or at home. I spent all day basking in the wonder of medicine, then I would come home and study for hours. I relied on my partner for keeping our household together more than ever, because I spent all day—all year, rather—in a state of discovery. Her life was largely the same, with the normal challenges of being a scientist, with the added bonus of getting less help from me. The shame built over the year. Again, how dare I?\nA year of glad. This has been an undeniable year of growth and joy, with these quibbles. It is clear that I was happier than I was during grad school. I know this from within myself, and reinforced by my wife\u0026rsquo;s comments on my mood. The pace of the day, and immediacy of problem solving were a welcome change.\nI recall, during the very first days preparing for med school during xTAP, having to do a simulated patient encounter complete with patient presentation to an attending physician. We were told about this encounter days in advance. And yet, I dreaded it. And near the last day of my final rotation, I did 8 of these in a row without breaking a sweat. Progress!\nI think, in a word, what I\u0026rsquo;ve experienced in the third year of med school is gratitude. Gratitude to be privileged to learn what I am learning. Gratitude for the experiences in my life that brought me here. Gratitude for the support from my wife. Gratitude to be involved in people\u0026rsquo;s lives when they are fragile. Ever since reading Braiding Sweetgrass I think one could call me \u0026ldquo;gratitude-pilled\u0026rdquo;. I also selfishly enjoyed the gratitude from patients as I put on my best doctor performance. In reflection on the year, I have spent time thinking of a phrase that I heard a number of times throughout med school from residents, \u0026ldquo;The worst day of residency is better than the best day of med school.\u0026rdquo; I find this hard to believe. This year has been magical. It is hard to imagine a year filled with more wonder and joy of caring for those in need. I will have to rely on the experience of those who have walked this path and trust that the rest of my training has plenty of magic to spare.\n","permalink":"https://www.zacharybillman.com/posts/ms3-year-is-magical/","summary":"\u003ch2 id=\"it-s-over-dot\"\u003eIt\u0026rsquo;s over.\u003c/h2\u003e\n\u003cp\u003eMy third year of medical school is officially behind me. I managed to get in a grand total of \u003cem\u003ezero\u003c/em\u003e blog posts during grad school, so here\u0026rsquo;s to a new year with hopefully some more thoughts being shared. I have a lot to reflect on from the past year. It was wonderful. I wish everyone could experience what I did this past year. I think it goes without saying:\u003c/p\u003e","title":"The third year of medical school is magical."},{"content":"I, like many others, picked up a new hobby during the pandemic. Other people\u0026rsquo;s hobbies may bring them joy. This could be for many reasons. There is the joy of creating something from scratch. You can revel in your thriftiness. You can embrace the pride when you recognize that your creation is on par (or better!) than what you can buy. I feel like these are embodied in the sourdough craze that caught fire early on in COVID. Dare I say that I did this before it was cool? \u0026#x1f60e; I baked two loaves of bread almost every weekend through med school. Maybe I should bring that back, it\u0026rsquo;s been a while since I brought out the ole\u0026rsquo; starter. My pandemic hobby is similar, but different in that it often feels like a chore, costs more money, and often turns out worse than what I can buy. Of course, I am talking about how I\u0026rsquo;ve started roasting my own coffee at home.\nI\u0026rsquo;m not sure where this idea was planted into my brain. I don\u0026rsquo;t think I know anyone who roasts their own beans, and I certainly didn\u0026rsquo;t know how. I didn\u0026rsquo;t even drink coffee regularly until after college! I guess that extra time on the computer sent me down a rabbithole I have yet to emerge from.\nFirst, I want to preface the following with a disclaimer: This is not a detailed guide about how to roast your own coffee. If you are interested, I recommend checking out the How To Roast Your Own Coffee guide at Sweet Maria\u0026rsquo;s as a starting point. There is also the /r/roasting subreddit if that is your cup of tea. My only warning is there will be a lot of smoke. Roast your coffee outside, for Pete\u0026rsquo;s sake!\nIt all started with a trusty popcorn popper. There are a few things you want when you roast coffee:\nAir hot enough to roast coffee Remove the chaff from the beans Turns out that a classic popcorn popper fits the bill, as long as it has an upwards airflow and doesn\u0026rsquo;t let the chaff fall into the heating element. There is a bit of a cult following for the West Bend Poppery 2 model, but that one seemed a bit pricey, so I settled for a very capable popper from Nostalgia.\nFigure 1: I got a good bit of mileage out of my popcorn popper. If you are interested in roasting your own coffee I would give it a whirl.\nThings were simple back then. I still bought most of the coffee I drank, but I roasted enough to enjoy some freshly roasted coffee as an occasional treat. I ordered 10 pounds of green beans from Sweet Maria\u0026rsquo;s and life was good.\nThen I became a bit of a coffee snob.\nI could only roast 100 grams of coffee at a time in the popcorn popper, which is only enough for one pot of coffee in the morning for me. So it was time to upgrade.\nI bought the SR800 fluid bed roaster, which upped my roasting capacity and gave me finer control on temperature and airflow. Suffice to say my roasts improved a lot! At this point, I would consider my coffee good enough to sell at a farmer\u0026rsquo;s market to break even.\nIf you ever find yourself on a coffee roasting forum and bring up the SR800, someone is bound to bring up the famous RazzoRoasting extension tube. If you look for advice for how to use the SR800, I swear it\u0026rsquo;s assumed that you have this very specific accessory. \u0026hellip;And so I bought one.\nDon\u0026rsquo;t worry, that is the extent of all of my coffee spending (for now). I am a very satisfied coffee roaster now. Check out this quick series of images going from the green beans to a nearly finished product! I can spend about 45 minutes and go from nothing to nearly 2 pounds of roasted beans, enough for about a week and a half of coffee. Not bad! The only downside is that now I feel like I need to buy coffee from local roasters to get my fix. There are certainly crueler fates.\nAs a sign off, I will share something that surprised me about coffee roasting. When I roast coffee, the most important cue to determine if the coffee is roasted is the sound. That\u0026rsquo;s right, not the color, not the smell, but the sound. When heating up a coffee bean, the water trapped inside eventually bursts out of the bean in a rapid expansion. This is called \u0026ldquo;first crack\u0026rdquo;, and indicates that the coffee is roasted enough to be drinkable. The expansion also releases the chaff from the bean. If you continue heating up the bean, you will eventually reach \u0026ldquo;second crack\u0026rdquo;. I think a solid medium roast is taken out just before second crack, so I try to take my coffee out to this point and it hasn\u0026rsquo;t proved me wrong yet.\nHappy coffee-ing! \u0026#x2615;\n","permalink":"https://www.zacharybillman.com/posts/roasting-coffee-at-home/","summary":"\u003cp\u003eI, like many others, picked up a new hobby during the pandemic. Other people\u0026rsquo;s hobbies may bring them joy. This could be for many reasons. There is the joy of creating something from scratch. You can revel in your thriftiness. You can embrace the pride when you recognize that your creation is on par (or better!) than what you can buy. I feel like these are embodied in the sourdough craze that caught fire early on in COVID.\n\u003cspan class=\"sidenote-number\"\u003e\u003csmall class=\"sidenote\"\u003e\nDare I say that I did this before it was cool? \u0026#x1f60e; I baked two loaves of bread almost every weekend through med school. Maybe I should bring that back, it\u0026rsquo;s been a while since I brought out the ole\u0026rsquo; starter.\n\u003c/small\u003e\u003c/span\u003e\nMy pandemic hobby is similar, but different in that it often feels like a chore, costs more money, and often turns out worse than what I can buy. Of course, I am talking about how I\u0026rsquo;ve started roasting my own coffee at home.\u003c/p\u003e","title":"Roasting coffee at home. ☕"},{"content":"It is an age-old question: how can one keep up with the continuous output of science? I remember at the beginning of my PhD struggling to figure out how anyone found out when a new paper came out. \u0026#x1f635; Did they sit on nature.com and spam the refresh button? Did they know when each journal released their latest issue?\nBehold the power of RSS! Most websites have a page that contains information about each subpage in a computer-readable format called RSS (Really Simple Syndication). Mine has one right here! These pages can be parsed by a number of RSS feed aggregators. The way these pages are set up make it such that they add any new information hosted at that domain. This is useful in the science world because you can find the RSS feed of a given journal, subscribe to it, then have every new article published online be delivered right to you.\nThere are a plethora of RSS feed aggregators you can pick from manage your feeds. I have previously used Feedly and Inoreader, which are great free solutions, but have moved on to selfhosting my own instance of FreshRSS.\nAfter making an account at your friendly local RSS feed aggregator, you can add whatever feeds your heart desires. To find a journal\u0026rsquo;s rss feed, I often just search \u0026ldquo;$JOURNAL_NAME rss feed\u0026rdquo; and poke around until I find something that looks right. Most of the aggregators will test the feed out first to make sure that you are trying to add a legitimate one. Here are a few of the heavy hitters to get you started:\nhttp://feeds.nature.com/nature/rss/current https://www.science.org/rss/express.xml https://www.cell.com/cell/inpress.rss Nothing like a constant stream of Cell, Science, and Nature to make your project feel like a real winner, eh?\nHere is what my own site looks like.\nFigure 1: My current FreshRSS setup. On the left I have my feeds separated into folders. In the middle you can see the titles of papers that appear in my feed.\nAnd after I hit J to move to the first item in the feed.\nFigure 2: With a title selected, you can see the abstract and authors.\nAfter collecting all of your desired RSS feeds, you cannot forego your responsibility of actually reading them! Most RSS feed aggregators have shortcuts to move through titles quickly (Typically J to move on to the next one and K to move up.) They always seem to use vi keybindings. A bunch of computer nerds have really cornered the keybinding market. I have let them take over my computing life. Each morning when I get into the lab, I quickly set up something, then head to my desk to hit J until the counter reaches zero.\nBut what about my very specific field? You can subscribe to all of the journals you want, but that doesn\u0026rsquo;t make the papers with your specific interests pop out. Fortunately, the NIH has this exact circumstance in mind.\nWhen you make a new search on PubMed you might notice the \u0026ldquo;Create RSS\u0026rdquo; button. Give it a click, then you will have a personal link you can add to your favorite RSS feed aggregator.\nFigure 3: Somehow I never noticed this button until I needed it.\nThis changed the game for me for keeping up with papers. Unfortunately, it doesn\u0026rsquo;t solve the problem of library management, or actually getting around to reading the papers you care about. I will leave library management as an exercise for the interested reader. Here\u0026rsquo;s a tip, the best solution uses the Zotero citation manager. Bonus points for using Zotfile for renaming your PDFs and Better BibTex for Zotero. \u0026#x1f609; I hope this helps you get your eyeballs on that science you crave. If you have solved the problem of accruing papers to read faster than you read them, let me know.\n","permalink":"https://www.zacharybillman.com/posts/rss-feeds-to-find-science-papers/","summary":"\u003cp\u003eIt is an age-old question: how can one keep up with the continuous output of science? I remember at the beginning of my PhD struggling to figure out how anyone found out when a new paper came out. \u0026#x1f635; Did they sit on nature.com and spam the refresh button? Did they know when each journal released their latest issue?\u003c/p\u003e\n\u003ch2 id=\"behold-the-power-of-rss\"\u003eBehold the power of RSS!\u003c/h2\u003e\n\u003cp\u003eMost websites have a page that contains information about each subpage in a computer-readable format called RSS (Really Simple Syndication). \u003ca href=\"https://zacharybillman.com/index.xml\"\u003eMine has one right here!\u003c/a\u003e These pages can be parsed by a number of RSS feed aggregators. The way these pages are set up make it such that they add any new information hosted at that domain. This is useful in the science world because you can find the RSS feed of a given journal, subscribe to it, then have every new article published online be delivered right to you.\u003c/p\u003e","title":"Using RSS feeds to keep on top of science."},{"content":"My interest in self-hosting began in my with my interests in internet privacy. Plastered all over the internet are stories about how much Google, Facebook and Amazon know about you. I deleted my Facebook account years ago, and I\u0026rsquo;m too paranoid to go back to the site because there\u0026rsquo;s a real possibility that Facebook has cached my account, ready to spin it back up in case I try to login again. The ads served to me were too accurate for my liking. This is despite almost never clicking on them! I have become convinced of the idea that, if you are not paying for the product, you are the product. From this assumption, it follows that anywhere I trust with my data that I am not paying for (like Google Drive, Google Photos, Dropbox, Facebook, Twitter) is using my data to earn money. We know that Google uses the labels you add to Photos to train it\u0026rsquo;s AI, and Facebook uses (at least) Instagram photos to train it\u0026rsquo;s AI. For some, the value proposition of allowing a company to use your data for a useful service in return is an acceptable one. I find this to be a reasonable stance, but I took my growing interest in internet privacy as a chance to learn about how I can take control of my data.\nInitially, I lurked on forums like /r/privacy to learn what I could do to avoid big-tech\u0026rsquo;s watchful eye. There were numerous comments along the lines of: \u0026ldquo;The only way to be in control of your data is to self-host your services.\u0026rdquo; I had no idea what this meant! Hard to believe that less than a year later, I learned to use (and love) Linux as my primary OS, and have happily replaced Google Photos, Google Drive and other services with my own self-hosted alternatives. Self-hosting, I have since learned, is when you run useful programs from your own computer. By doing so, you have complete knowledge of where and how your data is stored and how it is being used. It has the additional effect of being a bottomless time sink.\nTo begin, I needed an always-on computer to run these useful programs. I began with a humble Raspberry Pi.\nFigure 1: My humble Raspberry Pi and its hard drive. This dude currently tirelessly runs the excellent Adguard Home and downloads a backup of my data every night.\nThese are tiny, but capable computers that are great for fiddling with. The projects people develop for these are amazing and diverse. With RPi in hand, I began with the ambitious project of replacing Google Drive with Nextcloud. After much frustration with a bare metal installation, I found the NextcloudPi project. Surprisingly, it went pretty okay! At first, I was intimidated by Linux defaults, but over time I grew to appreciate, and indeed, prefer Linux as an operating system. My decision to use Linux over Windows/MacOS is because it is free and open source software (FOSS). This is a topic for a different post, but I think using FOSS when possible is a moral imperative of sorts. I used Nextcloud strictly from my home for a few months, without the ability to connect to it from the internet, to test the self-hosting waters. My first true cloud replacement spun up once I decided to access this lil\u0026rsquo; guy from the internet. To do so, I purchased a domain (not the one this site is hosted on) and pointed it to the IP of my house. I forwarded the appropriate ports of my router to the RPi.\nThis is when the real exploration began. I was able to access my files and images using Nextcloud, but the photo viewing service left something to be desired. No problem, why not spin up an instance of Photoprism? I use RSS feeds to keep on top of the latest science in the journals relevant to my field using Feedly. Why not host my own RSS feed aggregator so I can subscribe to as many feeds as I desire?\nThis cycle continued, and I accrued many cool applications, but in the back of my mind I worried about opening up my home network to the internet. I also struggled to run some programs because the RPi uses the arm64 architecture, and most services are written with amd64 in mind. These two forces eventually convinced me to purchase a server where I could manage all of my services remotely. Some would say that not owning the hardware that is running your own services is not \u0026ldquo;true\u0026rdquo; self-hosting. I think this is needlessly exclusive. Let everyone self host, dangit! Someday, when I have more stable internet and a more permanent home, I hope to host everything from my own home, but until then, I\u0026rsquo;m extremely pleased with my current stack. And that is where I am now. I happily host numerous services on my virtual private server that entirely replace Google Photos, Google Drive and GitHub for me. Even better, there are specialized services that fill a need I never realized I had. What\u0026rsquo;s more, if I ever want to spin up a new service, all I have to do is add it to my to docker-compose file and it will be up within minutes. What a world!\nI thought about making this into a \u0026ldquo;guide\u0026rdquo; style post. I nixed that idea because, quite frankly, I feel like I don\u0026rsquo;t know what I\u0026rsquo;m doing. I am really happy with my setup, but I don\u0026rsquo;t feel like I have the authority to tell people how to administer their own services. If you are interested, allow me to point you toward the guide that really got me rolling: Ultimate Traefik Docker Compose Guide.\nFor those of you wondering what I am currently hosting, check out my current list at the link and let me know what you think!\n","permalink":"https://www.zacharybillman.com/posts/my-selfhosting-journey/","summary":"\u003cp\u003eMy interest in self-hosting began in my with my interests in internet privacy. Plastered all over the internet are stories about how much Google, Facebook and Amazon know about you. I deleted my Facebook account years ago, and I\u0026rsquo;m too paranoid to go back to the site because there\u0026rsquo;s \u003ca href=\"https://www.reddit.com/r/privacy/comments/6nmjfh/facebook_account_fully_recovered_3_years_after/\"\u003ea real possibility that Facebook has cached my account, ready to spin it back up\u003c/a\u003e in case I try to login again. The ads served to me were too accurate for my liking.\n\u003cspan class=\"sidenote-number\"\u003e\u003csmall class=\"sidenote\"\u003e\nThis is despite almost never clicking on them!\n\u003c/small\u003e\u003c/span\u003e\nI have become convinced of the idea that, if you are not paying for the product, you are the product. From this assumption, it follows that anywhere I trust with my data that I am not paying for (like Google Drive, Google Photos, Dropbox, Facebook, Twitter) is using my data to earn money. We know that \u003ca href=\"https://www.theverge.com/2020/11/11/21559930/google-train-ai-photos-image-labelling-app-android-update\"\u003eGoogle uses the labels you add to Photos to train it\u0026rsquo;s AI\u003c/a\u003e, and \u003ca href=\"https://ai.facebook.com/blog/seer-the-start-of-a-more-powerful-flexible-and-accessible-era-for-computer-vision/\"\u003eFacebook uses (at least) Instagram photos to train it\u0026rsquo;s AI\u003c/a\u003e. For some, the value proposition of allowing a company to use your data for a useful service in return is an acceptable one. I find this to be a reasonable stance, but I took my growing interest in internet privacy as a chance to learn about how I can take control of my data.\u003c/p\u003e","title":"My selfhosting journey."},{"content":"N.B.: I hope to add screenshots for each of these eventually. For now, I hope links to each services\u0026rsquo; website will suffice.\nSeafile\nThis is a great tool for managing files. I moved to this from Nextcloud because I am of the philosophy that I would prefer services that do one thing excellently instead of many things well. Nextcloud is an incredible Office365 replacement, but I found myself using a fraction of what it was capable of providing. Enter Seafile. It is cloud file syncing with a robust encryption implementation, just what the doctor ordered.\nPhotoprism\nNextcloud\u0026rsquo;s implementation of photo management was a bit clumsy for my tastes, so I began on a hunt for a more feature complete option. I was very lucky to stumble upon Photoprism early on in my self hosting journey. I am a proud supporter of this project. It brings a ton to the table, and doesn\u0026rsquo;t leave me missing Google Photos one bit. It is also actively developed. For instance, as of 2022-07-02, there was a recent update that improved scrolling a ton, which was one of my remaining quibbles with it\u0026rsquo;s functionality. Some people complain that it doesn\u0026rsquo;t scale up for libraries of 10,000+ photos, but my 2000 photo library works swimmingly. On my phone, I use the Folder Sync app to automatically send any pictures I take on my phone to the Photoprism imports folder. Within 15 minutes of snapping a photo, it is there on my Photoprism instance. I highly recommend giving it a go.\nMealie\nI have to admit that the name leaves something to be desired. Fortunately, the service itself doesn\u0026rsquo;t fall short. Mealie is a recipe management application. It is able to parse your favorite recipe websites to create immortalized versions of the recipe. This helps fight detestable link rot that plagues the internet. It allows you to edit ingredient amounts, make comments about what you would change next time, and plan out your weekly meals. It helps that it is beautiful and intuitive to use. If only I could get my partner to use it\u0026hellip; I want to go on the record here and say that I think it is sensible that she doesn\u0026rsquo;t trust my self hosted services that much. In the early days of my self hosting journey, let\u0026rsquo;s just say that the up-time of my services were extremely finicky. I like to think they are more permanent now, especially because I am hosting everything on a VPS, but I certainly cannot compete with the stability of Google and Amazon. (Or pretty much any other paid service for that matter.) \u0026#x1f609;\nGitea\nGitea is a community managed, lightweight code hosting solution written in Go. I use it to manage my data analysis (using Private repos) and even host the source code for this very website! Using Gitea has given me the surface level introduction to the behemoth that is git. Fortunately, that is all I need. Once I have removed any sensitive data (like passwords, etc.) I will make my docker-compose file public. The docker-compose file is where I determine which services I pick to host, and how to configure them to my liking. Hopefully someone will find this useful.\nSyncthing\nIf I could only tell someone to self host a single service, I would have to pick Syncthing. It is a continuous file synchronization program, which means it keeps a specific file or folder the same between any device running Syncthing. I use it to keep my password database and my org-mode notes Now org-mode might be the biggest rabbithole of them all, and definitely the topic for another blog post. I use it to manage my TODO list, my lab notebook, my shopping lists, write this blog, and maintain my Zettelkasten note database. It is an immensely powerful tool. up to date between all of my devices. With Syncthing, all of my data is stored on my own devices and encrypted in transit.\nFreshRSS\nI keep up to date on the science in my field by subscribing to relevant RSS feeds. Yet another topic to write a post about. This really changed the game for my ability to keep on top of the latest research. 2022-07-14 Update: post complete! Check it out here. FreshRSS replaced Feedly for me, as I ran up against the number of feeds I could subscribe to on a free account. Also, when self hosting, I can save as many articles as my heart desires (even if I will never look at them again \u0026#x1f635; ).\nWallabag\nRemember Pocket for Firefox? (Yes, I know it still exists, okay?) Give Wallabag a spin, it is great for storing articles you want to read later. I set up FreshRSS to save articles to my Wallabag instance to keep for later.\nChangeDetection\nNow this is a fun one! ChangeDetection.io is a service that loads a webpage and checks to see if something has changed since the last time. This might not sound useful at first, but I recently used this to check for when a hot item for my new coffee roasting hobby was back in stock. I got an email the other day to let me know it was in stock. Pretty cool!\nHugo\nHugo is the static site generator I use to make this here blog! I was amazed at how much more response my site was using Hugo compare to when I paid a company to host a WordPress site. I\u0026rsquo;m sure WordPress could be fast, but I just wanted a barebones, pure html experience, and Hugo made it easy.\nCommento++\nYou may have noticed that I have some pretty snazzy comments sections on my site. I initially used Disqus, which you may recognize from a ton of sites around the internet, but didn\u0026rsquo;t like how it would serve ads through my comments section, and provided sign-ins using Google/Facebook/Twitter. I wanted to serve the simplest comments section I could, that still gave me the ability to migrate the comments to wherever I decide to keep my server. Go ahead and use the anonymous comment button, fill in your name, and you are off to the races.\nAuthelia\nThere are a few services I host that I really want to lock down. For these services, Authelia is great. It puts up a \u0026ldquo;Enter the 6 digit code on your phone\u0026rdquo; style 2 factor authentication in front of the services I choose. Or, if you follow the guide here, you can have it send you a DUO push, just like you are one of the big hitters out there. I feel much more secure with Authelia in front of Adminer, Traefik, and Portainer.\nBoring stuff that allows everything else to work!\nPostgreSQL database MariaDB database Traefik reverse proxy Umami privacy respecting site analytics Portainer for docker container management Redis in-memory data store Adminer database management traefik-socket-proxy to prevent pesky backdoors to my server! ","permalink":"https://www.zacharybillman.com/posts/zpb-current-selfhosted/","summary":"\u003cp\u003e\u003cem\u003eN.B.: I hope to add screenshots for each of these eventually. For now, I hope links to each services\u0026rsquo; website will suffice.\u003c/em\u003e\u003c/p\u003e\n\u003col\u003e\n\u003cli\u003e\n\u003cp\u003e\u003ca href=\"https://www.seafile.com/en/home/\"\u003eSeafile\u003c/a\u003e\u003c/p\u003e\n\u003cp\u003eThis is a great tool for managing files. I moved to this from Nextcloud because I am of the philosophy that I would prefer services that do one thing excellently instead of many things well. Nextcloud is an incredible Office365 replacement, but I found myself using a fraction of what it was capable of providing. Enter Seafile. It is cloud file syncing with a robust encryption implementation, just what the doctor ordered.\u003c/p\u003e","title":"What I'm currently selfhosting."},{"content":"My partner and I took a trip to the Mason Farm Biological Reserve the other day, and what a glorious day it was. This year, I\u0026rsquo;ve been quite busy in the lab, and missed a lot of the early spring warbler season, so I was very excited by the opportunity to check out the old stomping grounds.\nI brought the camera with me despite the fact we were going to be there around midday when the birds are much less active. I\u0026rsquo;m glad I did, because I got the best look at a common yellowthroat I\u0026rsquo;ve ever had. Normally these guys are flighty, staying close to the ground in small brush or tall grasses, but this one was putting on a proper show for the mating season. Even when you get a glimpse of one, it is usually just that, as they have jumped away before you can pull out the camera, taunting you with their iconic call. I was very pleased to capture a few choice shots of the bird. Hopefully there are more to come. While we were out, I also got a nice picture of a hermit thrush and a king snake.\nThese images have been compressed quite a bit for a lighter internet footprint. These have all been resized to 25% of their original size. If you would like the full sized images, let me know and I will send you a link!\n","permalink":"https://www.zacharybillman.com/posts/the-uncommon-yellowthroat/","summary":"\u003cp\u003eMy partner and I took a trip to the \u003ca href=\"https://ncbg.unc.edu/visit/mason-farm-biological-reserve/\"\u003eMason Farm Biological Reserve\u003c/a\u003e the other day, and what a glorious day it was. This year, I\u0026rsquo;ve been quite busy in the lab, and missed a lot of the early spring warbler season, so I was very excited by the opportunity to check out the old stomping grounds.\u003c/p\u003e\n\u003cp\u003eI brought the camera with me despite the fact we were going to be there around midday when the birds are much less active. I\u0026rsquo;m glad I did, because I got the best look at a common yellowthroat I\u0026rsquo;ve ever had.\n\u003cspan class=\"sidenote-number\"\u003e\u003csmall class=\"sidenote\"\u003e\nNormally these guys are flighty, staying close to the ground in small brush or tall grasses, but this one was putting on a proper show for the mating season. Even when you get a glimpse of one, it is usually just that, as they have jumped away before you can pull out the camera, taunting you with their \u003ca href=\"https://ebird.org/species/comyel#Modal-playlist\"\u003eiconic call\u003c/a\u003e.\n\u003c/small\u003e\u003c/span\u003e\nI was very pleased to capture a few choice shots of the bird. Hopefully there are more to come. While we were out, I also got a nice picture of a hermit thrush and a king snake.\u003c/p\u003e","title":"The (un)common yellowthroat."},{"content":"Welcome to my site! My name is Zachary Billman. I\u0026rsquo;m a UNC MD-PhD student in my 4th year of med school applying to pathology residency programs. I completed my PhD in Ed Miao\u0026rsquo;s lab. The curious reader may be thinking: \u0026ldquo;But Zach, Dr. Miao\u0026rsquo;s lab is at Duke, how did that come about?\u0026rdquo; What an astute question! Ed\u0026rsquo;s lab moved from UNC to Duke in early 2020, and I followed him down the street. My PhD was awarded by the UNC department of Microbiology and Immunology, but it just so happens that (nearly) all of my research took place at Duke. This move was quite a trial, especially when compounded with the onset of the pandemic. I suspect my research timeline suffered, though this is an extremely minor inconvenience compared to the tragedy the pandemic caused. This makes for very interesting basketball viewing parties with my Duke friends!\nMaybe having a diagram will make my training timeline make a bit more sense.\nHopefully that can clear up the winding road I\u0026rsquo;ve taken!\nMy research and scientific interests. I am broadly interested in innate immunology. I spent most of my time in graduate school studying the host-pathogen interaction between the intracellular fungus Histoplasma capsulatum and macrophages. There are many unstudied curiosities regarding the innate immune response to Histoplasma spp. and other intracellular fungi that I think are quite interesting. I also spent a considerable time thinking about the evolution of proteins involved in the programmed cell death pathway called pyroptosis.\nHobbies I may write about. Besides my science, I am interested in birding, baking sourdough bread (I swear I began years before the pandemic, though hearing of people baking bread brings me joy no matter when they first began!), board games, roasting coffee, and self-hosting free and open source software. Over the course of the pandemic, I have learned how to maintain a basic suite of services spread between a server I rent and a computer at home that have replaced my need for Google Photos and Google Drive. I\u0026rsquo;m hoping to be able to move away from these platforms entirely soon. I think they provide a great service, but at a substantial cost to privacy. Hopefully more to be said about my thoughts on FOSS soon! I also transitioned my old, (and quite frankly, embarrassingly slow) managed WordPress site with this lean, static site made in Hugo that I host myself. Now that I have mangled together some CSS to get my precious sidenotes up and running again, I\u0026rsquo;m ready to begin putting some ideas to paper. I love marginalia (the word to describe these notes on the side of this webpage). I\u0026rsquo;m not sure if this is unique to me, but I seem to get caught up in parenthetical / tangential thoughts very often, and I think using an Edward Tufte-esque sidenote is a great way for me to communicate in this way without distracting the reader too much. It seems marginalia such as this have been used throughout history, so perhaps it is normal, but most people can keep their thoughts focused better than me. The implementation I use is inspired by the Tufte CSS project and largely taken from this incredibly helpful post found at scripter.co. I\u0026rsquo;m quite proud of my progress in administering my server and self-hosting useful services.\nThe future of this site. On this site I plan to post updates about my journey through med school, grad school, and self-hosting I would like to share with the world. I have been helped immensely by many others\u0026rsquo; advice and I hope to impart similar tips to others someday. I suspect most posts will be about much lighter fare, like whatever hobbies tickle my fancy at the time.\n","permalink":"https://www.zacharybillman.com/posts/about-me/","summary":"\u003ch2 id=\"welcome-to-my-site\"\u003eWelcome to my site!\u003c/h2\u003e\n\u003cp\u003eMy name is Zachary Billman. I\u0026rsquo;m a UNC MD-PhD student in my 4th year of med school applying to pathology residency programs. I completed my PhD in Ed Miao\u0026rsquo;s lab. The curious reader may be thinking: \u0026ldquo;But Zach, Dr. Miao\u0026rsquo;s lab is at Duke, how did that come about?\u0026rdquo; What an astute question! Ed\u0026rsquo;s lab moved from UNC to Duke in early 2020, and I followed him down the street. My PhD was awarded by the UNC department of Microbiology and Immunology, but it just so happens that (nearly) all of my research took place at Duke.\n\u003cspan class=\"sidenote-number\"\u003e\u003csmall class=\"sidenote\"\u003e\nThis move was quite a trial, especially when compounded with the onset of the pandemic. I suspect my research timeline suffered, though this is an extremely minor inconvenience compared to the tragedy the pandemic caused.\n\u003c/small\u003e\u003c/span\u003e\nThis makes for very interesting basketball viewing parties with my Duke friends!\u003c/p\u003e","title":"About me. 👋"},{"content":"It\u0026rsquo;s over. My third year of medical school is officially behind me. I managed to get in a grand total of zero blog posts during grad school, so here\u0026rsquo;s to a new year with hopefully some more thoughts being shared. I have a lot to reflect on from the past year. It was wonderful. I wish everyone could experience what I did this past year. I think it goes without saying:\nI loved the third year of med school, but I do not want to do it again.\nA year of change. In the days leading up to my return to med school, I thought \u0026ldquo;Oh no, I really enjoy doing science, do I really have to go to med school?\u0026rdquo;. I also remember at the end of Step 1 and the first two years of med school thinking, \u0026ldquo;Oh no, I really enjoy med school, do I really have to do science again?\u0026rdquo;. I think I have a welcome problem of enjoying what I\u0026rsquo;m doing. The third year of med school is a shift. After years of memorizing and examinations, the doors to the promised land are finally opened. I have experienced nothing like it before It feels intentionally unsettling. You are thrown into the clinic with a modicum of guidance so you aren\u0026rsquo;t totally caught off guard, but you are thrown out to the wolves. I don\u0026rsquo;t mean this as a criticism of the system, it feels necessary. Third year medical students—commonly shorted to MS3s—have just one year to experience a broad swath of medicine and pick a specialty. So you had better be ready to dive in.\nTotal immersion I came to terms with my new reality quickly. Gone were the days of hitting the snooze button and going home when I pleased. I am now beholden to other people\u0026rsquo;s schedules. This came back relatively naturally. Maybe not hitting snooze. A regrettable personal failing of mine. I was, however, immediately faced with a new reality in the patient room. Patients come to the doctor for a number of reasons, but often seek relief. To get to the core of what ails them, they will tell you everything. I was not prepared for how vulnerable patients would be with me. I am not sure if this ever will feel natural. I hope it never does. I was told many stories of experiences living with scary diagnoses, and not knowing what to do with it. Family histories of all sorts. Personal details that were sometimes (oftentimes?) off the wall. I see all of these specifics as flailing, grasping at sand hoping that something could explain their pain. Sometimes it could. Usually it did not. But since I was in a white coat, I was privileged to hear it.\nI think my years spent in the lab have prepared me to face some of the challenges set before me. At the very least, having a few more years under my belt helped me approach the year with a bit of maturity. This seems to have paid off. I guess my recommendation is to simply get old before going to med school. Returning to studying The hospital is how I spent the majority of my time, but a new reality for me was also going back to daily studying. There is a strange dichotomy in medicine of \u0026ldquo;Oh, it doesn\u0026rsquo;t really matter\u0026rdquo; and \u0026ldquo;If you don\u0026rsquo;t get this class/score/grade then you won\u0026rsquo;t be able to be the kind of doctor you want to be, so you had better get your act together.\u0026rdquo; Simultaneously there are no expectations and immense responsibility for the looming specter of Step 2. I\u0026rsquo;m glad that studying regularly came back easily enough. I was concerned I would experience a studying whiplash. I\u0026rsquo;m glad it never came. I did UWorld and Anki nearly every day for a full year and felt alright.\nBecoming invisible I quickly learned I needed to change my understanding of my contribution to the team. Exiting grad school, people understood that they could come to me for help. I was a resource, a seasoned veteran of the lab. If someone needed an experiment done, I could do it, and be trusted to do it. In med school as a third year, I was nothing. A fly on the wall; a worm beneath the feet of the real doctors. In science, I felt like I was treated as a peer with even my committee members with multiple R01s. Even if I didn\u0026rsquo;t understand the science perfectly, I could contribute some different perspective. In medicine, sometimes not being recognized at all by my attendings was the best outcome. Which happened regularly. My role, was not as a contributor—as it was in science—it was simply to get in the reps. Once I understood that the expectations of me were below the ground, I understood that everything I did in third year was for myself. This is taken at face value by the team at times. I would spend 30 minutes working on a presentation, pre-rounding, the works, and at the end of my part, the intern would nod, then turn to the senior resident and say \u0026ldquo;I was thinking that we\u0026hellip;\u0026rdquo; without thinking of my work. This is perhaps a bit of cognitive restructuring, but recognizing this is what gave me the freedom to embed myself in the hospital flow, without a single worry about the outcome. Simply doing my best was the best thing I could do. Obviously. But this was not apparent to me at first. I needed more quality repetitions to develop good habits in the future. And also experience as much of medicine as possible to find what I want to do with my life. This permission allowed me to approach specialties I do not care about with the awe and respect they deserve.\nA year of wonder. Med school prepares you for the standardized tests. I think this is generally useful. The tests on aggregate are reasonable and evaluate your ability to think through common clinical scenarios. There will always be oddball questions that come out of left field, but I let these flow over me. No need to perseverate on the small stuff. The time for that can come later.\nWhat I didn\u0026rsquo;t realize is how much of the \u0026ldquo;classic\u0026rdquo; material we are fed in the first couple years of med school would come to the forefront. The \u0026ldquo;sandpaper rash\u0026rdquo; of scarlet fever really does feel like sandpaper. Nikolsky\u0026rsquo;s sign actually works. Tripoding for epiglottitis gets the physicians worked up. Don\u0026rsquo;t forget about von Willebrand\u0026rsquo;s disease when someone seems to be bleeding a bit too much. TB is out there, watch for hemoptosis. Night sweats, unintended weight loss, is cancer until proven otherwise. And yes, it really can be lupus.\nIn general, facing the unknown with a sense of earnestness was the way I felt best able to respect those who gathered and passed down the medical knowledge I am privileged to learn today. Sometimes, my excitement to see aspects of medicine would rouse a curious response from the residents. I project here, but I felt a sense of surprise, like that of a doting parent seeing their child experience something new, after forgetting the astonishment they once felt.\nEarnestness is next to med studentlyness.\nPerhaps what I\u0026rsquo;m getting at here is that I found it important to bask in the privilege of seeing the pathology I encountered in med school, and to remind the residents of this sensation. I felt childish at times—and perhaps overanimated—but I found this excitement was to my and my resident\u0026rsquo;s benefit.\nMy surgery rotation overflowed with examples of wonder of medicine. Partially because of the team I worked with, and the rest because of the undeniable coolness of surgery. The OR is a cool place. The orderliness and chaos ebb. The spans of steady, industrious work are interrupted with staccato notes of bedlam. The anatomy I learned in class was ever present, but the surgeons bemoaned \u0026ldquo;normal anatomic variation\u0026rdquo;.\nI was struck with wonder at the sight of human anatomy as it unfolded before me. What I was able to experience in the OR felt like the culmination of centuries of human curiosity. There is an ancientness to medicine that I catch flashes of—I could perform the physical exam on humans hundred of millions of years ago and interrogate the same pathologies as I do in the hospital today—and viewing the exposed anatomy is a pressure-bagged infusion of this collective wonder. To gaze upon the peristalsing of the small intestine, or steady beating of the heart is a sight to behold, indeed.\nA year of shame. It weighs upon me the circumstances that resulted in these transcendent experiences. Not one patient was in the hospital without reason. What to make of these patients with horrible pathology? I still feel unsettled about how the cause of their pain sparked wonder. How dare I gain, merely by the circumstance of having their care managed at UNC, Which, as a tertiary care center, layers on more complexity. Many patients end up at UNC because they have no where else they can go for help. And this signs them up for med students? For shame. from the very essence of their malady? I do not know what to do with my discomfort, but I think it is best that I dwell in it. With this, I respect the people before me in the hospital and recognize their humanity.\nBut I often complained of what I say here I was lucky to do. I find myself resentful of my future schedule; when was I supposed to learn that I will be working 13 hour days, 6 days a week for the rest of my life? And what of having a family? Medicine by necessity requires sacrifice. I happened to sign up for sacrifices years before I recognized how profound they were. How might I balance this dread and with the joy of practicing medicine? And why do I seem more concerned about this than others? Am I not grateful enough? Am I not capable of the sacrifices that others seem to offer so effortlessly? I don\u0026rsquo;t necessarily think this to be true, but these questions erode at my will to pursue medicine.\nPerhaps most shameful of all is how my understanding of the patient-provider interaction evolved over the year. It began as an exploration of an open book, a tabula rasa that held within it a diagnosis and how to best intervene. On my first day in the outpatient clinic, it was clear that this is not the case. My preceptor had only 20 minutes for me to ① interview the patient and perform the physical exam, ② present with a plan, ③ return to the room and do everything again, ④ write orders, educate, and get the patient out of the door. It simply is not amenable to the free form, personable, curious interview I hoped to perform. By the end of the year, I had optimized how I asked questions to keep patients from going off the rails. When prerounding in medicine, I was there to extract information and not much else. Small talk had to go, there was no time. I like to chat, so this came at a loss of who I think I am. I am not sure how to do this well, while still feeling like Zachary. And from what I gather from the interns, that may just come later in my career. I found myself questioning, \u0026ldquo;Is this the \u0026lsquo;patient interaction\u0026rsquo; that has been mythologized throughout my training?\u0026rdquo; The carrot at the end of the stick dangled before me with a \u0026ldquo;You are so lucky to be able to do this, so you had better not complain of any abuse that comes your way.\u0026rdquo; It wasn\u0026rsquo;t a genuine interaction as much as me leading the patient along to tell me what I wanted to know. Of course, I used open ended questions, but only open enough. Leave the door a bit too open and next thing you know, you are talking about their dog\u0026rsquo;s breeder while you constantly stare at your watch, imagining what your attending will say when you return. I feel like I am alone in missing the core human element that funnels sprightly youths into medicine. Or worse, finding it a façade.\nThe shame extends beyond the hospital. One aspect of my life that has changed most dramatically is the sheer amount of time I felt I needed to dedicate to medicine, whether at the hospital or at home. I spent all day basking in the wonder of medicine, then I would come home and study for hours. I relied on my partner for keeping our household together more than ever, because I spent all day—all year, rather—in a state of discovery. Her life was largely the same, with the normal challenges of being a scientist, with the added bonus of getting less help from me. The shame built over the year. Again, how dare I?\nA year of glad. This has been an undeniable year of growth and joy, with these quibbles. It is clear that I was happier than I was during grad school. I know this from within myself, and reinforced by my wife\u0026rsquo;s comments on my mood. The pace of the day, and immediacy of problem solving were a welcome change.\nI recall, during the very first days preparing for med school during xTAP, having to do a simulated patient encounter complete with patient presentation to an attending physician. We were told about this encounter days in advance. And yet, I dreaded it. And near the last day of my final rotation, I did 8 of these in a row without breaking a sweat. Progress!\nI think, in a word, what I\u0026rsquo;ve experienced in the third year of med school is gratitude. Gratitude to be privileged to learn what I am learning. Gratitude for the experiences in my life that brought me here. Gratitude for the support from my wife. Gratitude to be involved in people\u0026rsquo;s lives when they are fragile. Ever since reading Braiding Sweetgrass I think one could call me \u0026ldquo;gratitude-pilled\u0026rdquo;. I also selfishly enjoyed the gratitude from patients as I put on my best doctor performance. In reflection on the year, I have spent time thinking of a phrase that I heard a number of times throughout med school from residents, \u0026ldquo;The worst day of residency is better than the best day of med school.\u0026rdquo; I find this hard to believe. This year has been magical. It is hard to imagine a year filled with more wonder and joy of caring for those in need. I will have to rely on the experience of those who have walked this path and trust that the rest of my training has plenty of magic to spare.\n","permalink":"https://www.zacharybillman.com/posts/ms3-year-is-magical/","summary":"\u003ch2 id=\"it-s-over-dot\"\u003eIt\u0026rsquo;s over.\u003c/h2\u003e\n\u003cp\u003eMy third year of medical school is officially behind me. I managed to get in a grand total of \u003cem\u003ezero\u003c/em\u003e blog posts during grad school, so here\u0026rsquo;s to a new year with hopefully some more thoughts being shared. I have a lot to reflect on from the past year. It was wonderful. I wish everyone could experience what I did this past year. I think it goes without saying:\u003c/p\u003e","title":"The third year of medical school is magical."},{"content":"I, like many others, picked up a new hobby during the pandemic. Other people\u0026rsquo;s hobbies may bring them joy. This could be for many reasons. There is the joy of creating something from scratch. You can revel in your thriftiness. You can embrace the pride when you recognize that your creation is on par (or better!) than what you can buy. I feel like these are embodied in the sourdough craze that caught fire early on in COVID. Dare I say that I did this before it was cool? \u0026#x1f60e; I baked two loaves of bread almost every weekend through med school. Maybe I should bring that back, it\u0026rsquo;s been a while since I brought out the ole\u0026rsquo; starter. My pandemic hobby is similar, but different in that it often feels like a chore, costs more money, and often turns out worse than what I can buy. Of course, I am talking about how I\u0026rsquo;ve started roasting my own coffee at home.\nI\u0026rsquo;m not sure where this idea was planted into my brain. I don\u0026rsquo;t think I know anyone who roasts their own beans, and I certainly didn\u0026rsquo;t know how. I didn\u0026rsquo;t even drink coffee regularly until after college! I guess that extra time on the computer sent me down a rabbithole I have yet to emerge from.\nFirst, I want to preface the following with a disclaimer: This is not a detailed guide about how to roast your own coffee. If you are interested, I recommend checking out the How To Roast Your Own Coffee guide at Sweet Maria\u0026rsquo;s as a starting point. There is also the /r/roasting subreddit if that is your cup of tea. My only warning is there will be a lot of smoke. Roast your coffee outside, for Pete\u0026rsquo;s sake!\nIt all started with a trusty popcorn popper. There are a few things you want when you roast coffee:\nAir hot enough to roast coffee Remove the chaff from the beans Turns out that a classic popcorn popper fits the bill, as long as it has an upwards airflow and doesn\u0026rsquo;t let the chaff fall into the heating element. There is a bit of a cult following for the West Bend Poppery 2 model, but that one seemed a bit pricey, so I settled for a very capable popper from Nostalgia.\nFigure 1: I got a good bit of mileage out of my popcorn popper. If you are interested in roasting your own coffee I would give it a whirl.\nThings were simple back then. I still bought most of the coffee I drank, but I roasted enough to enjoy some freshly roasted coffee as an occasional treat. I ordered 10 pounds of green beans from Sweet Maria\u0026rsquo;s and life was good.\nThen I became a bit of a coffee snob.\nI could only roast 100 grams of coffee at a time in the popcorn popper, which is only enough for one pot of coffee in the morning for me. So it was time to upgrade.\nI bought the SR800 fluid bed roaster, which upped my roasting capacity and gave me finer control on temperature and airflow. Suffice to say my roasts improved a lot! At this point, I would consider my coffee good enough to sell at a farmer\u0026rsquo;s market to break even.\nIf you ever find yourself on a coffee roasting forum and bring up the SR800, someone is bound to bring up the famous RazzoRoasting extension tube. If you look for advice for how to use the SR800, I swear it\u0026rsquo;s assumed that you have this very specific accessory. \u0026hellip;And so I bought one.\nDon\u0026rsquo;t worry, that is the extent of all of my coffee spending (for now). I am a very satisfied coffee roaster now. Check out this quick series of images going from the green beans to a nearly finished product! I can spend about 45 minutes and go from nothing to nearly 2 pounds of roasted beans, enough for about a week and a half of coffee. Not bad! The only downside is that now I feel like I need to buy coffee from local roasters to get my fix. There are certainly crueler fates.\nAs a sign off, I will share something that surprised me about coffee roasting. When I roast coffee, the most important cue to determine if the coffee is roasted is the sound. That\u0026rsquo;s right, not the color, not the smell, but the sound. When heating up a coffee bean, the water trapped inside eventually bursts out of the bean in a rapid expansion. This is called \u0026ldquo;first crack\u0026rdquo;, and indicates that the coffee is roasted enough to be drinkable. The expansion also releases the chaff from the bean. If you continue heating up the bean, you will eventually reach \u0026ldquo;second crack\u0026rdquo;. I think a solid medium roast is taken out just before second crack, so I try to take my coffee out to this point and it hasn\u0026rsquo;t proved me wrong yet.\nHappy coffee-ing! \u0026#x2615;\n","permalink":"https://www.zacharybillman.com/posts/roasting-coffee-at-home/","summary":"\u003cp\u003eI, like many others, picked up a new hobby during the pandemic. Other people\u0026rsquo;s hobbies may bring them joy. This could be for many reasons. There is the joy of creating something from scratch. You can revel in your thriftiness. You can embrace the pride when you recognize that your creation is on par (or better!) than what you can buy. I feel like these are embodied in the sourdough craze that caught fire early on in COVID.\n\u003cspan class=\"sidenote-number\"\u003e\u003csmall class=\"sidenote\"\u003e\nDare I say that I did this before it was cool? \u0026#x1f60e; I baked two loaves of bread almost every weekend through med school. Maybe I should bring that back, it\u0026rsquo;s been a while since I brought out the ole\u0026rsquo; starter.\n\u003c/small\u003e\u003c/span\u003e\nMy pandemic hobby is similar, but different in that it often feels like a chore, costs more money, and often turns out worse than what I can buy. Of course, I am talking about how I\u0026rsquo;ve started roasting my own coffee at home.\u003c/p\u003e","title":"Roasting coffee at home. ☕"},{"content":"It is an age-old question: how can one keep up with the continuous output of science? I remember at the beginning of my PhD struggling to figure out how anyone found out when a new paper came out. \u0026#x1f635; Did they sit on nature.com and spam the refresh button? Did they know when each journal released their latest issue?\nBehold the power of RSS! Most websites have a page that contains information about each subpage in a computer-readable format called RSS (Really Simple Syndication). Mine has one right here! These pages can be parsed by a number of RSS feed aggregators. The way these pages are set up make it such that they add any new information hosted at that domain. This is useful in the science world because you can find the RSS feed of a given journal, subscribe to it, then have every new article published online be delivered right to you.\nThere are a plethora of RSS feed aggregators you can pick from manage your feeds. I have previously used Feedly and Inoreader, which are great free solutions, but have moved on to selfhosting my own instance of FreshRSS.\nAfter making an account at your friendly local RSS feed aggregator, you can add whatever feeds your heart desires. To find a journal\u0026rsquo;s rss feed, I often just search \u0026ldquo;$JOURNAL_NAME rss feed\u0026rdquo; and poke around until I find something that looks right. Most of the aggregators will test the feed out first to make sure that you are trying to add a legitimate one. Here are a few of the heavy hitters to get you started:\nhttp://feeds.nature.com/nature/rss/current https://www.science.org/rss/express.xml https://www.cell.com/cell/inpress.rss Nothing like a constant stream of Cell, Science, and Nature to make your project feel like a real winner, eh?\nHere is what my own site looks like.\nFigure 1: My current FreshRSS setup. On the left I have my feeds separated into folders. In the middle you can see the titles of papers that appear in my feed.\nAnd after I hit J to move to the first item in the feed.\nFigure 2: With a title selected, you can see the abstract and authors.\nAfter collecting all of your desired RSS feeds, you cannot forego your responsibility of actually reading them! Most RSS feed aggregators have shortcuts to move through titles quickly (Typically J to move on to the next one and K to move up.) They always seem to use vi keybindings. A bunch of computer nerds have really cornered the keybinding market. I have let them take over my computing life. Each morning when I get into the lab, I quickly set up something, then head to my desk to hit J until the counter reaches zero.\nBut what about my very specific field? You can subscribe to all of the journals you want, but that doesn\u0026rsquo;t make the papers with your specific interests pop out. Fortunately, the NIH has this exact circumstance in mind.\nWhen you make a new search on PubMed you might notice the \u0026ldquo;Create RSS\u0026rdquo; button. Give it a click, then you will have a personal link you can add to your favorite RSS feed aggregator.\nFigure 3: Somehow I never noticed this button until I needed it.\nThis changed the game for me for keeping up with papers. Unfortunately, it doesn\u0026rsquo;t solve the problem of library management, or actually getting around to reading the papers you care about. I will leave library management as an exercise for the interested reader. Here\u0026rsquo;s a tip, the best solution uses the Zotero citation manager. Bonus points for using Zotfile for renaming your PDFs and Better BibTex for Zotero. \u0026#x1f609; I hope this helps you get your eyeballs on that science you crave. If you have solved the problem of accruing papers to read faster than you read them, let me know.\n","permalink":"https://www.zacharybillman.com/posts/rss-feeds-to-find-science-papers/","summary":"\u003cp\u003eIt is an age-old question: how can one keep up with the continuous output of science? I remember at the beginning of my PhD struggling to figure out how anyone found out when a new paper came out. \u0026#x1f635; Did they sit on nature.com and spam the refresh button? Did they know when each journal released their latest issue?\u003c/p\u003e\n\u003ch2 id=\"behold-the-power-of-rss\"\u003eBehold the power of RSS!\u003c/h2\u003e\n\u003cp\u003eMost websites have a page that contains information about each subpage in a computer-readable format called RSS (Really Simple Syndication). \u003ca href=\"https://zacharybillman.com/index.xml\"\u003eMine has one right here!\u003c/a\u003e These pages can be parsed by a number of RSS feed aggregators. The way these pages are set up make it such that they add any new information hosted at that domain. This is useful in the science world because you can find the RSS feed of a given journal, subscribe to it, then have every new article published online be delivered right to you.\u003c/p\u003e","title":"Using RSS feeds to keep on top of science."},{"content":"My interest in self-hosting began in my with my interests in internet privacy. Plastered all over the internet are stories about how much Google, Facebook and Amazon know about you. I deleted my Facebook account years ago, and I\u0026rsquo;m too paranoid to go back to the site because there\u0026rsquo;s a real possibility that Facebook has cached my account, ready to spin it back up in case I try to login again. The ads served to me were too accurate for my liking. This is despite almost never clicking on them! I have become convinced of the idea that, if you are not paying for the product, you are the product. From this assumption, it follows that anywhere I trust with my data that I am not paying for (like Google Drive, Google Photos, Dropbox, Facebook, Twitter) is using my data to earn money. We know that Google uses the labels you add to Photos to train it\u0026rsquo;s AI, and Facebook uses (at least) Instagram photos to train it\u0026rsquo;s AI. For some, the value proposition of allowing a company to use your data for a useful service in return is an acceptable one. I find this to be a reasonable stance, but I took my growing interest in internet privacy as a chance to learn about how I can take control of my data.\nInitially, I lurked on forums like /r/privacy to learn what I could do to avoid big-tech\u0026rsquo;s watchful eye. There were numerous comments along the lines of: \u0026ldquo;The only way to be in control of your data is to self-host your services.\u0026rdquo; I had no idea what this meant! Hard to believe that less than a year later, I learned to use (and love) Linux as my primary OS, and have happily replaced Google Photos, Google Drive and other services with my own self-hosted alternatives. Self-hosting, I have since learned, is when you run useful programs from your own computer. By doing so, you have complete knowledge of where and how your data is stored and how it is being used. It has the additional effect of being a bottomless time sink.\nTo begin, I needed an always-on computer to run these useful programs. I began with a humble Raspberry Pi.\nFigure 1: My humble Raspberry Pi and its hard drive. This dude currently tirelessly runs the excellent Adguard Home and downloads a backup of my data every night.\nThese are tiny, but capable computers that are great for fiddling with. The projects people develop for these are amazing and diverse. With RPi in hand, I began with the ambitious project of replacing Google Drive with Nextcloud. After much frustration with a bare metal installation, I found the NextcloudPi project. Surprisingly, it went pretty okay! At first, I was intimidated by Linux defaults, but over time I grew to appreciate, and indeed, prefer Linux as an operating system. My decision to use Linux over Windows/MacOS is because it is free and open source software (FOSS). This is a topic for a different post, but I think using FOSS when possible is a moral imperative of sorts. I used Nextcloud strictly from my home for a few months, without the ability to connect to it from the internet, to test the self-hosting waters. My first true cloud replacement spun up once I decided to access this lil\u0026rsquo; guy from the internet. To do so, I purchased a domain (not the one this site is hosted on) and pointed it to the IP of my house. I forwarded the appropriate ports of my router to the RPi.\nThis is when the real exploration began. I was able to access my files and images using Nextcloud, but the photo viewing service left something to be desired. No problem, why not spin up an instance of Photoprism? I use RSS feeds to keep on top of the latest science in the journals relevant to my field using Feedly. Why not host my own RSS feed aggregator so I can subscribe to as many feeds as I desire?\nThis cycle continued, and I accrued many cool applications, but in the back of my mind I worried about opening up my home network to the internet. I also struggled to run some programs because the RPi uses the arm64 architecture, and most services are written with amd64 in mind. These two forces eventually convinced me to purchase a server where I could manage all of my services remotely. Some would say that not owning the hardware that is running your own services is not \u0026ldquo;true\u0026rdquo; self-hosting. I think this is needlessly exclusive. Let everyone self host, dangit! Someday, when I have more stable internet and a more permanent home, I hope to host everything from my own home, but until then, I\u0026rsquo;m extremely pleased with my current stack. And that is where I am now. I happily host numerous services on my virtual private server that entirely replace Google Photos, Google Drive and GitHub for me. Even better, there are specialized services that fill a need I never realized I had. What\u0026rsquo;s more, if I ever want to spin up a new service, all I have to do is add it to my to docker-compose file and it will be up within minutes. What a world!\nI thought about making this into a \u0026ldquo;guide\u0026rdquo; style post. I nixed that idea because, quite frankly, I feel like I don\u0026rsquo;t know what I\u0026rsquo;m doing. I am really happy with my setup, but I don\u0026rsquo;t feel like I have the authority to tell people how to administer their own services. If you are interested, allow me to point you toward the guide that really got me rolling: Ultimate Traefik Docker Compose Guide.\nFor those of you wondering what I am currently hosting, check out my current list at the link and let me know what you think!\n","permalink":"https://www.zacharybillman.com/posts/my-selfhosting-journey/","summary":"\u003cp\u003eMy interest in self-hosting began in my with my interests in internet privacy. Plastered all over the internet are stories about how much Google, Facebook and Amazon know about you. I deleted my Facebook account years ago, and I\u0026rsquo;m too paranoid to go back to the site because there\u0026rsquo;s \u003ca href=\"https://www.reddit.com/r/privacy/comments/6nmjfh/facebook_account_fully_recovered_3_years_after/\"\u003ea real possibility that Facebook has cached my account, ready to spin it back up\u003c/a\u003e in case I try to login again. The ads served to me were too accurate for my liking.\n\u003cspan class=\"sidenote-number\"\u003e\u003csmall class=\"sidenote\"\u003e\nThis is despite almost never clicking on them!\n\u003c/small\u003e\u003c/span\u003e\nI have become convinced of the idea that, if you are not paying for the product, you are the product. From this assumption, it follows that anywhere I trust with my data that I am not paying for (like Google Drive, Google Photos, Dropbox, Facebook, Twitter) is using my data to earn money. We know that \u003ca href=\"https://www.theverge.com/2020/11/11/21559930/google-train-ai-photos-image-labelling-app-android-update\"\u003eGoogle uses the labels you add to Photos to train it\u0026rsquo;s AI\u003c/a\u003e, and \u003ca href=\"https://ai.facebook.com/blog/seer-the-start-of-a-more-powerful-flexible-and-accessible-era-for-computer-vision/\"\u003eFacebook uses (at least) Instagram photos to train it\u0026rsquo;s AI\u003c/a\u003e. For some, the value proposition of allowing a company to use your data for a useful service in return is an acceptable one. I find this to be a reasonable stance, but I took my growing interest in internet privacy as a chance to learn about how I can take control of my data.\u003c/p\u003e","title":"My selfhosting journey."},{"content":"N.B.: I hope to add screenshots for each of these eventually. For now, I hope links to each services\u0026rsquo; website will suffice.\nSeafile\nThis is a great tool for managing files. I moved to this from Nextcloud because I am of the philosophy that I would prefer services that do one thing excellently instead of many things well. Nextcloud is an incredible Office365 replacement, but I found myself using a fraction of what it was capable of providing. Enter Seafile. It is cloud file syncing with a robust encryption implementation, just what the doctor ordered.\nPhotoprism\nNextcloud\u0026rsquo;s implementation of photo management was a bit clumsy for my tastes, so I began on a hunt for a more feature complete option. I was very lucky to stumble upon Photoprism early on in my self hosting journey. I am a proud supporter of this project. It brings a ton to the table, and doesn\u0026rsquo;t leave me missing Google Photos one bit. It is also actively developed. For instance, as of 2022-07-02, there was a recent update that improved scrolling a ton, which was one of my remaining quibbles with it\u0026rsquo;s functionality. Some people complain that it doesn\u0026rsquo;t scale up for libraries of 10,000+ photos, but my 2000 photo library works swimmingly. On my phone, I use the Folder Sync app to automatically send any pictures I take on my phone to the Photoprism imports folder. Within 15 minutes of snapping a photo, it is there on my Photoprism instance. I highly recommend giving it a go.\nMealie\nI have to admit that the name leaves something to be desired. Fortunately, the service itself doesn\u0026rsquo;t fall short. Mealie is a recipe management application. It is able to parse your favorite recipe websites to create immortalized versions of the recipe. This helps fight detestable link rot that plagues the internet. It allows you to edit ingredient amounts, make comments about what you would change next time, and plan out your weekly meals. It helps that it is beautiful and intuitive to use. If only I could get my partner to use it\u0026hellip; I want to go on the record here and say that I think it is sensible that she doesn\u0026rsquo;t trust my self hosted services that much. In the early days of my self hosting journey, let\u0026rsquo;s just say that the up-time of my services were extremely finicky. I like to think they are more permanent now, especially because I am hosting everything on a VPS, but I certainly cannot compete with the stability of Google and Amazon. (Or pretty much any other paid service for that matter.) \u0026#x1f609;\nGitea\nGitea is a community managed, lightweight code hosting solution written in Go. I use it to manage my data analysis (using Private repos) and even host the source code for this very website! Using Gitea has given me the surface level introduction to the behemoth that is git. Fortunately, that is all I need. Once I have removed any sensitive data (like passwords, etc.) I will make my docker-compose file public. The docker-compose file is where I determine which services I pick to host, and how to configure them to my liking. Hopefully someone will find this useful.\nSyncthing\nIf I could only tell someone to self host a single service, I would have to pick Syncthing. It is a continuous file synchronization program, which means it keeps a specific file or folder the same between any device running Syncthing. I use it to keep my password database and my org-mode notes Now org-mode might be the biggest rabbithole of them all, and definitely the topic for another blog post. I use it to manage my TODO list, my lab notebook, my shopping lists, write this blog, and maintain my Zettelkasten note database. It is an immensely powerful tool. up to date between all of my devices. With Syncthing, all of my data is stored on my own devices and encrypted in transit.\nFreshRSS\nI keep up to date on the science in my field by subscribing to relevant RSS feeds. Yet another topic to write a post about. This really changed the game for my ability to keep on top of the latest research. 2022-07-14 Update: post complete! Check it out here. FreshRSS replaced Feedly for me, as I ran up against the number of feeds I could subscribe to on a free account. Also, when self hosting, I can save as many articles as my heart desires (even if I will never look at them again \u0026#x1f635; ).\nWallabag\nRemember Pocket for Firefox? (Yes, I know it still exists, okay?) Give Wallabag a spin, it is great for storing articles you want to read later. I set up FreshRSS to save articles to my Wallabag instance to keep for later.\nChangeDetection\nNow this is a fun one! ChangeDetection.io is a service that loads a webpage and checks to see if something has changed since the last time. This might not sound useful at first, but I recently used this to check for when a hot item for my new coffee roasting hobby was back in stock. I got an email the other day to let me know it was in stock. Pretty cool!\nHugo\nHugo is the static site generator I use to make this here blog! I was amazed at how much more response my site was using Hugo compare to when I paid a company to host a WordPress site. I\u0026rsquo;m sure WordPress could be fast, but I just wanted a barebones, pure html experience, and Hugo made it easy.\nCommento++\nYou may have noticed that I have some pretty snazzy comments sections on my site. I initially used Disqus, which you may recognize from a ton of sites around the internet, but didn\u0026rsquo;t like how it would serve ads through my comments section, and provided sign-ins using Google/Facebook/Twitter. I wanted to serve the simplest comments section I could, that still gave me the ability to migrate the comments to wherever I decide to keep my server. Go ahead and use the anonymous comment button, fill in your name, and you are off to the races.\nAuthelia\nThere are a few services I host that I really want to lock down. For these services, Authelia is great. It puts up a \u0026ldquo;Enter the 6 digit code on your phone\u0026rdquo; style 2 factor authentication in front of the services I choose. Or, if you follow the guide here, you can have it send you a DUO push, just like you are one of the big hitters out there. I feel much more secure with Authelia in front of Adminer, Traefik, and Portainer.\nBoring stuff that allows everything else to work!\nPostgreSQL database MariaDB database Traefik reverse proxy Umami privacy respecting site analytics Portainer for docker container management Redis in-memory data store Adminer database management traefik-socket-proxy to prevent pesky backdoors to my server! ","permalink":"https://www.zacharybillman.com/posts/zpb-current-selfhosted/","summary":"\u003cp\u003e\u003cem\u003eN.B.: I hope to add screenshots for each of these eventually. For now, I hope links to each services\u0026rsquo; website will suffice.\u003c/em\u003e\u003c/p\u003e\n\u003col\u003e\n\u003cli\u003e\n\u003cp\u003e\u003ca href=\"https://www.seafile.com/en/home/\"\u003eSeafile\u003c/a\u003e\u003c/p\u003e\n\u003cp\u003eThis is a great tool for managing files. I moved to this from Nextcloud because I am of the philosophy that I would prefer services that do one thing excellently instead of many things well. Nextcloud is an incredible Office365 replacement, but I found myself using a fraction of what it was capable of providing. Enter Seafile. It is cloud file syncing with a robust encryption implementation, just what the doctor ordered.\u003c/p\u003e","title":"What I'm currently selfhosting."},{"content":"My partner and I took a trip to the Mason Farm Biological Reserve the other day, and what a glorious day it was. This year, I\u0026rsquo;ve been quite busy in the lab, and missed a lot of the early spring warbler season, so I was very excited by the opportunity to check out the old stomping grounds.\nI brought the camera with me despite the fact we were going to be there around midday when the birds are much less active. I\u0026rsquo;m glad I did, because I got the best look at a common yellowthroat I\u0026rsquo;ve ever had. Normally these guys are flighty, staying close to the ground in small brush or tall grasses, but this one was putting on a proper show for the mating season. Even when you get a glimpse of one, it is usually just that, as they have jumped away before you can pull out the camera, taunting you with their iconic call. I was very pleased to capture a few choice shots of the bird. Hopefully there are more to come. While we were out, I also got a nice picture of a hermit thrush and a king snake.\nThese images have been compressed quite a bit for a lighter internet footprint. These have all been resized to 25% of their original size. If you would like the full sized images, let me know and I will send you a link!\n","permalink":"https://www.zacharybillman.com/posts/the-uncommon-yellowthroat/","summary":"\u003cp\u003eMy partner and I took a trip to the \u003ca href=\"https://ncbg.unc.edu/visit/mason-farm-biological-reserve/\"\u003eMason Farm Biological Reserve\u003c/a\u003e the other day, and what a glorious day it was. This year, I\u0026rsquo;ve been quite busy in the lab, and missed a lot of the early spring warbler season, so I was very excited by the opportunity to check out the old stomping grounds.\u003c/p\u003e\n\u003cp\u003eI brought the camera with me despite the fact we were going to be there around midday when the birds are much less active. I\u0026rsquo;m glad I did, because I got the best look at a common yellowthroat I\u0026rsquo;ve ever had.\n\u003cspan class=\"sidenote-number\"\u003e\u003csmall class=\"sidenote\"\u003e\nNormally these guys are flighty, staying close to the ground in small brush or tall grasses, but this one was putting on a proper show for the mating season. Even when you get a glimpse of one, it is usually just that, as they have jumped away before you can pull out the camera, taunting you with their \u003ca href=\"https://ebird.org/species/comyel#Modal-playlist\"\u003eiconic call\u003c/a\u003e.\n\u003c/small\u003e\u003c/span\u003e\nI was very pleased to capture a few choice shots of the bird. Hopefully there are more to come. While we were out, I also got a nice picture of a hermit thrush and a king snake.\u003c/p\u003e","title":"The (un)common yellowthroat."},{"content":"Welcome to my site! My name is Zachary Billman. I\u0026rsquo;m a UNC MD-PhD student in my 4th year of med school applying to pathology residency programs. I completed my PhD in Ed Miao\u0026rsquo;s lab. The curious reader may be thinking: \u0026ldquo;But Zach, Dr. Miao\u0026rsquo;s lab is at Duke, how did that come about?\u0026rdquo; What an astute question! Ed\u0026rsquo;s lab moved from UNC to Duke in early 2020, and I followed him down the street. My PhD was awarded by the UNC department of Microbiology and Immunology, but it just so happens that (nearly) all of my research took place at Duke. This move was quite a trial, especially when compounded with the onset of the pandemic. I suspect my research timeline suffered, though this is an extremely minor inconvenience compared to the tragedy the pandemic caused. This makes for very interesting basketball viewing parties with my Duke friends!\nMaybe having a diagram will make my training timeline make a bit more sense.\nFigure 1: An overview of my research training. I first began working for Dr. Sean Murphy in undergrad, then worked as a research scientist/lab manager for 3 years before heading to UNC for my MSTP training. During grad school, my lab moved from UNC to Duke, though my degree was awarded by UNC. The \u0026ldquo;Present\u0026rdquo; diamond was used on an older version of my CV and represents September 1st, 2025. Created using PlantUML.\nHopefully that can clear up the winding road I\u0026rsquo;ve taken a bit!\nMy research and scientific interests. I am broadly interested in innate immunology. I spent most of my time in graduate school studying the host-pathogen interaction between the intracellular fungus Histoplasma capsulatum and macrophages. There are many unstudied curiosities regarding the innate immune response to Histoplasma spp. and other intracellular fungi that I think are quite interesting. I also spent a considerable time thinking about the evolution of proteins involved in the programmed cell death pathway called pyroptosis.\nHobbies I may write about. Besides my science, I am interested in birding, baking sourdough bread (I swear I began years before the pandemic, though hearing of people baking bread brings me joy no matter when they first began!), board games, roasting coffee, and self-hosting free and open source software. Over the course of the pandemic, I have learned how to maintain a basic suite of services spread between a server I rent and a computer at home that have replaced my need for Google Photos and Google Drive. I\u0026rsquo;m hoping to be able to move away from these platforms entirely soon. I think they provide a great service, but at a substantial cost to privacy. Hopefully more to be said about my thoughts on FOSS soon! I also transitioned my old, (and quite frankly, embarrassingly slow) managed WordPress site with this lean, static site made in Hugo that I host myself. Now that I have mangled together some CSS to get my precious sidenotes up and running again, I\u0026rsquo;m ready to begin putting some ideas to paper. I love marginalia (the word to describe these notes on the side of this webpage). I\u0026rsquo;m not sure if this is unique to me, but I seem to get caught up in parenthetical / tangential thoughts very often, and I think using an Edward Tufte-esque sidenote is a great way for me to communicate in this way without distracting the reader too much. It seems marginalia such as this have been used throughout history, so perhaps it is normal, but most people can keep their thoughts focused better than me. The implementation I use is inspired by the Tufte CSS project and largely taken from this incredibly helpful post found at scripter.co. I\u0026rsquo;m quite proud of my progress in administering my server and self-hosting useful services.\nThe future of this site. On this site I plan to post updates about my journey through med school, grad school, and self-hosting I would like to share with the world. I have been helped immensely by many others\u0026rsquo; advice and I hope to impart similar tips to others someday. I suspect most posts will be about much lighter fare, like whatever hobbies tickle my fancy at the time.\n","permalink":"https://www.zacharybillman.com/posts/about-me/","summary":"\u003ch2 id=\"welcome-to-my-site\"\u003eWelcome to my site!\u003c/h2\u003e\n\u003cp\u003eMy name is Zachary Billman. I\u0026rsquo;m a UNC MD-PhD student in my 4th year of med school applying to pathology residency programs. I completed my PhD in Ed Miao\u0026rsquo;s lab. The curious reader may be thinking: \u0026ldquo;But Zach, Dr. Miao\u0026rsquo;s lab is at Duke, how did that come about?\u0026rdquo; What an astute question! Ed\u0026rsquo;s lab moved from UNC to Duke in early 2020, and I followed him down the street. My PhD was awarded by the UNC department of Microbiology and Immunology, but it just so happens that (nearly) all of my research took place at Duke.\n\u003cspan class=\"sidenote-number\"\u003e\u003csmall class=\"sidenote\"\u003e\nThis move was quite a trial, especially when compounded with the onset of the pandemic. I suspect my research timeline suffered, though this is an extremely minor inconvenience compared to the tragedy the pandemic caused.\n\u003c/small\u003e\u003c/span\u003e\nThis makes for very interesting basketball viewing parties with my Duke friends!\u003c/p\u003e","title":"About me. 👋"},{"content":"It\u0026rsquo;s over. My third year of medical school is officially behind me. I managed to get in a grand total of zero blog posts during grad school, so here\u0026rsquo;s to a new year with hopefully some more thoughts being shared. I have a lot to reflect on from the past year. It was wonderful. I wish everyone could experience what I did this past year. I think it goes without saying:\nI loved the third year of med school, but I do not want to do it again.\nA year of change. In the days leading up to my return to med school, I thought \u0026ldquo;Oh no, I really enjoy doing science, do I really have to go to med school?\u0026rdquo;. I also remember at the end of Step 1 and the first two years of med school thinking, \u0026ldquo;Oh no, I really enjoy med school, do I really have to do science again?\u0026rdquo;. I think I have a welcome problem of enjoying what I\u0026rsquo;m doing. The third year of med school is a shift. After years of memorizing and examinations, the doors to the promised land are finally opened. I have experienced nothing like it before It feels intentionally unsettling. You are thrown into the clinic with a modicum of guidance so you aren\u0026rsquo;t totally caught off guard, but you are thrown out to the wolves. I don\u0026rsquo;t mean this as a criticism of the system, it feels necessary. Third year medical students—commonly shorted to MS3s—have just one year to experience a broad swath of medicine and pick a specialty. So you had better be ready to dive in.\nTotal immersion I came to terms with my new reality quickly. Gone were the days of hitting the snooze button and going home when I pleased. I am now beholden to other people\u0026rsquo;s schedules. This came back relatively naturally. Maybe not hitting snooze. A regrettable personal failing of mine. I was, however, immediately faced with a new reality in the patient room. Patients come to the doctor for a number of reasons, but often seek relief. To get to the core of what ails them, they will tell you everything. I was not prepared for how vulnerable patients would be with me. I am not sure if this ever will feel natural. I hope it never does. I was told many stories of experiences living with scary diagnoses, and not knowing what to do with it. Family histories of all sorts. Personal details that were sometimes (oftentimes?) off the wall. I see all of these specifics as flailing, grasping at sand hoping that something could explain their pain. Sometimes it could. Usually it did not. But since I was in a white coat, I was privileged to hear it.\nI think my years spent in the lab have prepared me to face some of the challenges set before me. At the very least, having a few more years under my belt helped me approach the year with a bit of maturity. This seems to have paid off. I guess my recommendation is to simply get old before going to med school. Returning to studying The hospital is how I spent the majority of my time, but a new reality for me was also going back to daily studying. There is a strange dichotomy in medicine of \u0026ldquo;Oh, it doesn\u0026rsquo;t really matter\u0026rdquo; and \u0026ldquo;If you don\u0026rsquo;t get this class/score/grade then you won\u0026rsquo;t be able to be the kind of doctor you want to be, so you had better get your act together.\u0026rdquo; Simultaneously there are no expectations and immense responsibility for the looming specter of Step 2. I\u0026rsquo;m glad that studying regularly came back easily enough. I was concerned I would experience a studying whiplash. I\u0026rsquo;m glad it never came. I did UWorld and Anki nearly every day for a full year and felt alright.\nBecoming invisible I quickly learned I needed to change my understanding of my contribution to the team. Exiting grad school, people understood that they could come to me for help. I was a resource, a seasoned veteran of the lab. If someone needed an experiment done, I could do it, and be trusted to do it. In med school as a third year, I was nothing. A fly on the wall; a worm beneath the feet of the real doctors. In science, I felt like I was treated as a peer with even my committee members with multiple R01s. Even if I didn\u0026rsquo;t understand the science perfectly, I could contribute some different perspective. In medicine, sometimes not being recognized at all by my attendings was the best outcome. Which happened regularly. My role, was not as a contributor—as it was in science—it was simply to get in the reps. Once I understood that the expectations of me were below the ground, I understood that everything I did in third year was for myself. This is taken at face value by the team at times. I would spend 30 minutes working on a presentation, pre-rounding, the works, and at the end of my part, the intern would nod, then turn to the senior resident and say \u0026ldquo;I was thinking that we\u0026hellip;\u0026rdquo; without thinking of my work. This is perhaps a bit of cognitive restructuring, but recognizing this is what gave me the freedom to embed myself in the hospital flow, without a single worry about the outcome. Simply doing my best was the best thing I could do. Obviously. But this was not apparent to me at first. I needed more quality repetitions to develop good habits in the future. And also experience as much of medicine as possible to find what I want to do with my life. This permission allowed me to approach specialties I do not care about with the awe and respect they deserve.\nA year of wonder. Med school prepares you for the standardized tests. I think this is generally useful. The tests on aggregate are reasonable and evaluate your ability to think through common clinical scenarios. There will always be oddball questions that come out of left field, but I let these flow over me. No need to perseverate on the small stuff. The time for that can come later.\nWhat I didn\u0026rsquo;t realize is how much of the \u0026ldquo;classic\u0026rdquo; material we are fed in the first couple years of med school would come to the forefront. The \u0026ldquo;sandpaper rash\u0026rdquo; of scarlet fever really does feel like sandpaper. Nikolsky\u0026rsquo;s sign actually works. Tripoding for epiglottitis gets the physicians worked up. Don\u0026rsquo;t forget about von Willebrand\u0026rsquo;s disease when someone seems to be bleeding a bit too much. TB is out there, watch for hemoptosis. Night sweats, unintended weight loss, is cancer until proven otherwise. And yes, it really can be lupus.\nIn general, facing the unknown with a sense of earnestness was the way I felt best able to respect those who gathered and passed down the medical knowledge I am privileged to learn today. Sometimes, my excitement to see aspects of medicine would rouse a curious response from the residents. I project here, but I felt a sense of surprise, like that of a doting parent seeing their child experience something new, after forgetting the astonishment they once felt.\nEarnestness is next to med studentlyness.\nPerhaps what I\u0026rsquo;m getting at here is that I found it important to bask in the privilege of seeing the pathology I encountered in med school, and to remind the residents of this sensation. I felt childish at times—and perhaps overanimated—but I found this excitement was to my and my resident\u0026rsquo;s benefit.\nMy surgery rotation overflowed with examples of wonder of medicine. Partially because of the team I worked with, and the rest because of the undeniable coolness of surgery. The OR is a cool place. The orderliness and chaos ebb. The spans of steady, industrious work are interrupted with staccato notes of bedlam. The anatomy I learned in class was ever present, but the surgeons bemoaned \u0026ldquo;normal anatomic variation\u0026rdquo;.\nI was struck with wonder at the sight of human anatomy as it unfolded before me. What I was able to experience in the OR felt like the culmination of centuries of human curiosity. There is an ancientness to medicine that I catch flashes of—I could perform the physical exam on humans hundred of millions of years ago and interrogate the same pathologies as I do in the hospital today—and viewing the exposed anatomy is a pressure-bagged infusion of this collective wonder. To gaze upon the peristalsing of the small intestine, or steady beating of the heart is a sight to behold, indeed.\nA year of shame. It weighs upon me the circumstances that resulted in these transcendent experiences. Not one patient was in the hospital without reason. What to make of these patients with horrible pathology? I still feel unsettled about how the cause of their pain sparked wonder. How dare I gain, merely by the circumstance of having their care managed at UNC, Which, as a tertiary care center, layers on more complexity. Many patients end up at UNC because they have no where else they can go for help. And this signs them up for med students? For shame. from the very essence of their malady? I do not know what to do with my discomfort, but I think it is best that I dwell in it. With this, I respect the people before me in the hospital and recognize their humanity.\nBut I often complained of what I say here I was lucky to do. I find myself resentful of my future schedule; when was I supposed to learn that I will be working 13 hour days, 6 days a week for the rest of my life? And what of having a family? Medicine by necessity requires sacrifice. I happened to sign up for sacrifices years before I recognized how profound they were. How might I balance this dread and with the joy of practicing medicine? And why do I seem more concerned about this than others? Am I not grateful enough? Am I not capable of the sacrifices that others seem to offer so effortlessly? I don\u0026rsquo;t necessarily think this to be true, but these questions erode at my will to pursue medicine.\nPerhaps most shameful of all is how my understanding of the patient-provider interaction evolved over the year. It began as an exploration of an open book, a tabula rasa that held within it a diagnosis and how to best intervene. On my first day in the outpatient clinic, it was clear that this is not the case. My preceptor had only 20 minutes for me to ① interview the patient and perform the physical exam, ② present with a plan, ③ return to the room and do everything again, ④ write orders, educate, and get the patient out of the door. It simply is not amenable to the free form, personable, curious interview I hoped to perform. By the end of the year, I had optimized how I asked questions to keep patients from going off the rails. When prerounding in medicine, I was there to extract information and not much else. Small talk had to go, there was no time. I like to chat, so this came at a loss of who I think I am. I am not sure how to do this well, while still feeling like Zachary. And from what I gather from the interns, that may just come later in my career. I found myself questioning, \u0026ldquo;Is this the \u0026lsquo;patient interaction\u0026rsquo; that has been mythologized throughout my training?\u0026rdquo; The carrot at the end of the stick dangled before me with a \u0026ldquo;You are so lucky to be able to do this, so you had better not complain of any abuse that comes your way.\u0026rdquo; It wasn\u0026rsquo;t a genuine interaction as much as me leading the patient along to tell me what I wanted to know. Of course, I used open ended questions, but only open enough. Leave the door a bit too open and next thing you know, you are talking about their dog\u0026rsquo;s breeder while you constantly stare at your watch, imagining what your attending will say when you return. I feel like I am alone in missing the core human element that funnels sprightly youths into medicine. Or worse, finding it a façade.\nThe shame extends beyond the hospital. One aspect of my life that has changed most dramatically is the sheer amount of time I felt I needed to dedicate to medicine, whether at the hospital or at home. I spent all day basking in the wonder of medicine, then I would come home and study for hours. I relied on my partner for keeping our household together more than ever, because I spent all day—all year, rather—in a state of discovery. Her life was largely the same, with the normal challenges of being a scientist, with the added bonus of getting less help from me. The shame built over the year. Again, how dare I?\nA year of glad. This has been an undeniable year of growth and joy, with these quibbles. It is clear that I was happier than I was during grad school. I know this from within myself, and reinforced by my wife\u0026rsquo;s comments on my mood. The pace of the day, and immediacy of problem solving were a welcome change.\nI recall, during the very first days preparing for med school during xTAP, having to do a simulated patient encounter complete with patient presentation to an attending physician. We were told about this encounter days in advance. And yet, I dreaded it. And near the last day of my final rotation, I did 8 of these in a row without breaking a sweat. Progress!\nI think, in a word, what I\u0026rsquo;ve experienced in the third year of med school is gratitude. Gratitude to be privileged to learn what I am learning. Gratitude for the experiences in my life that brought me here. Gratitude for the support from my wife. Gratitude to be involved in people\u0026rsquo;s lives when they are fragile. Ever since reading Braiding Sweetgrass I think one could call me \u0026ldquo;gratitude-pilled\u0026rdquo;. I also selfishly enjoyed the gratitude from patients as I put on my best doctor performance. In reflection on the year, I have spent time thinking of a phrase that I heard a number of times throughout med school from residents, \u0026ldquo;The worst day of residency is better than the best day of med school.\u0026rdquo; I find this hard to believe. This year has been magical. It is hard to imagine a year filled with more wonder and joy of caring for those in need. I will have to rely on the experience of those who have walked this path and trust that the rest of my training has plenty of magic to spare.\n","permalink":"https://www.zacharybillman.com/posts/ms3-year-is-magical/","summary":"\u003ch2 id=\"it-s-over-dot\"\u003eIt\u0026rsquo;s over.\u003c/h2\u003e\n\u003cp\u003eMy third year of medical school is officially behind me. I managed to get in a grand total of \u003cem\u003ezero\u003c/em\u003e blog posts during grad school, so here\u0026rsquo;s to a new year with hopefully some more thoughts being shared. I have a lot to reflect on from the past year. It was wonderful. I wish everyone could experience what I did this past year. I think it goes without saying:\u003c/p\u003e","title":"The third year of medical school is magical."},{"content":"I, like many others, picked up a new hobby during the pandemic. Other people\u0026rsquo;s hobbies may bring them joy. This could be for many reasons. There is the joy of creating something from scratch. You can revel in your thriftiness. You can embrace the pride when you recognize that your creation is on par (or better!) than what you can buy. I feel like these are embodied in the sourdough craze that caught fire early on in COVID. Dare I say that I did this before it was cool? \u0026#x1f60e; I baked two loaves of bread almost every weekend through med school. Maybe I should bring that back, it\u0026rsquo;s been a while since I brought out the ole\u0026rsquo; starter. My pandemic hobby is similar, but different in that it often feels like a chore, costs more money, and often turns out worse than what I can buy. Of course, I am talking about how I\u0026rsquo;ve started roasting my own coffee at home.\nI\u0026rsquo;m not sure where this idea was planted into my brain. I don\u0026rsquo;t think I know anyone who roasts their own beans, and I certainly didn\u0026rsquo;t know how. I didn\u0026rsquo;t even drink coffee regularly until after college! I guess that extra time on the computer sent me down a rabbithole I have yet to emerge from.\nFirst, I want to preface the following with a disclaimer: This is not a detailed guide about how to roast your own coffee. If you are interested, I recommend checking out the How To Roast Your Own Coffee guide at Sweet Maria\u0026rsquo;s as a starting point. There is also the /r/roasting subreddit if that is your cup of tea. My only warning is there will be a lot of smoke. Roast your coffee outside, for Pete\u0026rsquo;s sake!\nIt all started with a trusty popcorn popper. There are a few things you want when you roast coffee:\nAir hot enough to roast coffee Remove the chaff from the beans Turns out that a classic popcorn popper fits the bill, as long as it has an upwards airflow and doesn\u0026rsquo;t let the chaff fall into the heating element. There is a bit of a cult following for the West Bend Poppery 2 model, but that one seemed a bit pricey, so I settled for a very capable popper from Nostalgia.\nFigure 1: I got a good bit of mileage out of my popcorn popper. If you are interested in roasting your own coffee I would give it a whirl.\nThings were simple back then. I still bought most of the coffee I drank, but I roasted enough to enjoy some freshly roasted coffee as an occasional treat. I ordered 10 pounds of green beans from Sweet Maria\u0026rsquo;s and life was good.\nThen I became a bit of a coffee snob.\nI could only roast 100 grams of coffee at a time in the popcorn popper, which is only enough for one pot of coffee in the morning for me. So it was time to upgrade.\nI bought the SR800 fluid bed roaster, which upped my roasting capacity and gave me finer control on temperature and airflow. Suffice to say my roasts improved a lot! At this point, I would consider my coffee good enough to sell at a farmer\u0026rsquo;s market to break even.\nIf you ever find yourself on a coffee roasting forum and bring up the SR800, someone is bound to bring up the famous RazzoRoasting extension tube. If you look for advice for how to use the SR800, I swear it\u0026rsquo;s assumed that you have this very specific accessory. \u0026hellip;And so I bought one.\nDon\u0026rsquo;t worry, that is the extent of all of my coffee spending (for now). I am a very satisfied coffee roaster now. Check out this quick series of images going from the green beans to a nearly finished product! I can spend about 45 minutes and go from nothing to nearly 2 pounds of roasted beans, enough for about a week and a half of coffee. Not bad! The only downside is that now I feel like I need to buy coffee from local roasters to get my fix. There are certainly crueler fates.\nAs a sign off, I will share something that surprised me about coffee roasting. When I roast coffee, the most important cue to determine if the coffee is roasted is the sound. That\u0026rsquo;s right, not the color, not the smell, but the sound. When heating up a coffee bean, the water trapped inside eventually bursts out of the bean in a rapid expansion. This is called \u0026ldquo;first crack\u0026rdquo;, and indicates that the coffee is roasted enough to be drinkable. The expansion also releases the chaff from the bean. If you continue heating up the bean, you will eventually reach \u0026ldquo;second crack\u0026rdquo;. I think a solid medium roast is taken out just before second crack, so I try to take my coffee out to this point and it hasn\u0026rsquo;t proved me wrong yet.\nHappy coffee-ing! \u0026#x2615;\n","permalink":"https://www.zacharybillman.com/posts/roasting-coffee-at-home/","summary":"\u003cp\u003eI, like many others, picked up a new hobby during the pandemic. Other people\u0026rsquo;s hobbies may bring them joy. This could be for many reasons. There is the joy of creating something from scratch. You can revel in your thriftiness. You can embrace the pride when you recognize that your creation is on par (or better!) than what you can buy. I feel like these are embodied in the sourdough craze that caught fire early on in COVID.\n\u003cspan class=\"sidenote-number\"\u003e\u003csmall class=\"sidenote\"\u003e\nDare I say that I did this before it was cool? \u0026#x1f60e; I baked two loaves of bread almost every weekend through med school. Maybe I should bring that back, it\u0026rsquo;s been a while since I brought out the ole\u0026rsquo; starter.\n\u003c/small\u003e\u003c/span\u003e\nMy pandemic hobby is similar, but different in that it often feels like a chore, costs more money, and often turns out worse than what I can buy. Of course, I am talking about how I\u0026rsquo;ve started roasting my own coffee at home.\u003c/p\u003e","title":"Roasting coffee at home. ☕"},{"content":"It is an age-old question: how can one keep up with the continuous output of science? I remember at the beginning of my PhD struggling to figure out how anyone found out when a new paper came out. \u0026#x1f635; Did they sit on nature.com and spam the refresh button? Did they know when each journal released their latest issue?\nBehold the power of RSS! Most websites have a page that contains information about each subpage in a computer-readable format called RSS (Really Simple Syndication). Mine has one right here! These pages can be parsed by a number of RSS feed aggregators. The way these pages are set up make it such that they add any new information hosted at that domain. This is useful in the science world because you can find the RSS feed of a given journal, subscribe to it, then have every new article published online be delivered right to you.\nThere are a plethora of RSS feed aggregators you can pick from manage your feeds. I have previously used Feedly and Inoreader, which are great free solutions, but have moved on to selfhosting my own instance of FreshRSS.\nAfter making an account at your friendly local RSS feed aggregator, you can add whatever feeds your heart desires. To find a journal\u0026rsquo;s rss feed, I often just search \u0026ldquo;$JOURNAL_NAME rss feed\u0026rdquo; and poke around until I find something that looks right. Most of the aggregators will test the feed out first to make sure that you are trying to add a legitimate one. Here are a few of the heavy hitters to get you started:\nhttp://feeds.nature.com/nature/rss/current https://www.science.org/rss/express.xml https://www.cell.com/cell/inpress.rss Nothing like a constant stream of Cell, Science, and Nature to make your project feel like a real winner, eh?\nHere is what my own site looks like.\nFigure 1: My current FreshRSS setup. On the left I have my feeds separated into folders. In the middle you can see the titles of papers that appear in my feed.\nAnd after I hit J to move to the first item in the feed.\nFigure 2: With a title selected, you can see the abstract and authors.\nAfter collecting all of your desired RSS feeds, you cannot forego your responsibility of actually reading them! Most RSS feed aggregators have shortcuts to move through titles quickly (Typically J to move on to the next one and K to move up.) They always seem to use vi keybindings. A bunch of computer nerds have really cornered the keybinding market. I have let them take over my computing life. Each morning when I get into the lab, I quickly set up something, then head to my desk to hit J until the counter reaches zero.\nBut what about my very specific field? You can subscribe to all of the journals you want, but that doesn\u0026rsquo;t make the papers with your specific interests pop out. Fortunately, the NIH has this exact circumstance in mind.\nWhen you make a new search on PubMed you might notice the \u0026ldquo;Create RSS\u0026rdquo; button. Give it a click, then you will have a personal link you can add to your favorite RSS feed aggregator.\nFigure 3: Somehow I never noticed this button until I needed it.\nThis changed the game for me for keeping up with papers. Unfortunately, it doesn\u0026rsquo;t solve the problem of library management, or actually getting around to reading the papers you care about. I will leave library management as an exercise for the interested reader. Here\u0026rsquo;s a tip, the best solution uses the Zotero citation manager. Bonus points for using Zotfile for renaming your PDFs and Better BibTex for Zotero. \u0026#x1f609; I hope this helps you get your eyeballs on that science you crave. If you have solved the problem of accruing papers to read faster than you read them, let me know.\n","permalink":"https://www.zacharybillman.com/posts/rss-feeds-to-find-science-papers/","summary":"\u003cp\u003eIt is an age-old question: how can one keep up with the continuous output of science? I remember at the beginning of my PhD struggling to figure out how anyone found out when a new paper came out. \u0026#x1f635; Did they sit on nature.com and spam the refresh button? Did they know when each journal released their latest issue?\u003c/p\u003e\n\u003ch2 id=\"behold-the-power-of-rss\"\u003eBehold the power of RSS!\u003c/h2\u003e\n\u003cp\u003eMost websites have a page that contains information about each subpage in a computer-readable format called RSS (Really Simple Syndication). \u003ca href=\"https://zacharybillman.com/index.xml\"\u003eMine has one right here!\u003c/a\u003e These pages can be parsed by a number of RSS feed aggregators. The way these pages are set up make it such that they add any new information hosted at that domain. This is useful in the science world because you can find the RSS feed of a given journal, subscribe to it, then have every new article published online be delivered right to you.\u003c/p\u003e","title":"Using RSS feeds to keep on top of science."},{"content":"My interest in self-hosting began in my with my interests in internet privacy. Plastered all over the internet are stories about how much Google, Facebook and Amazon know about you. I deleted my Facebook account years ago, and I\u0026rsquo;m too paranoid to go back to the site because there\u0026rsquo;s a real possibility that Facebook has cached my account, ready to spin it back up in case I try to login again. The ads served to me were too accurate for my liking. This is despite almost never clicking on them! I have become convinced of the idea that, if you are not paying for the product, you are the product. From this assumption, it follows that anywhere I trust with my data that I am not paying for (like Google Drive, Google Photos, Dropbox, Facebook, Twitter) is using my data to earn money. We know that Google uses the labels you add to Photos to train it\u0026rsquo;s AI, and Facebook uses (at least) Instagram photos to train it\u0026rsquo;s AI. For some, the value proposition of allowing a company to use your data for a useful service in return is an acceptable one. I find this to be a reasonable stance, but I took my growing interest in internet privacy as a chance to learn about how I can take control of my data.\nInitially, I lurked on forums like /r/privacy to learn what I could do to avoid big-tech\u0026rsquo;s watchful eye. There were numerous comments along the lines of: \u0026ldquo;The only way to be in control of your data is to self-host your services.\u0026rdquo; I had no idea what this meant! Hard to believe that less than a year later, I learned to use (and love) Linux as my primary OS, and have happily replaced Google Photos, Google Drive and other services with my own self-hosted alternatives. Self-hosting, I have since learned, is when you run useful programs from your own computer. By doing so, you have complete knowledge of where and how your data is stored and how it is being used. It has the additional effect of being a bottomless time sink.\nTo begin, I needed an always-on computer to run these useful programs. I began with a humble Raspberry Pi.\nFigure 1: My humble Raspberry Pi and its hard drive. This dude currently tirelessly runs the excellent Adguard Home and downloads a backup of my data every night.\nThese are tiny, but capable computers that are great for fiddling with. The projects people develop for these are amazing and diverse. With RPi in hand, I began with the ambitious project of replacing Google Drive with Nextcloud. After much frustration with a bare metal installation, I found the NextcloudPi project. Surprisingly, it went pretty okay! At first, I was intimidated by Linux defaults, but over time I grew to appreciate, and indeed, prefer Linux as an operating system. My decision to use Linux over Windows/MacOS is because it is free and open source software (FOSS). This is a topic for a different post, but I think using FOSS when possible is a moral imperative of sorts. I used Nextcloud strictly from my home for a few months, without the ability to connect to it from the internet, to test the self-hosting waters. My first true cloud replacement spun up once I decided to access this lil\u0026rsquo; guy from the internet. To do so, I purchased a domain (not the one this site is hosted on) and pointed it to the IP of my house. I forwarded the appropriate ports of my router to the RPi.\nThis is when the real exploration began. I was able to access my files and images using Nextcloud, but the photo viewing service left something to be desired. No problem, why not spin up an instance of Photoprism? I use RSS feeds to keep on top of the latest science in the journals relevant to my field using Feedly. Why not host my own RSS feed aggregator so I can subscribe to as many feeds as I desire?\nThis cycle continued, and I accrued many cool applications, but in the back of my mind I worried about opening up my home network to the internet. I also struggled to run some programs because the RPi uses the arm64 architecture, and most services are written with amd64 in mind. These two forces eventually convinced me to purchase a server where I could manage all of my services remotely. Some would say that not owning the hardware that is running your own services is not \u0026ldquo;true\u0026rdquo; self-hosting. I think this is needlessly exclusive. Let everyone self host, dangit! Someday, when I have more stable internet and a more permanent home, I hope to host everything from my own home, but until then, I\u0026rsquo;m extremely pleased with my current stack. And that is where I am now. I happily host numerous services on my virtual private server that entirely replace Google Photos, Google Drive and GitHub for me. Even better, there are specialized services that fill a need I never realized I had. What\u0026rsquo;s more, if I ever want to spin up a new service, all I have to do is add it to my to docker-compose file and it will be up within minutes. What a world!\nI thought about making this into a \u0026ldquo;guide\u0026rdquo; style post. I nixed that idea because, quite frankly, I feel like I don\u0026rsquo;t know what I\u0026rsquo;m doing. I am really happy with my setup, but I don\u0026rsquo;t feel like I have the authority to tell people how to administer their own services. If you are interested, allow me to point you toward the guide that really got me rolling: Ultimate Traefik Docker Compose Guide.\nFor those of you wondering what I am currently hosting, check out my current list at the link and let me know what you think!\n","permalink":"https://www.zacharybillman.com/posts/my-selfhosting-journey/","summary":"\u003cp\u003eMy interest in self-hosting began in my with my interests in internet privacy. Plastered all over the internet are stories about how much Google, Facebook and Amazon know about you. I deleted my Facebook account years ago, and I\u0026rsquo;m too paranoid to go back to the site because there\u0026rsquo;s \u003ca href=\"https://www.reddit.com/r/privacy/comments/6nmjfh/facebook_account_fully_recovered_3_years_after/\"\u003ea real possibility that Facebook has cached my account, ready to spin it back up\u003c/a\u003e in case I try to login again. The ads served to me were too accurate for my liking.\n\u003cspan class=\"sidenote-number\"\u003e\u003csmall class=\"sidenote\"\u003e\nThis is despite almost never clicking on them!\n\u003c/small\u003e\u003c/span\u003e\nI have become convinced of the idea that, if you are not paying for the product, you are the product. From this assumption, it follows that anywhere I trust with my data that I am not paying for (like Google Drive, Google Photos, Dropbox, Facebook, Twitter) is using my data to earn money. We know that \u003ca href=\"https://www.theverge.com/2020/11/11/21559930/google-train-ai-photos-image-labelling-app-android-update\"\u003eGoogle uses the labels you add to Photos to train it\u0026rsquo;s AI\u003c/a\u003e, and \u003ca href=\"https://ai.facebook.com/blog/seer-the-start-of-a-more-powerful-flexible-and-accessible-era-for-computer-vision/\"\u003eFacebook uses (at least) Instagram photos to train it\u0026rsquo;s AI\u003c/a\u003e. For some, the value proposition of allowing a company to use your data for a useful service in return is an acceptable one. I find this to be a reasonable stance, but I took my growing interest in internet privacy as a chance to learn about how I can take control of my data.\u003c/p\u003e","title":"My selfhosting journey."},{"content":"N.B.: I hope to add screenshots for each of these eventually. For now, I hope links to each services\u0026rsquo; website will suffice.\nSeafile\nThis is a great tool for managing files. I moved to this from Nextcloud because I am of the philosophy that I would prefer services that do one thing excellently instead of many things well. Nextcloud is an incredible Office365 replacement, but I found myself using a fraction of what it was capable of providing. Enter Seafile. It is cloud file syncing with a robust encryption implementation, just what the doctor ordered.\nPhotoprism\nNextcloud\u0026rsquo;s implementation of photo management was a bit clumsy for my tastes, so I began on a hunt for a more feature complete option. I was very lucky to stumble upon Photoprism early on in my self hosting journey. I am a proud supporter of this project. It brings a ton to the table, and doesn\u0026rsquo;t leave me missing Google Photos one bit. It is also actively developed. For instance, as of 2022-07-02, there was a recent update that improved scrolling a ton, which was one of my remaining quibbles with it\u0026rsquo;s functionality. Some people complain that it doesn\u0026rsquo;t scale up for libraries of 10,000+ photos, but my 2000 photo library works swimmingly. On my phone, I use the Folder Sync app to automatically send any pictures I take on my phone to the Photoprism imports folder. Within 15 minutes of snapping a photo, it is there on my Photoprism instance. I highly recommend giving it a go.\nMealie\nI have to admit that the name leaves something to be desired. Fortunately, the service itself doesn\u0026rsquo;t fall short. Mealie is a recipe management application. It is able to parse your favorite recipe websites to create immortalized versions of the recipe. This helps fight detestable link rot that plagues the internet. It allows you to edit ingredient amounts, make comments about what you would change next time, and plan out your weekly meals. It helps that it is beautiful and intuitive to use. If only I could get my partner to use it\u0026hellip; I want to go on the record here and say that I think it is sensible that she doesn\u0026rsquo;t trust my self hosted services that much. In the early days of my self hosting journey, let\u0026rsquo;s just say that the up-time of my services were extremely finicky. I like to think they are more permanent now, especially because I am hosting everything on a VPS, but I certainly cannot compete with the stability of Google and Amazon. (Or pretty much any other paid service for that matter.) \u0026#x1f609;\nGitea\nGitea is a community managed, lightweight code hosting solution written in Go. I use it to manage my data analysis (using Private repos) and even host the source code for this very website! Using Gitea has given me the surface level introduction to the behemoth that is git. Fortunately, that is all I need. Once I have removed any sensitive data (like passwords, etc.) I will make my docker-compose file public. The docker-compose file is where I determine which services I pick to host, and how to configure them to my liking. Hopefully someone will find this useful.\nSyncthing\nIf I could only tell someone to self host a single service, I would have to pick Syncthing. It is a continuous file synchronization program, which means it keeps a specific file or folder the same between any device running Syncthing. I use it to keep my password database and my org-mode notes Now org-mode might be the biggest rabbithole of them all, and definitely the topic for another blog post. I use it to manage my TODO list, my lab notebook, my shopping lists, write this blog, and maintain my Zettelkasten note database. It is an immensely powerful tool. up to date between all of my devices. With Syncthing, all of my data is stored on my own devices and encrypted in transit.\nFreshRSS\nI keep up to date on the science in my field by subscribing to relevant RSS feeds. Yet another topic to write a post about. This really changed the game for my ability to keep on top of the latest research. 2022-07-14 Update: post complete! Check it out here. FreshRSS replaced Feedly for me, as I ran up against the number of feeds I could subscribe to on a free account. Also, when self hosting, I can save as many articles as my heart desires (even if I will never look at them again \u0026#x1f635; ).\nWallabag\nRemember Pocket for Firefox? (Yes, I know it still exists, okay?) Give Wallabag a spin, it is great for storing articles you want to read later. I set up FreshRSS to save articles to my Wallabag instance to keep for later.\nChangeDetection\nNow this is a fun one! ChangeDetection.io is a service that loads a webpage and checks to see if something has changed since the last time. This might not sound useful at first, but I recently used this to check for when a hot item for my new coffee roasting hobby was back in stock. I got an email the other day to let me know it was in stock. Pretty cool!\nHugo\nHugo is the static site generator I use to make this here blog! I was amazed at how much more response my site was using Hugo compare to when I paid a company to host a WordPress site. I\u0026rsquo;m sure WordPress could be fast, but I just wanted a barebones, pure html experience, and Hugo made it easy.\nCommento++\nYou may have noticed that I have some pretty snazzy comments sections on my site. I initially used Disqus, which you may recognize from a ton of sites around the internet, but didn\u0026rsquo;t like how it would serve ads through my comments section, and provided sign-ins using Google/Facebook/Twitter. I wanted to serve the simplest comments section I could, that still gave me the ability to migrate the comments to wherever I decide to keep my server. Go ahead and use the anonymous comment button, fill in your name, and you are off to the races.\nAuthelia\nThere are a few services I host that I really want to lock down. For these services, Authelia is great. It puts up a \u0026ldquo;Enter the 6 digit code on your phone\u0026rdquo; style 2 factor authentication in front of the services I choose. Or, if you follow the guide here, you can have it send you a DUO push, just like you are one of the big hitters out there. I feel much more secure with Authelia in front of Adminer, Traefik, and Portainer.\nBoring stuff that allows everything else to work!\nPostgreSQL database MariaDB database Traefik reverse proxy Umami privacy respecting site analytics Portainer for docker container management Redis in-memory data store Adminer database management traefik-socket-proxy to prevent pesky backdoors to my server! ","permalink":"https://www.zacharybillman.com/posts/zpb-current-selfhosted/","summary":"\u003cp\u003e\u003cem\u003eN.B.: I hope to add screenshots for each of these eventually. For now, I hope links to each services\u0026rsquo; website will suffice.\u003c/em\u003e\u003c/p\u003e\n\u003col\u003e\n\u003cli\u003e\n\u003cp\u003e\u003ca href=\"https://www.seafile.com/en/home/\"\u003eSeafile\u003c/a\u003e\u003c/p\u003e\n\u003cp\u003eThis is a great tool for managing files. I moved to this from Nextcloud because I am of the philosophy that I would prefer services that do one thing excellently instead of many things well. Nextcloud is an incredible Office365 replacement, but I found myself using a fraction of what it was capable of providing. Enter Seafile. It is cloud file syncing with a robust encryption implementation, just what the doctor ordered.\u003c/p\u003e","title":"What I'm currently selfhosting."},{"content":"My partner and I took a trip to the Mason Farm Biological Reserve the other day, and what a glorious day it was. This year, I\u0026rsquo;ve been quite busy in the lab, and missed a lot of the early spring warbler season, so I was very excited by the opportunity to check out the old stomping grounds.\nI brought the camera with me despite the fact we were going to be there around midday when the birds are much less active. I\u0026rsquo;m glad I did, because I got the best look at a common yellowthroat I\u0026rsquo;ve ever had. Normally these guys are flighty, staying close to the ground in small brush or tall grasses, but this one was putting on a proper show for the mating season. Even when you get a glimpse of one, it is usually just that, as they have jumped away before you can pull out the camera, taunting you with their iconic call. I was very pleased to capture a few choice shots of the bird. Hopefully there are more to come. While we were out, I also got a nice picture of a hermit thrush and a king snake.\nThese images have been compressed quite a bit for a lighter internet footprint. These have all been resized to 25% of their original size. If you would like the full sized images, let me know and I will send you a link!\n","permalink":"https://www.zacharybillman.com/posts/the-uncommon-yellowthroat/","summary":"\u003cp\u003eMy partner and I took a trip to the \u003ca href=\"https://ncbg.unc.edu/visit/mason-farm-biological-reserve/\"\u003eMason Farm Biological Reserve\u003c/a\u003e the other day, and what a glorious day it was. This year, I\u0026rsquo;ve been quite busy in the lab, and missed a lot of the early spring warbler season, so I was very excited by the opportunity to check out the old stomping grounds.\u003c/p\u003e\n\u003cp\u003eI brought the camera with me despite the fact we were going to be there around midday when the birds are much less active. I\u0026rsquo;m glad I did, because I got the best look at a common yellowthroat I\u0026rsquo;ve ever had.\n\u003cspan class=\"sidenote-number\"\u003e\u003csmall class=\"sidenote\"\u003e\nNormally these guys are flighty, staying close to the ground in small brush or tall grasses, but this one was putting on a proper show for the mating season. Even when you get a glimpse of one, it is usually just that, as they have jumped away before you can pull out the camera, taunting you with their \u003ca href=\"https://ebird.org/species/comyel#Modal-playlist\"\u003eiconic call\u003c/a\u003e.\n\u003c/small\u003e\u003c/span\u003e\nI was very pleased to capture a few choice shots of the bird. Hopefully there are more to come. While we were out, I also got a nice picture of a hermit thrush and a king snake.\u003c/p\u003e","title":"The (un)common yellowthroat."},{"content":"Welcome to my site! My name is Zachary Billman. I\u0026rsquo;m a UNC MD-PhD student in my 4th year of med school applying to pathology residency programs. I completed my PhD in Ed Miao\u0026rsquo;s lab. The curious reader may be thinking: \u0026ldquo;But Zach, Dr. Miao\u0026rsquo;s lab is at Duke, how did that come about?\u0026rdquo; What an astute question! Ed\u0026rsquo;s lab moved from UNC to Duke in early 2020, and I followed him down the street. My PhD was awarded by the UNC department of Microbiology and Immunology, but it just so happens that (nearly) all of my research took place at Duke. This move was quite a trial, especially when compounded with the onset of the pandemic. I suspect my research timeline suffered, though this is an extremely minor inconvenience compared to the tragedy the pandemic caused. This makes for very interesting basketball viewing parties with my Duke friends!\nMaybe having a diagram will make my training timeline make a bit more sense.\nFigure 1: An overview of my research training. I first began working for Dr. Sean Murphy in undergrad, then worked as a research scientist/lab manager for 3 years before heading to UNC for my MSTP training. During grad school, my lab moved from UNC to Duke, though my degree was awarded by UNC. The \u0026ldquo;Present\u0026rdquo; diamond was used on an older version of my CV and represents September 1st, 2025. Created using PlantUML.\nHopefully that can clear up the winding road I\u0026rsquo;ve taken a bit!\nMy research and scientific interests. I am broadly interested in innate immunology. I spent most of my time in graduate school studying the host-pathogen interaction between the intracellular fungus Histoplasma capsulatum and macrophages. There are many unstudied curiosities regarding the innate immune response to Histoplasma spp. and other intracellular fungi that I think are quite interesting. I also spent a considerable time thinking about the evolution of proteins involved in the programmed cell death pathway called pyroptosis.\nHobbies I may write about. Besides my science, I am interested in birding, baking sourdough bread (I swear I began years before the pandemic, though hearing of people baking bread brings me joy no matter when they first began!), board games, roasting coffee, and self-hosting free and open source software. Over the course of the pandemic, I have learned how to maintain a basic suite of services spread between a server I rent and a computer at home that have replaced my need for Google Photos and Google Drive. I\u0026rsquo;m hoping to be able to move away from these platforms entirely soon. I think they provide a great service, but at a substantial cost to privacy. Hopefully more to be said about my thoughts on FOSS soon! I also transitioned my old, (and quite frankly, embarrassingly slow) managed WordPress site with this lean, static site made in Hugo that I host myself. Now that I have mangled together some CSS to get my precious sidenotes up and running again, I\u0026rsquo;m ready to begin putting some ideas to paper. I love marginalia (the word to describe these notes on the side of this webpage). I\u0026rsquo;m not sure if this is unique to me, but I seem to get caught up in parenthetical / tangential thoughts very often, and I think using an Edward Tufte-esque sidenote is a great way for me to communicate in this way without distracting the reader too much. It seems marginalia such as this have been used throughout history, so perhaps it is normal, but most people can keep their thoughts focused better than me. The implementation I use is inspired by the Tufte CSS project and largely taken from this incredibly helpful post found at scripter.co. I\u0026rsquo;m quite proud of my progress in administering my server and self-hosting useful services.\nThe future of this site. On this site I plan to post updates about my journey through med school, grad school, and self-hosting I would like to share with the world. I have been helped immensely by many others\u0026rsquo; advice and I hope to impart similar tips to others someday. I suspect most posts will be about much lighter fare, like whatever hobbies tickle my fancy at the time.\n","permalink":"https://www.zacharybillman.com/posts/about-me/","summary":"\u003ch2 id=\"welcome-to-my-site\"\u003eWelcome to my site!\u003c/h2\u003e\n\u003cp\u003eMy name is Zachary Billman. I\u0026rsquo;m a UNC MD-PhD student in my 4th year of med school applying to pathology residency programs. I completed my PhD in Ed Miao\u0026rsquo;s lab. The curious reader may be thinking: \u0026ldquo;But Zach, Dr. Miao\u0026rsquo;s lab is at Duke, how did that come about?\u0026rdquo; What an astute question! Ed\u0026rsquo;s lab moved from UNC to Duke in early 2020, and I followed him down the street. My PhD was awarded by the UNC department of Microbiology and Immunology, but it just so happens that (nearly) all of my research took place at Duke.\n\u003cspan class=\"sidenote-number\"\u003e\u003csmall class=\"sidenote\"\u003e\nThis move was quite a trial, especially when compounded with the onset of the pandemic. I suspect my research timeline suffered, though this is an extremely minor inconvenience compared to the tragedy the pandemic caused.\n\u003c/small\u003e\u003c/span\u003e\nThis makes for very interesting basketball viewing parties with my Duke friends!\u003c/p\u003e","title":"About me. 👋"},{"content":"It\u0026rsquo;s over. My third year of medical school is officially behind me. I managed to get in a grand total of zero blog posts during grad school, so here\u0026rsquo;s to a new year with hopefully some more thoughts being shared. I have a lot to reflect on from the past year. It was wonderful. I wish everyone could experience what I did this past year. I think it goes without saying:\nI loved the third year of med school, but I do not want to do it again.\nA year of change. In the days leading up to my return to med school, I thought \u0026ldquo;Oh no, I really enjoy doing science, do I really have to go to med school?\u0026rdquo;. I also remember at the end of Step 1 and the first two years of med school thinking, \u0026ldquo;Oh no, I really enjoy med school, do I really have to do science again?\u0026rdquo;. I think I have a welcome problem of enjoying what I\u0026rsquo;m doing. The third year of med school is a shift. After years of memorizing and examinations, the doors to the promised land are finally opened. I have experienced nothing like it before It feels intentionally unsettling. You are thrown into the clinic with a modicum of guidance so you aren\u0026rsquo;t totally caught off guard, but you are thrown out to the wolves. I don\u0026rsquo;t mean this as a criticism of the system, it feels necessary. Third year medical students—commonly shorted to MS3s—have just one year to experience a broad swath of medicine and pick a specialty. So you had better be ready to dive in.\nTotal immersion I came to terms with my new reality quickly. Gone were the days of hitting the snooze button and going home when I pleased. I am now beholden to other people\u0026rsquo;s schedules. This came back relatively naturally. Maybe not hitting snooze. A regrettable personal failing of mine. I was, however, immediately faced with a new reality in the patient room. Patients come to the doctor for a number of reasons, but often seek relief. To get to the core of what ails them, they will tell you everything. I was not prepared for how vulnerable patients would be with me. I am not sure if this ever will feel natural. I hope it never does. I was told many stories of experiences living with scary diagnoses, and not knowing what to do with it. Family histories of all sorts. Personal details that were sometimes (oftentimes?) off the wall. I see all of these specifics as flailing, grasping at sand hoping that something could explain their pain. Sometimes it could. Usually it did not. But since I was in a white coat, I was privileged to hear it.\nI think my years spent in the lab have prepared me to face some of the challenges set before me. At the very least, having a few more years under my belt helped me approach the year with a bit of maturity. This seems to have paid off. I guess my recommendation is to simply get old before going to med school. Returning to studying The hospital is how I spent the majority of my time, but a new reality for me was also going back to daily studying. There is a strange dichotomy in medicine of \u0026ldquo;Oh, it doesn\u0026rsquo;t really matter\u0026rdquo; and \u0026ldquo;If you don\u0026rsquo;t get this class/score/grade then you won\u0026rsquo;t be able to be the kind of doctor you want to be, so you had better get your act together.\u0026rdquo; Simultaneously there are no expectations and immense responsibility for the looming specter of Step 2. I\u0026rsquo;m glad that studying regularly came back easily enough. I was concerned I would experience a studying whiplash. I\u0026rsquo;m glad it never came. I did UWorld and Anki nearly every day for a full year and felt alright.\nBecoming invisible I quickly learned I needed to change my understanding of my contribution to the team. Exiting grad school, people understood that they could come to me for help. I was a resource, a seasoned veteran of the lab. If someone needed an experiment done, I could do it, and be trusted to do it. In med school as a third year, I was nothing. A fly on the wall; a worm beneath the feet of the real doctors. In science, I felt like I was treated as a peer with even my committee members with multiple R01s. Even if I didn\u0026rsquo;t understand the science perfectly, I could contribute some different perspective. In medicine, sometimes not being recognized at all by my attendings was the best outcome. Which happened regularly. My role, was not as a contributor—as it was in science—it was simply to get in the reps. Once I understood that the expectations of me were below the ground, I understood that everything I did in third year was for myself. This is taken at face value by the team at times. I would spend 30 minutes working on a presentation, pre-rounding, the works, and at the end of my part, the intern would nod, then turn to the senior resident and say \u0026ldquo;I was thinking that we\u0026hellip;\u0026rdquo; without thinking of my work. This is perhaps a bit of cognitive restructuring, but recognizing this is what gave me the freedom to embed myself in the hospital flow, without a single worry about the outcome. Simply doing my best was the best thing I could do. Obviously. But this was not apparent to me at first. I needed more quality repetitions to develop good habits in the future. And also experience as much of medicine as possible to find what I want to do with my life. This permission allowed me to approach specialties I do not care about with the awe and respect they deserve.\nA year of wonder. Med school prepares you for the standardized tests. I think this is generally useful. The tests on aggregate are reasonable and evaluate your ability to think through common clinical scenarios. There will always be oddball questions that come out of left field, but I let these flow over me. No need to perseverate on the small stuff. The time for that can come later.\nWhat I didn\u0026rsquo;t realize is how much of the \u0026ldquo;classic\u0026rdquo; material we are fed in the first couple years of med school would come to the forefront. The \u0026ldquo;sandpaper rash\u0026rdquo; of scarlet fever really does feel like sandpaper. Nikolsky\u0026rsquo;s sign actually works. Tripoding for epiglottitis gets the physicians worked up. Don\u0026rsquo;t forget about von Willebrand\u0026rsquo;s disease when someone seems to be bleeding a bit too much. TB is out there, watch for hemoptosis. Night sweats, unintended weight loss, is cancer until proven otherwise. And yes, it really can be lupus.\nIn general, facing the unknown with a sense of earnestness was the way I felt best able to respect those who gathered and passed down the medical knowledge I am privileged to learn today. Sometimes, my excitement to see aspects of medicine would rouse a curious response from the residents. I project here, but I felt a sense of surprise, like that of a doting parent seeing their child experience something new, after forgetting the astonishment they once felt.\nEarnestness is next to med studentlyness.\nPerhaps what I\u0026rsquo;m getting at here is that I found it important to bask in the privilege of seeing the pathology I encountered in med school, and to remind the residents of this sensation. I felt childish at times—and perhaps overanimated—but I found this excitement was to my and my resident\u0026rsquo;s benefit.\nMy surgery rotation overflowed with examples of wonder of medicine. Partially because of the team I worked with, and the rest because of the undeniable coolness of surgery. The OR is a cool place. The orderliness and chaos ebb. The spans of steady, industrious work are interrupted with staccato notes of bedlam. The anatomy I learned in class was ever present, but the surgeons bemoaned \u0026ldquo;normal anatomic variation\u0026rdquo;.\nI was struck with wonder at the sight of human anatomy as it unfolded before me. What I was able to experience in the OR felt like the culmination of centuries of human curiosity. There is an ancientness to medicine that I catch flashes of—I could perform the physical exam on humans hundred of millions of years ago and interrogate the same pathologies as I do in the hospital today—and viewing the exposed anatomy is a pressure-bagged infusion of this collective wonder. To gaze upon the peristalsing of the small intestine, or steady beating of the heart is a sight to behold, indeed.\nA year of shame. It weighs upon me the circumstances that resulted in these transcendent experiences. Not one patient was in the hospital without reason. What to make of these patients with horrible pathology? I still feel unsettled about how the cause of their pain sparked wonder. How dare I gain, merely by the circumstance of having their care managed at UNC, Which, as a tertiary care center, layers on more complexity. Many patients end up at UNC because they have no where else they can go for help. And this signs them up for med students? For shame. from the very essence of their malady? I do not know what to do with my discomfort, but I think it is best that I dwell in it. With this, I respect the people before me in the hospital and recognize their humanity.\nBut I often complained of what I say here I was lucky to do. I find myself resentful of my future schedule; when was I supposed to learn that I will be working 13 hour days, 6 days a week for the rest of my life? And what of having a family? Medicine by necessity requires sacrifice. I happened to sign up for sacrifices years before I recognized how profound they were. How might I balance this dread and with the joy of practicing medicine? And why do I seem more concerned about this than others? Am I not grateful enough? Am I not capable of the sacrifices that others seem to offer so effortlessly? I don\u0026rsquo;t necessarily think this to be true, but these questions erode at my will to pursue medicine.\nPerhaps most shameful of all is how my understanding of the patient-provider interaction evolved over the year. It began as an exploration of an open book, a tabula rasa that held within it a diagnosis and how to best intervene. On my first day in the outpatient clinic, it was clear that this is not the case. My preceptor had only 20 minutes for me to ① interview the patient and perform the physical exam, ② present with a plan, ③ return to the room and do everything again, ④ write orders, educate, and get the patient out of the door. It simply is not amenable to the free form, personable, curious interview I hoped to perform. By the end of the year, I had optimized how I asked questions to keep patients from going off the rails. When prerounding in medicine, I was there to extract information and not much else. Small talk had to go, there was no time. I like to chat, so this came at a loss of who I think I am. I am not sure how to do this well, while still feeling like Zachary. And from what I gather from the interns, that may just come later in my career. I found myself questioning, \u0026ldquo;Is this the \u0026lsquo;patient interaction\u0026rsquo; that has been mythologized throughout my training?\u0026rdquo; The carrot at the end of the stick dangled before me with a \u0026ldquo;You are so lucky to be able to do this, so you had better not complain of any abuse that comes your way.\u0026rdquo; It wasn\u0026rsquo;t a genuine interaction as much as me leading the patient along to tell me what I wanted to know. Of course, I used open ended questions, but only open enough. Leave the door a bit too open and next thing you know, you are talking about their dog\u0026rsquo;s breeder while you constantly stare at your watch, imagining what your attending will say when you return. I feel like I am alone in missing the core human element that funnels sprightly youths into medicine. Or worse, finding it a façade.\nThe shame extends beyond the hospital. One aspect of my life that has changed most dramatically is the sheer amount of time I felt I needed to dedicate to medicine, whether at the hospital or at home. I spent all day basking in the wonder of medicine, then I would come home and study for hours. I relied on my partner for keeping our household together more than ever, because I spent all day—all year, rather—in a state of discovery. Her life was largely the same, with the normal challenges of being a scientist, with the added bonus of getting less help from me. The shame built over the year. Again, how dare I?\nA year of glad. This has been an undeniable year of growth and joy, with these quibbles. It is clear that I was happier than I was during grad school. I know this from within myself, and reinforced by my wife\u0026rsquo;s comments on my mood. The pace of the day, and immediacy of problem solving were a welcome change.\nI recall, during the very first days preparing for med school during xTAP, having to do a simulated patient encounter complete with patient presentation to an attending physician. We were told about this encounter days in advance. And yet, I dreaded it. And near the last day of my final rotation, I did 8 of these in a row without breaking a sweat. Progress!\nI think, in a word, what I\u0026rsquo;ve experienced in the third year of med school is gratitude. Gratitude to be privileged to learn what I am learning. Gratitude for the experiences in my life that brought me here. Gratitude for the support from my wife. Gratitude to be involved in people\u0026rsquo;s lives when they are fragile. Ever since reading Braiding Sweetgrass I think one could call me \u0026ldquo;gratitude-pilled\u0026rdquo;. I also selfishly enjoyed the gratitude from patients as I put on my best doctor performance. In reflection on the year, I have spent time thinking of a phrase that I heard a number of times throughout med school from residents, \u0026ldquo;The worst day of residency is better than the best day of med school.\u0026rdquo; I find this hard to believe. This year has been magical. It is hard to imagine a year filled with more wonder and joy of caring for those in need. I will have to rely on the experience of those who have walked this path and trust that the rest of my training has plenty of magic to spare.\n","permalink":"https://www.zacharybillman.com/posts/ms3-year-is-magical/","summary":"\u003ch2 id=\"it-s-over-dot\"\u003eIt\u0026rsquo;s over.\u003c/h2\u003e\n\u003cp\u003eMy third year of medical school is officially behind me. I managed to get in a grand total of \u003cem\u003ezero\u003c/em\u003e blog posts during grad school, so here\u0026rsquo;s to a new year with hopefully some more thoughts being shared. I have a lot to reflect on from the past year. It was wonderful. I wish everyone could experience what I did this past year. I think it goes without saying:\u003c/p\u003e","title":"The third year of medical school is magical."},{"content":"I, like many others, picked up a new hobby during the pandemic. Other people\u0026rsquo;s hobbies may bring them joy. This could be for many reasons. There is the joy of creating something from scratch. You can revel in your thriftiness. You can embrace the pride when you recognize that your creation is on par (or better!) than what you can buy. I feel like these are embodied in the sourdough craze that caught fire early on in COVID. Dare I say that I did this before it was cool? \u0026#x1f60e; I baked two loaves of bread almost every weekend through med school. Maybe I should bring that back, it\u0026rsquo;s been a while since I brought out the ole\u0026rsquo; starter. My pandemic hobby is similar, but different in that it often feels like a chore, costs more money, and often turns out worse than what I can buy. Of course, I am talking about how I\u0026rsquo;ve started roasting my own coffee at home.\nI\u0026rsquo;m not sure where this idea was planted into my brain. I don\u0026rsquo;t think I know anyone who roasts their own beans, and I certainly didn\u0026rsquo;t know how. I didn\u0026rsquo;t even drink coffee regularly until after college! I guess that extra time on the computer sent me down a rabbithole I have yet to emerge from.\nFirst, I want to preface the following with a disclaimer: This is not a detailed guide about how to roast your own coffee. If you are interested, I recommend checking out the How To Roast Your Own Coffee guide at Sweet Maria\u0026rsquo;s as a starting point. There is also the /r/roasting subreddit if that is your cup of tea. My only warning is there will be a lot of smoke. Roast your coffee outside, for Pete\u0026rsquo;s sake!\nIt all started with a trusty popcorn popper. There are a few things you want when you roast coffee:\nAir hot enough to roast coffee Remove the chaff from the beans Turns out that a classic popcorn popper fits the bill, as long as it has an upwards airflow and doesn\u0026rsquo;t let the chaff fall into the heating element. There is a bit of a cult following for the West Bend Poppery 2 model, but that one seemed a bit pricey, so I settled for a very capable popper from Nostalgia.\nFigure 1: I got a good bit of mileage out of my popcorn popper. If you are interested in roasting your own coffee I would give it a whirl.\nThings were simple back then. I still bought most of the coffee I drank, but I roasted enough to enjoy some freshly roasted coffee as an occasional treat. I ordered 10 pounds of green beans from Sweet Maria\u0026rsquo;s and life was good.\nThen I became a bit of a coffee snob.\nI could only roast 100 grams of coffee at a time in the popcorn popper, which is only enough for one pot of coffee in the morning for me. So it was time to upgrade.\nI bought the SR800 fluid bed roaster, which upped my roasting capacity and gave me finer control on temperature and airflow. Suffice to say my roasts improved a lot! At this point, I would consider my coffee good enough to sell at a farmer\u0026rsquo;s market to break even.\nIf you ever find yourself on a coffee roasting forum and bring up the SR800, someone is bound to bring up the famous RazzoRoasting extension tube. If you look for advice for how to use the SR800, I swear it\u0026rsquo;s assumed that you have this very specific accessory. \u0026hellip;And so I bought one.\nDon\u0026rsquo;t worry, that is the extent of all of my coffee spending (for now). I am a very satisfied coffee roaster now. Check out this quick series of images going from the green beans to a nearly finished product! I can spend about 45 minutes and go from nothing to nearly 2 pounds of roasted beans, enough for about a week and a half of coffee. Not bad! The only downside is that now I feel like I need to buy coffee from local roasters to get my fix. There are certainly crueler fates.\nAs a sign off, I will share something that surprised me about coffee roasting. When I roast coffee, the most important cue to determine if the coffee is roasted is the sound. That\u0026rsquo;s right, not the color, not the smell, but the sound. When heating up a coffee bean, the water trapped inside eventually bursts out of the bean in a rapid expansion. This is called \u0026ldquo;first crack\u0026rdquo;, and indicates that the coffee is roasted enough to be drinkable. The expansion also releases the chaff from the bean. If you continue heating up the bean, you will eventually reach \u0026ldquo;second crack\u0026rdquo;. I think a solid medium roast is taken out just before second crack, so I try to take my coffee out to this point and it hasn\u0026rsquo;t proved me wrong yet.\nHappy coffee-ing! \u0026#x2615;\n","permalink":"https://www.zacharybillman.com/posts/roasting-coffee-at-home/","summary":"\u003cp\u003eI, like many others, picked up a new hobby during the pandemic. Other people\u0026rsquo;s hobbies may bring them joy. This could be for many reasons. There is the joy of creating something from scratch. You can revel in your thriftiness. You can embrace the pride when you recognize that your creation is on par (or better!) than what you can buy. I feel like these are embodied in the sourdough craze that caught fire early on in COVID.\n\u003cspan class=\"sidenote-number\"\u003e\u003csmall class=\"sidenote\"\u003e\nDare I say that I did this before it was cool? \u0026#x1f60e; I baked two loaves of bread almost every weekend through med school. Maybe I should bring that back, it\u0026rsquo;s been a while since I brought out the ole\u0026rsquo; starter.\n\u003c/small\u003e\u003c/span\u003e\nMy pandemic hobby is similar, but different in that it often feels like a chore, costs more money, and often turns out worse than what I can buy. Of course, I am talking about how I\u0026rsquo;ve started roasting my own coffee at home.\u003c/p\u003e","title":"Roasting coffee at home. ☕"},{"content":"It is an age-old question: how can one keep up with the continuous output of science? I remember at the beginning of my PhD struggling to figure out how anyone found out when a new paper came out. \u0026#x1f635; Did they sit on nature.com and spam the refresh button? Did they know when each journal released their latest issue?\nBehold the power of RSS! Most websites have a page that contains information about each subpage in a computer-readable format called RSS (Really Simple Syndication). Mine has one right here! These pages can be parsed by a number of RSS feed aggregators. The way these pages are set up make it such that they add any new information hosted at that domain. This is useful in the science world because you can find the RSS feed of a given journal, subscribe to it, then have every new article published online be delivered right to you.\nThere are a plethora of RSS feed aggregators you can pick from manage your feeds. I have previously used Feedly and Inoreader, which are great free solutions, but have moved on to selfhosting my own instance of FreshRSS.\nAfter making an account at your friendly local RSS feed aggregator, you can add whatever feeds your heart desires. To find a journal\u0026rsquo;s rss feed, I often just search \u0026ldquo;$JOURNAL_NAME rss feed\u0026rdquo; and poke around until I find something that looks right. Most of the aggregators will test the feed out first to make sure that you are trying to add a legitimate one. Here are a few of the heavy hitters to get you started:\nhttp://feeds.nature.com/nature/rss/current https://www.science.org/rss/express.xml https://www.cell.com/cell/inpress.rss Nothing like a constant stream of Cell, Science, and Nature to make your project feel like a real winner, eh?\nHere is what my own site looks like.\nFigure 1: My current FreshRSS setup. On the left I have my feeds separated into folders. In the middle you can see the titles of papers that appear in my feed.\nAnd after I hit J to move to the first item in the feed.\nFigure 2: With a title selected, you can see the abstract and authors.\nAfter collecting all of your desired RSS feeds, you cannot forego your responsibility of actually reading them! Most RSS feed aggregators have shortcuts to move through titles quickly (Typically J to move on to the next one and K to move up.) They always seem to use vi keybindings. A bunch of computer nerds have really cornered the keybinding market. I have let them take over my computing life. Each morning when I get into the lab, I quickly set up something, then head to my desk to hit J until the counter reaches zero.\nBut what about my very specific field? You can subscribe to all of the journals you want, but that doesn\u0026rsquo;t make the papers with your specific interests pop out. Fortunately, the NIH has this exact circumstance in mind.\nWhen you make a new search on PubMed you might notice the \u0026ldquo;Create RSS\u0026rdquo; button. Give it a click, then you will have a personal link you can add to your favorite RSS feed aggregator.\nFigure 3: Somehow I never noticed this button until I needed it.\nThis changed the game for me for keeping up with papers. Unfortunately, it doesn\u0026rsquo;t solve the problem of library management, or actually getting around to reading the papers you care about. I will leave library management as an exercise for the interested reader. Here\u0026rsquo;s a tip, the best solution uses the Zotero citation manager. Bonus points for using Zotfile for renaming your PDFs and Better BibTex for Zotero. \u0026#x1f609; I hope this helps you get your eyeballs on that science you crave. If you have solved the problem of accruing papers to read faster than you read them, let me know.\n","permalink":"https://www.zacharybillman.com/posts/rss-feeds-to-find-science-papers/","summary":"\u003cp\u003eIt is an age-old question: how can one keep up with the continuous output of science? I remember at the beginning of my PhD struggling to figure out how anyone found out when a new paper came out. \u0026#x1f635; Did they sit on nature.com and spam the refresh button? Did they know when each journal released their latest issue?\u003c/p\u003e\n\u003ch2 id=\"behold-the-power-of-rss\"\u003eBehold the power of RSS!\u003c/h2\u003e\n\u003cp\u003eMost websites have a page that contains information about each subpage in a computer-readable format called RSS (Really Simple Syndication). \u003ca href=\"https://zacharybillman.com/index.xml\"\u003eMine has one right here!\u003c/a\u003e These pages can be parsed by a number of RSS feed aggregators. The way these pages are set up make it such that they add any new information hosted at that domain. This is useful in the science world because you can find the RSS feed of a given journal, subscribe to it, then have every new article published online be delivered right to you.\u003c/p\u003e","title":"Using RSS feeds to keep on top of science."},{"content":"My interest in self-hosting began in my with my interests in internet privacy. Plastered all over the internet are stories about how much Google, Facebook and Amazon know about you. I deleted my Facebook account years ago, and I\u0026rsquo;m too paranoid to go back to the site because there\u0026rsquo;s a real possibility that Facebook has cached my account, ready to spin it back up in case I try to login again. The ads served to me were too accurate for my liking. This is despite almost never clicking on them! I have become convinced of the idea that, if you are not paying for the product, you are the product. From this assumption, it follows that anywhere I trust with my data that I am not paying for (like Google Drive, Google Photos, Dropbox, Facebook, Twitter) is using my data to earn money. We know that Google uses the labels you add to Photos to train it\u0026rsquo;s AI, and Facebook uses (at least) Instagram photos to train it\u0026rsquo;s AI. For some, the value proposition of allowing a company to use your data for a useful service in return is an acceptable one. I find this to be a reasonable stance, but I took my growing interest in internet privacy as a chance to learn about how I can take control of my data.\nInitially, I lurked on forums like /r/privacy to learn what I could do to avoid big-tech\u0026rsquo;s watchful eye. There were numerous comments along the lines of: \u0026ldquo;The only way to be in control of your data is to self-host your services.\u0026rdquo; I had no idea what this meant! Hard to believe that less than a year later, I learned to use (and love) Linux as my primary OS, and have happily replaced Google Photos, Google Drive and other services with my own self-hosted alternatives. Self-hosting, I have since learned, is when you run useful programs from your own computer. By doing so, you have complete knowledge of where and how your data is stored and how it is being used. It has the additional effect of being a bottomless time sink.\nTo begin, I needed an always-on computer to run these useful programs. I began with a humble Raspberry Pi.\nFigure 1: My humble Raspberry Pi and its hard drive. This dude currently tirelessly runs the excellent Adguard Home and downloads a backup of my data every night.\nThese are tiny, but capable computers that are great for fiddling with. The projects people develop for these are amazing and diverse. With RPi in hand, I began with the ambitious project of replacing Google Drive with Nextcloud. After much frustration with a bare metal installation, I found the NextcloudPi project. Surprisingly, it went pretty okay! At first, I was intimidated by Linux defaults, but over time I grew to appreciate, and indeed, prefer Linux as an operating system. My decision to use Linux over Windows/MacOS is because it is free and open source software (FOSS). This is a topic for a different post, but I think using FOSS when possible is a moral imperative of sorts. I used Nextcloud strictly from my home for a few months, without the ability to connect to it from the internet, to test the self-hosting waters. My first true cloud replacement spun up once I decided to access this lil\u0026rsquo; guy from the internet. To do so, I purchased a domain (not the one this site is hosted on) and pointed it to the IP of my house. I forwarded the appropriate ports of my router to the RPi.\nThis is when the real exploration began. I was able to access my files and images using Nextcloud, but the photo viewing service left something to be desired. No problem, why not spin up an instance of Photoprism? I use RSS feeds to keep on top of the latest science in the journals relevant to my field using Feedly. Why not host my own RSS feed aggregator so I can subscribe to as many feeds as I desire?\nThis cycle continued, and I accrued many cool applications, but in the back of my mind I worried about opening up my home network to the internet. I also struggled to run some programs because the RPi uses the arm64 architecture, and most services are written with amd64 in mind. These two forces eventually convinced me to purchase a server where I could manage all of my services remotely. Some would say that not owning the hardware that is running your own services is not \u0026ldquo;true\u0026rdquo; self-hosting. I think this is needlessly exclusive. Let everyone self host, dangit! Someday, when I have more stable internet and a more permanent home, I hope to host everything from my own home, but until then, I\u0026rsquo;m extremely pleased with my current stack. And that is where I am now. I happily host numerous services on my virtual private server that entirely replace Google Photos, Google Drive and GitHub for me. Even better, there are specialized services that fill a need I never realized I had. What\u0026rsquo;s more, if I ever want to spin up a new service, all I have to do is add it to my to docker-compose file and it will be up within minutes. What a world!\nI thought about making this into a \u0026ldquo;guide\u0026rdquo; style post. I nixed that idea because, quite frankly, I feel like I don\u0026rsquo;t know what I\u0026rsquo;m doing. I am really happy with my setup, but I don\u0026rsquo;t feel like I have the authority to tell people how to administer their own services. If you are interested, allow me to point you toward the guide that really got me rolling: Ultimate Traefik Docker Compose Guide.\nFor those of you wondering what I am currently hosting, check out my current list at the link and let me know what you think!\n","permalink":"https://www.zacharybillman.com/posts/my-selfhosting-journey/","summary":"\u003cp\u003eMy interest in self-hosting began in my with my interests in internet privacy. Plastered all over the internet are stories about how much Google, Facebook and Amazon know about you. I deleted my Facebook account years ago, and I\u0026rsquo;m too paranoid to go back to the site because there\u0026rsquo;s \u003ca href=\"https://www.reddit.com/r/privacy/comments/6nmjfh/facebook_account_fully_recovered_3_years_after/\"\u003ea real possibility that Facebook has cached my account, ready to spin it back up\u003c/a\u003e in case I try to login again. The ads served to me were too accurate for my liking.\n\u003cspan class=\"sidenote-number\"\u003e\u003csmall class=\"sidenote\"\u003e\nThis is despite almost never clicking on them!\n\u003c/small\u003e\u003c/span\u003e\nI have become convinced of the idea that, if you are not paying for the product, you are the product. From this assumption, it follows that anywhere I trust with my data that I am not paying for (like Google Drive, Google Photos, Dropbox, Facebook, Twitter) is using my data to earn money. We know that \u003ca href=\"https://www.theverge.com/2020/11/11/21559930/google-train-ai-photos-image-labelling-app-android-update\"\u003eGoogle uses the labels you add to Photos to train it\u0026rsquo;s AI\u003c/a\u003e, and \u003ca href=\"https://ai.facebook.com/blog/seer-the-start-of-a-more-powerful-flexible-and-accessible-era-for-computer-vision/\"\u003eFacebook uses (at least) Instagram photos to train it\u0026rsquo;s AI\u003c/a\u003e. For some, the value proposition of allowing a company to use your data for a useful service in return is an acceptable one. I find this to be a reasonable stance, but I took my growing interest in internet privacy as a chance to learn about how I can take control of my data.\u003c/p\u003e","title":"My selfhosting journey."},{"content":"N.B.: I hope to add screenshots for each of these eventually. For now, I hope links to each services\u0026rsquo; website will suffice.\nSeafile\nThis is a great tool for managing files. I moved to this from Nextcloud because I am of the philosophy that I would prefer services that do one thing excellently instead of many things well. Nextcloud is an incredible Office365 replacement, but I found myself using a fraction of what it was capable of providing. Enter Seafile. It is cloud file syncing with a robust encryption implementation, just what the doctor ordered.\nPhotoprism\nNextcloud\u0026rsquo;s implementation of photo management was a bit clumsy for my tastes, so I began on a hunt for a more feature complete option. I was very lucky to stumble upon Photoprism early on in my self hosting journey. I am a proud supporter of this project. It brings a ton to the table, and doesn\u0026rsquo;t leave me missing Google Photos one bit. It is also actively developed. For instance, as of 2022-07-02, there was a recent update that improved scrolling a ton, which was one of my remaining quibbles with it\u0026rsquo;s functionality. Some people complain that it doesn\u0026rsquo;t scale up for libraries of 10,000+ photos, but my 2000 photo library works swimmingly. On my phone, I use the Folder Sync app to automatically send any pictures I take on my phone to the Photoprism imports folder. Within 15 minutes of snapping a photo, it is there on my Photoprism instance. I highly recommend giving it a go.\nMealie\nI have to admit that the name leaves something to be desired. Fortunately, the service itself doesn\u0026rsquo;t fall short. Mealie is a recipe management application. It is able to parse your favorite recipe websites to create immortalized versions of the recipe. This helps fight detestable link rot that plagues the internet. It allows you to edit ingredient amounts, make comments about what you would change next time, and plan out your weekly meals. It helps that it is beautiful and intuitive to use. If only I could get my partner to use it\u0026hellip; I want to go on the record here and say that I think it is sensible that she doesn\u0026rsquo;t trust my self hosted services that much. In the early days of my self hosting journey, let\u0026rsquo;s just say that the up-time of my services were extremely finicky. I like to think they are more permanent now, especially because I am hosting everything on a VPS, but I certainly cannot compete with the stability of Google and Amazon. (Or pretty much any other paid service for that matter.) \u0026#x1f609;\nGitea\nGitea is a community managed, lightweight code hosting solution written in Go. I use it to manage my data analysis (using Private repos) and even host the source code for this very website! Using Gitea has given me the surface level introduction to the behemoth that is git. Fortunately, that is all I need. Once I have removed any sensitive data (like passwords, etc.) I will make my docker-compose file public. The docker-compose file is where I determine which services I pick to host, and how to configure them to my liking. Hopefully someone will find this useful.\nSyncthing\nIf I could only tell someone to self host a single service, I would have to pick Syncthing. It is a continuous file synchronization program, which means it keeps a specific file or folder the same between any device running Syncthing. I use it to keep my password database and my org-mode notes Now org-mode might be the biggest rabbithole of them all, and definitely the topic for another blog post. I use it to manage my TODO list, my lab notebook, my shopping lists, write this blog, and maintain my Zettelkasten note database. It is an immensely powerful tool. up to date between all of my devices. With Syncthing, all of my data is stored on my own devices and encrypted in transit.\nFreshRSS\nI keep up to date on the science in my field by subscribing to relevant RSS feeds. Yet another topic to write a post about. This really changed the game for my ability to keep on top of the latest research. 2022-07-14 Update: post complete! Check it out here. FreshRSS replaced Feedly for me, as I ran up against the number of feeds I could subscribe to on a free account. Also, when self hosting, I can save as many articles as my heart desires (even if I will never look at them again \u0026#x1f635; ).\nWallabag\nRemember Pocket for Firefox? (Yes, I know it still exists, okay?) Give Wallabag a spin, it is great for storing articles you want to read later. I set up FreshRSS to save articles to my Wallabag instance to keep for later.\nChangeDetection\nNow this is a fun one! ChangeDetection.io is a service that loads a webpage and checks to see if something has changed since the last time. This might not sound useful at first, but I recently used this to check for when a hot item for my new coffee roasting hobby was back in stock. I got an email the other day to let me know it was in stock. Pretty cool!\nHugo\nHugo is the static site generator I use to make this here blog! I was amazed at how much more response my site was using Hugo compare to when I paid a company to host a WordPress site. I\u0026rsquo;m sure WordPress could be fast, but I just wanted a barebones, pure html experience, and Hugo made it easy.\nCommento++\nYou may have noticed that I have some pretty snazzy comments sections on my site. I initially used Disqus, which you may recognize from a ton of sites around the internet, but didn\u0026rsquo;t like how it would serve ads through my comments section, and provided sign-ins using Google/Facebook/Twitter. I wanted to serve the simplest comments section I could, that still gave me the ability to migrate the comments to wherever I decide to keep my server. Go ahead and use the anonymous comment button, fill in your name, and you are off to the races.\nAuthelia\nThere are a few services I host that I really want to lock down. For these services, Authelia is great. It puts up a \u0026ldquo;Enter the 6 digit code on your phone\u0026rdquo; style 2 factor authentication in front of the services I choose. Or, if you follow the guide here, you can have it send you a DUO push, just like you are one of the big hitters out there. I feel much more secure with Authelia in front of Adminer, Traefik, and Portainer.\nBoring stuff that allows everything else to work!\nPostgreSQL database MariaDB database Traefik reverse proxy Umami privacy respecting site analytics Portainer for docker container management Redis in-memory data store Adminer database management traefik-socket-proxy to prevent pesky backdoors to my server! ","permalink":"https://www.zacharybillman.com/posts/zpb-current-selfhosted/","summary":"\u003cp\u003e\u003cem\u003eN.B.: I hope to add screenshots for each of these eventually. For now, I hope links to each services\u0026rsquo; website will suffice.\u003c/em\u003e\u003c/p\u003e\n\u003col\u003e\n\u003cli\u003e\n\u003cp\u003e\u003ca href=\"https://www.seafile.com/en/home/\"\u003eSeafile\u003c/a\u003e\u003c/p\u003e\n\u003cp\u003eThis is a great tool for managing files. I moved to this from Nextcloud because I am of the philosophy that I would prefer services that do one thing excellently instead of many things well. Nextcloud is an incredible Office365 replacement, but I found myself using a fraction of what it was capable of providing. Enter Seafile. It is cloud file syncing with a robust encryption implementation, just what the doctor ordered.\u003c/p\u003e","title":"What I'm currently selfhosting."},{"content":"My partner and I took a trip to the Mason Farm Biological Reserve the other day, and what a glorious day it was. This year, I\u0026rsquo;ve been quite busy in the lab, and missed a lot of the early spring warbler season, so I was very excited by the opportunity to check out the old stomping grounds.\nI brought the camera with me despite the fact we were going to be there around midday when the birds are much less active. I\u0026rsquo;m glad I did, because I got the best look at a common yellowthroat I\u0026rsquo;ve ever had. Normally these guys are flighty, staying close to the ground in small brush or tall grasses, but this one was putting on a proper show for the mating season. Even when you get a glimpse of one, it is usually just that, as they have jumped away before you can pull out the camera, taunting you with their iconic call. I was very pleased to capture a few choice shots of the bird. Hopefully there are more to come. While we were out, I also got a nice picture of a hermit thrush and a king snake.\nThese images have been compressed quite a bit for a lighter internet footprint. These have all been resized to 25% of their original size. If you would like the full sized images, let me know and I will send you a link!\n","permalink":"https://www.zacharybillman.com/posts/the-uncommon-yellowthroat/","summary":"\u003cp\u003eMy partner and I took a trip to the \u003ca href=\"https://ncbg.unc.edu/visit/mason-farm-biological-reserve/\"\u003eMason Farm Biological Reserve\u003c/a\u003e the other day, and what a glorious day it was. This year, I\u0026rsquo;ve been quite busy in the lab, and missed a lot of the early spring warbler season, so I was very excited by the opportunity to check out the old stomping grounds.\u003c/p\u003e\n\u003cp\u003eI brought the camera with me despite the fact we were going to be there around midday when the birds are much less active. I\u0026rsquo;m glad I did, because I got the best look at a common yellowthroat I\u0026rsquo;ve ever had.\n\u003cspan class=\"sidenote-number\"\u003e\u003csmall class=\"sidenote\"\u003e\nNormally these guys are flighty, staying close to the ground in small brush or tall grasses, but this one was putting on a proper show for the mating season. Even when you get a glimpse of one, it is usually just that, as they have jumped away before you can pull out the camera, taunting you with their \u003ca href=\"https://ebird.org/species/comyel#Modal-playlist\"\u003eiconic call\u003c/a\u003e.\n\u003c/small\u003e\u003c/span\u003e\nI was very pleased to capture a few choice shots of the bird. Hopefully there are more to come. While we were out, I also got a nice picture of a hermit thrush and a king snake.\u003c/p\u003e","title":"The (un)common yellowthroat."},{"content":"Welcome to my site! My name is Zachary Billman. I\u0026rsquo;m a UNC MD-PhD student in my 4th year of med school applying to pathology residency programs. I completed my PhD in Ed Miao\u0026rsquo;s lab. The curious reader may be thinking: \u0026ldquo;But Zach, Dr. Miao\u0026rsquo;s lab is at Duke, how did that come about?\u0026rdquo; What an astute question! Ed\u0026rsquo;s lab moved from UNC to Duke in early 2020, and I followed him down the street. My PhD was awarded by the UNC department of Microbiology and Immunology, but it just so happens that (nearly) all of my research took place at Duke. This move was quite a trial, especially when compounded with the onset of the pandemic. I suspect my research timeline suffered, though this is an extremely minor inconvenience compared to the tragedy the pandemic caused. This makes for very interesting basketball viewing parties with my Duke friends!\nMaybe having a diagram will make my training timeline make a bit more sense.\nFigure 1: An overview of my research training. I first began working for Dr. Sean Murphy in undergrad, then worked as a research scientist/lab manager for 3 years before heading to UNC for my MSTP training. During grad school, my lab moved from UNC to Duke, though my degree was awarded by UNC. The \u0026ldquo;Present\u0026rdquo; diamond was used on an older version of my CV and represents September 1st, 2025. Created using PlantUML.\nHopefully that can clear up the winding road I\u0026rsquo;ve taken a bit!\nMy research and scientific interests. I am broadly interested in innate immunology. I spent most of my time in graduate school studying the host-pathogen interaction between the intracellular fungus Histoplasma capsulatum and macrophages. There are many unstudied curiosities regarding the innate immune response to Histoplasma spp. and other intracellular fungi that I think are quite interesting. I also spent a considerable time thinking about the evolution of proteins involved in the programmed cell death pathway called pyroptosis.\nHobbies I may write about. Besides my science, I am interested in birding, baking sourdough bread (I swear I began years before the pandemic, though hearing of people baking bread brings me joy no matter when they first began!), board games, roasting coffee, and self-hosting free and open source software. Over the course of the pandemic, I have learned how to maintain a basic suite of services spread between a server I rent and a computer at home that have replaced my need for Google Photos and Google Drive. I\u0026rsquo;m hoping to be able to move away from these platforms entirely soon. I think they provide a great service, but at a substantial cost to privacy. Hopefully more to be said about my thoughts on FOSS soon! I also transitioned my old, (and quite frankly, embarrassingly slow) managed WordPress site with this lean, static site made in Hugo that I host myself. Now that I have mangled together some CSS to get my precious sidenotes up and running again, I\u0026rsquo;m ready to begin putting some ideas to paper. I love marginalia (the word to describe these notes on the side of this webpage). I\u0026rsquo;m not sure if this is unique to me, but I seem to get caught up in parenthetical / tangential thoughts very often, and I think using an Edward Tufte-esque sidenote is a great way for me to communicate in this way without distracting the reader too much. It seems marginalia such as this have been used throughout history, so perhaps it is normal, but most people can keep their thoughts focused better than me. The implementation I use is inspired by the Tufte CSS project and largely taken from this incredibly helpful post found at scripter.co. I\u0026rsquo;m quite proud of my progress in administering my server and self-hosting useful services.\nThe future of this site. On this site I plan to post updates about my journey through med school, grad school, and self-hosting I would like to share with the world. I have been helped immensely by many others\u0026rsquo; advice and I hope to impart similar tips to others someday. I suspect most posts will be about much lighter fare, like whatever hobbies tickle my fancy at the time.\n","permalink":"https://www.zacharybillman.com/posts/about-me/","summary":"\u003ch2 id=\"welcome-to-my-site\"\u003eWelcome to my site!\u003c/h2\u003e\n\u003cp\u003eMy name is Zachary Billman. I\u0026rsquo;m a UNC MD-PhD student in my 4th year of med school applying to pathology residency programs. I completed my PhD in Ed Miao\u0026rsquo;s lab. The curious reader may be thinking: \u0026ldquo;But Zach, Dr. Miao\u0026rsquo;s lab is at Duke, how did that come about?\u0026rdquo; What an astute question! Ed\u0026rsquo;s lab moved from UNC to Duke in early 2020, and I followed him down the street. My PhD was awarded by the UNC department of Microbiology and Immunology, but it just so happens that (nearly) all of my research took place at Duke.\n\u003cspan class=\"sidenote-number\"\u003e\u003csmall class=\"sidenote\"\u003e\nThis move was quite a trial, especially when compounded with the onset of the pandemic. I suspect my research timeline suffered, though this is an extremely minor inconvenience compared to the tragedy the pandemic caused.\n\u003c/small\u003e\u003c/span\u003e\nThis makes for very interesting basketball viewing parties with my Duke friends!\u003c/p\u003e","title":"About me. 👋"},{"content":"It\u0026rsquo;s over. My third year of medical school is officially behind me. I managed to get in a grand total of zero blog posts during grad school, so here\u0026rsquo;s to a new year with hopefully some more thoughts being shared. I have a lot to reflect on from the past year. It was wonderful. I wish everyone could experience what I did this past year. I think it goes without saying:\nI loved the third year of med school, but I do not want to do it again.\nA year of change. In the days leading up to my return to med school, I thought \u0026ldquo;Oh no, I really enjoy doing science, do I really have to go to med school?\u0026rdquo;. I also remember at the end of Step 1 and the first two years of med school thinking, \u0026ldquo;Oh no, I really enjoy med school, do I really have to do science again?\u0026rdquo;. I think I have a welcome problem of enjoying what I\u0026rsquo;m doing. The third year of med school is a shift. After years of memorizing and examinations, the doors to the promised land are finally opened. I have experienced nothing like it before It feels intentionally unsettling. You are thrown into the clinic with a modicum of guidance so you aren\u0026rsquo;t totally caught off guard, but you are thrown out to the wolves. I don\u0026rsquo;t mean this as a criticism of the system, it feels necessary. Third year medical students—commonly shorted to MS3s—have just one year to experience a broad swath of medicine and pick a specialty. So you had better be ready to dive in.\nTotal immersion I came to terms with my new reality quickly. Gone were the days of hitting the snooze button and going home when I pleased. I am now beholden to other people\u0026rsquo;s schedules. This came back relatively naturally. Maybe not hitting snooze. A regrettable personal failing of mine. I was, however, immediately faced with a new reality in the patient room. Patients come to the doctor for a number of reasons, but often seek relief. To get to the core of what ails them, they will tell you everything. I was not prepared for how vulnerable patients would be with me. I am not sure if this ever will feel natural. I hope it never does. I was told many stories of experiences living with scary diagnoses, and not knowing what to do with it. Family histories of all sorts. Personal details that were sometimes (oftentimes?) off the wall. I see all of these specifics as flailing, grasping at sand hoping that something could explain their pain. Sometimes it could. Usually it did not. But since I was in a white coat, I was privileged to hear it.\nI think my years spent in the lab have prepared me to face some of the challenges set before me. At the very least, having a few more years under my belt helped me approach the year with a bit of maturity. This seems to have paid off. I guess my recommendation is to simply get old before going to med school. Returning to studying The hospital is how I spent the majority of my time, but a new reality for me was also going back to daily studying. There is a strange dichotomy in medicine of \u0026ldquo;Oh, it doesn\u0026rsquo;t really matter\u0026rdquo; and \u0026ldquo;If you don\u0026rsquo;t get this class/score/grade then you won\u0026rsquo;t be able to be the kind of doctor you want to be, so you had better get your act together.\u0026rdquo; Simultaneously there are no expectations and immense responsibility for the looming specter of Step 2. I\u0026rsquo;m glad that studying regularly came back easily enough. I was concerned I would experience a studying whiplash. I\u0026rsquo;m glad it never came. I did UWorld and Anki nearly every day for a full year and felt alright.\nBecoming invisible I quickly learned I needed to change my understanding of my contribution to the team. Exiting grad school, people understood that they could come to me for help. I was a resource, a seasoned veteran of the lab. If someone needed an experiment done, I could do it, and be trusted to do it. In med school as a third year, I was nothing. A fly on the wall; a worm beneath the feet of the real doctors. In science, I felt like I was treated as a peer with even my committee members with multiple R01s. Even if I didn\u0026rsquo;t understand the science perfectly, I could contribute some different perspective. In medicine, sometimes not being recognized at all by my attendings was the best outcome. Which happened regularly. My role, was not as a contributor—as it was in science—it was simply to get in the reps. Once I understood that the expectations of me were below the ground, I understood that everything I did in third year was for myself. This is taken at face value by the team at times. I would spend 30 minutes working on a presentation, pre-rounding, the works, and at the end of my part, the intern would nod, then turn to the senior resident and say \u0026ldquo;I was thinking that we\u0026hellip;\u0026rdquo; without thinking of my work. This is perhaps a bit of cognitive restructuring, but recognizing this is what gave me the freedom to embed myself in the hospital flow, without a single worry about the outcome. Simply doing my best was the best thing I could do. Obviously. But this was not apparent to me at first. I needed more quality repetitions to develop good habits in the future. And also experience as much of medicine as possible to find what I want to do with my life. This permission allowed me to approach specialties I do not care about with the awe and respect they deserve.\nA year of wonder. Med school prepares you for the standardized tests. I think this is generally useful. The tests on aggregate are reasonable and evaluate your ability to think through common clinical scenarios. There will always be oddball questions that come out of left field, but I let these flow over me. No need to perseverate on the small stuff. The time for that can come later.\nWhat I didn\u0026rsquo;t realize is how much of the \u0026ldquo;classic\u0026rdquo; material we are fed in the first couple years of med school would come to the forefront. The \u0026ldquo;sandpaper rash\u0026rdquo; of scarlet fever really does feel like sandpaper. Nikolsky\u0026rsquo;s sign actually works. Tripoding for epiglottitis gets the physicians worked up. Don\u0026rsquo;t forget about von Willebrand\u0026rsquo;s disease when someone seems to be bleeding a bit too much. TB is out there, watch for hemoptosis. Night sweats, unintended weight loss, is cancer until proven otherwise. And yes, it really can be lupus.\nIn general, facing the unknown with a sense of earnestness was the way I felt best able to respect those who gathered and passed down the medical knowledge I am privileged to learn today. Sometimes, my excitement to see aspects of medicine would rouse a curious response from the residents. I project here, but I felt a sense of surprise, like that of a doting parent seeing their child experience something new, after forgetting the astonishment they once felt.\nEarnestness is next to med studentlyness.\nPerhaps what I\u0026rsquo;m getting at here is that I found it important to bask in the privilege of seeing the pathology I encountered in med school, and to remind the residents of this sensation. I felt childish at times—and perhaps overanimated—but I found this excitement was to my and my resident\u0026rsquo;s benefit.\nMy surgery rotation overflowed with examples of wonder of medicine. Partially because of the team I worked with, and the rest because of the undeniable coolness of surgery. The OR is a cool place. The orderliness and chaos ebb. The spans of steady, industrious work are interrupted with staccato notes of bedlam. The anatomy I learned in class was ever present, but the surgeons bemoaned \u0026ldquo;normal anatomic variation\u0026rdquo;.\nI was struck with wonder at the sight of human anatomy as it unfolded before me. What I was able to experience in the OR felt like the culmination of centuries of human curiosity. There is an ancientness to medicine that I catch flashes of—I could perform the physical exam on humans hundred of millions of years ago and interrogate the same pathologies as I do in the hospital today—and viewing the exposed anatomy is a pressure-bagged infusion of this collective wonder. To gaze upon the peristalsing of the small intestine, or steady beating of the heart is a sight to behold, indeed.\nA year of shame. It weighs upon me the circumstances that resulted in these transcendent experiences. Not one patient was in the hospital without reason. What to make of these patients with horrible pathology? I still feel unsettled about how the cause of their pain sparked wonder. How dare I gain, merely by the circumstance of having their care managed at UNC, Which, as a tertiary care center, layers on more complexity. Many patients end up at UNC because they have no where else they can go for help. And this signs them up for med students? For shame. from the very essence of their malady? I do not know what to do with my discomfort, but I think it is best that I dwell in it. With this, I respect the people before me in the hospital and recognize their humanity.\nBut I often complained of what I say here I was lucky to do. I find myself resentful of my future schedule; when was I supposed to learn that I will be working 13 hour days, 6 days a week for the rest of my life? And what of having a family? Medicine by necessity requires sacrifice. I happened to sign up for sacrifices years before I recognized how profound they were. How might I balance this dread and with the joy of practicing medicine? And why do I seem more concerned about this than others? Am I not grateful enough? Am I not capable of the sacrifices that others seem to offer so effortlessly? I don\u0026rsquo;t necessarily think this to be true, but these questions erode at my will to pursue medicine.\nPerhaps most shameful of all is how my understanding of the patient-provider interaction evolved over the year. It began as an exploration of an open book, a tabula rasa that held within it a diagnosis and how to best intervene. On my first day in the outpatient clinic, it was clear that this is not the case. My preceptor had only 20 minutes for me to ① interview the patient and perform the physical exam, ② present with a plan, ③ return to the room and do everything again, ④ write orders, educate, and get the patient out of the door. It simply is not amenable to the free form, personable, curious interview I hoped to perform. By the end of the year, I had optimized how I asked questions to keep patients from going off the rails. When prerounding in medicine, I was there to extract information and not much else. Small talk had to go, there was no time. I like to chat, so this came at a loss of who I think I am. I am not sure how to do this well, while still feeling like Zachary. And from what I gather from the interns, that may just come later in my career. I found myself questioning, \u0026ldquo;Is this the \u0026lsquo;patient interaction\u0026rsquo; that has been mythologized throughout my training?\u0026rdquo; The carrot at the end of the stick dangled before me with a \u0026ldquo;You are so lucky to be able to do this, so you had better not complain of any abuse that comes your way.\u0026rdquo; It wasn\u0026rsquo;t a genuine interaction as much as me leading the patient along to tell me what I wanted to know. Of course, I used open ended questions, but only open enough. Leave the door a bit too open and next thing you know, you are talking about their dog\u0026rsquo;s breeder while you constantly stare at your watch, imagining what your attending will say when you return. I feel like I am alone in missing the core human element that funnels sprightly youths into medicine. Or worse, finding it a façade.\nThe shame extends beyond the hospital. One aspect of my life that has changed most dramatically is the sheer amount of time I felt I needed to dedicate to medicine, whether at the hospital or at home. I spent all day basking in the wonder of medicine, then I would come home and study for hours. I relied on my partner for keeping our household together more than ever, because I spent all day—all year, rather—in a state of discovery. Her life was largely the same, with the normal challenges of being a scientist, with the added bonus of getting less help from me. The shame built over the year. Again, how dare I?\nA year of glad. This has been an undeniable year of growth and joy, with these quibbles. It is clear that I was happier than I was during grad school. I know this from within myself, and reinforced by my wife\u0026rsquo;s comments on my mood. The pace of the day, and immediacy of problem solving were a welcome change.\nI recall, during the very first days preparing for med school during xTAP, having to do a simulated patient encounter complete with patient presentation to an attending physician. We were told about this encounter days in advance. And yet, I dreaded it. And near the last day of my final rotation, I did 8 of these in a row without breaking a sweat. Progress!\nI think, in a word, what I\u0026rsquo;ve experienced in the third year of med school is gratitude. Gratitude to be privileged to learn what I am learning. Gratitude for the experiences in my life that brought me here. Gratitude for the support from my wife. Gratitude to be involved in people\u0026rsquo;s lives when they are fragile. Ever since reading Braiding Sweetgrass I think one could call me \u0026ldquo;gratitude-pilled\u0026rdquo;. I also selfishly enjoyed the gratitude from patients as I put on my best doctor performance. In reflection on the year, I have spent time thinking of a phrase that I heard a number of times throughout med school from residents, \u0026ldquo;The worst day of residency is better than the best day of med school.\u0026rdquo; I find this hard to believe. This year has been magical. It is hard to imagine a year filled with more wonder and joy of caring for those in need. I will have to rely on the experience of those who have walked this path and trust that the rest of my training has plenty of magic to spare.\n","permalink":"https://www.zacharybillman.com/posts/ms3-year-is-magical/","summary":"\u003ch2 id=\"it-s-over-dot\"\u003eIt\u0026rsquo;s over.\u003c/h2\u003e\n\u003cp\u003eMy third year of medical school is officially behind me. I managed to get in a grand total of \u003cem\u003ezero\u003c/em\u003e blog posts during grad school, so here\u0026rsquo;s to a new year with hopefully some more thoughts being shared. I have a lot to reflect on from the past year. It was wonderful. I wish everyone could experience what I did this past year. I think it goes without saying:\u003c/p\u003e","title":"The third year of medical school is magical."},{"content":"I, like many others, picked up a new hobby during the pandemic. Other people\u0026rsquo;s hobbies may bring them joy. This could be for many reasons. There is the joy of creating something from scratch. You can revel in your thriftiness. You can embrace the pride when you recognize that your creation is on par (or better!) than what you can buy. I feel like these are embodied in the sourdough craze that caught fire early on in COVID. Dare I say that I did this before it was cool? \u0026#x1f60e; I baked two loaves of bread almost every weekend through med school. Maybe I should bring that back, it\u0026rsquo;s been a while since I brought out the ole\u0026rsquo; starter. My pandemic hobby is similar, but different in that it often feels like a chore, costs more money, and often turns out worse than what I can buy. Of course, I am talking about how I\u0026rsquo;ve started roasting my own coffee at home.\nI\u0026rsquo;m not sure where this idea was planted into my brain. I don\u0026rsquo;t think I know anyone who roasts their own beans, and I certainly didn\u0026rsquo;t know how. I didn\u0026rsquo;t even drink coffee regularly until after college! I guess that extra time on the computer sent me down a rabbithole I have yet to emerge from.\nFirst, I want to preface the following with a disclaimer: This is not a detailed guide about how to roast your own coffee. If you are interested, I recommend checking out the How To Roast Your Own Coffee guide at Sweet Maria\u0026rsquo;s as a starting point. There is also the /r/roasting subreddit if that is your cup of tea. My only warning is there will be a lot of smoke. Roast your coffee outside, for Pete\u0026rsquo;s sake!\nIt all started with a trusty popcorn popper. There are a few things you want when you roast coffee:\nAir hot enough to roast coffee Remove the chaff from the beans Turns out that a classic popcorn popper fits the bill, as long as it has an upwards airflow and doesn\u0026rsquo;t let the chaff fall into the heating element. There is a bit of a cult following for the West Bend Poppery 2 model, but that one seemed a bit pricey, so I settled for a very capable popper from Nostalgia.\nFigure 1: I got a good bit of mileage out of my popcorn popper. If you are interested in roasting your own coffee I would give it a whirl.\nThings were simple back then. I still bought most of the coffee I drank, but I roasted enough to enjoy some freshly roasted coffee as an occasional treat. I ordered 10 pounds of green beans from Sweet Maria\u0026rsquo;s and life was good.\nThen I became a bit of a coffee snob.\nI could only roast 100 grams of coffee at a time in the popcorn popper, which is only enough for one pot of coffee in the morning for me. So it was time to upgrade.\nI bought the SR800 fluid bed roaster, which upped my roasting capacity and gave me finer control on temperature and airflow. Suffice to say my roasts improved a lot! At this point, I would consider my coffee good enough to sell at a farmer\u0026rsquo;s market to break even.\nIf you ever find yourself on a coffee roasting forum and bring up the SR800, someone is bound to bring up the famous RazzoRoasting extension tube. If you look for advice for how to use the SR800, I swear it\u0026rsquo;s assumed that you have this very specific accessory. \u0026hellip;And so I bought one.\nDon\u0026rsquo;t worry, that is the extent of all of my coffee spending (for now). I am a very satisfied coffee roaster now. Check out this quick series of images going from the green beans to a nearly finished product! I can spend about 45 minutes and go from nothing to nearly 2 pounds of roasted beans, enough for about a week and a half of coffee. Not bad! The only downside is that now I feel like I need to buy coffee from local roasters to get my fix. There are certainly crueler fates.\nAs a sign off, I will share something that surprised me about coffee roasting. When I roast coffee, the most important cue to determine if the coffee is roasted is the sound. That\u0026rsquo;s right, not the color, not the smell, but the sound. When heating up a coffee bean, the water trapped inside eventually bursts out of the bean in a rapid expansion. This is called \u0026ldquo;first crack\u0026rdquo;, and indicates that the coffee is roasted enough to be drinkable. The expansion also releases the chaff from the bean. If you continue heating up the bean, you will eventually reach \u0026ldquo;second crack\u0026rdquo;. I think a solid medium roast is taken out just before second crack, so I try to take my coffee out to this point and it hasn\u0026rsquo;t proved me wrong yet.\nHappy coffee-ing! \u0026#x2615;\n","permalink":"https://www.zacharybillman.com/posts/roasting-coffee-at-home/","summary":"\u003cp\u003eI, like many others, picked up a new hobby during the pandemic. Other people\u0026rsquo;s hobbies may bring them joy. This could be for many reasons. There is the joy of creating something from scratch. You can revel in your thriftiness. You can embrace the pride when you recognize that your creation is on par (or better!) than what you can buy. I feel like these are embodied in the sourdough craze that caught fire early on in COVID.\n\u003cspan class=\"sidenote-number\"\u003e\u003csmall class=\"sidenote\"\u003e\nDare I say that I did this before it was cool? \u0026#x1f60e; I baked two loaves of bread almost every weekend through med school. Maybe I should bring that back, it\u0026rsquo;s been a while since I brought out the ole\u0026rsquo; starter.\n\u003c/small\u003e\u003c/span\u003e\nMy pandemic hobby is similar, but different in that it often feels like a chore, costs more money, and often turns out worse than what I can buy. Of course, I am talking about how I\u0026rsquo;ve started roasting my own coffee at home.\u003c/p\u003e","title":"Roasting coffee at home. ☕"},{"content":"It is an age-old question: how can one keep up with the continuous output of science? I remember at the beginning of my PhD struggling to figure out how anyone found out when a new paper came out. \u0026#x1f635; Did they sit on nature.com and spam the refresh button? Did they know when each journal released their latest issue?\nBehold the power of RSS! Most websites have a page that contains information about each subpage in a computer-readable format called RSS (Really Simple Syndication). Mine has one right here! These pages can be parsed by a number of RSS feed aggregators. The way these pages are set up make it such that they add any new information hosted at that domain. This is useful in the science world because you can find the RSS feed of a given journal, subscribe to it, then have every new article published online be delivered right to you.\nThere are a plethora of RSS feed aggregators you can pick from manage your feeds. I have previously used Feedly and Inoreader, which are great free solutions, but have moved on to selfhosting my own instance of FreshRSS.\nAfter making an account at your friendly local RSS feed aggregator, you can add whatever feeds your heart desires. To find a journal\u0026rsquo;s rss feed, I often just search \u0026ldquo;$JOURNAL_NAME rss feed\u0026rdquo; and poke around until I find something that looks right. Most of the aggregators will test the feed out first to make sure that you are trying to add a legitimate one. Here are a few of the heavy hitters to get you started:\nhttp://feeds.nature.com/nature/rss/current https://www.science.org/rss/express.xml https://www.cell.com/cell/inpress.rss Nothing like a constant stream of Cell, Science, and Nature to make your project feel like a real winner, eh?\nHere is what my own site looks like.\nFigure 1: My current FreshRSS setup. On the left I have my feeds separated into folders. In the middle you can see the titles of papers that appear in my feed.\nAnd after I hit J to move to the first item in the feed.\nFigure 2: With a title selected, you can see the abstract and authors.\nAfter collecting all of your desired RSS feeds, you cannot forego your responsibility of actually reading them! Most RSS feed aggregators have shortcuts to move through titles quickly (Typically J to move on to the next one and K to move up.) They always seem to use vi keybindings. A bunch of computer nerds have really cornered the keybinding market. I have let them take over my computing life. Each morning when I get into the lab, I quickly set up something, then head to my desk to hit J until the counter reaches zero.\nBut what about my very specific field? You can subscribe to all of the journals you want, but that doesn\u0026rsquo;t make the papers with your specific interests pop out. Fortunately, the NIH has this exact circumstance in mind.\nWhen you make a new search on PubMed you might notice the \u0026ldquo;Create RSS\u0026rdquo; button. Give it a click, then you will have a personal link you can add to your favorite RSS feed aggregator.\nFigure 3: Somehow I never noticed this button until I needed it.\nThis changed the game for me for keeping up with papers. Unfortunately, it doesn\u0026rsquo;t solve the problem of library management, or actually getting around to reading the papers you care about. I will leave library management as an exercise for the interested reader. Here\u0026rsquo;s a tip, the best solution uses the Zotero citation manager. Bonus points for using Zotfile for renaming your PDFs and Better BibTex for Zotero. \u0026#x1f609; I hope this helps you get your eyeballs on that science you crave. If you have solved the problem of accruing papers to read faster than you read them, let me know.\n","permalink":"https://www.zacharybillman.com/posts/rss-feeds-to-find-science-papers/","summary":"\u003cp\u003eIt is an age-old question: how can one keep up with the continuous output of science? I remember at the beginning of my PhD struggling to figure out how anyone found out when a new paper came out. \u0026#x1f635; Did they sit on nature.com and spam the refresh button? Did they know when each journal released their latest issue?\u003c/p\u003e\n\u003ch2 id=\"behold-the-power-of-rss\"\u003eBehold the power of RSS!\u003c/h2\u003e\n\u003cp\u003eMost websites have a page that contains information about each subpage in a computer-readable format called RSS (Really Simple Syndication). \u003ca href=\"https://zacharybillman.com/index.xml\"\u003eMine has one right here!\u003c/a\u003e These pages can be parsed by a number of RSS feed aggregators. The way these pages are set up make it such that they add any new information hosted at that domain. This is useful in the science world because you can find the RSS feed of a given journal, subscribe to it, then have every new article published online be delivered right to you.\u003c/p\u003e","title":"Using RSS feeds to keep on top of science."},{"content":"My interest in self-hosting began in my with my interests in internet privacy. Plastered all over the internet are stories about how much Google, Facebook and Amazon know about you. I deleted my Facebook account years ago, and I\u0026rsquo;m too paranoid to go back to the site because there\u0026rsquo;s a real possibility that Facebook has cached my account, ready to spin it back up in case I try to login again. The ads served to me were too accurate for my liking. This is despite almost never clicking on them! I have become convinced of the idea that, if you are not paying for the product, you are the product. From this assumption, it follows that anywhere I trust with my data that I am not paying for (like Google Drive, Google Photos, Dropbox, Facebook, Twitter) is using my data to earn money. We know that Google uses the labels you add to Photos to train it\u0026rsquo;s AI, and Facebook uses (at least) Instagram photos to train it\u0026rsquo;s AI. For some, the value proposition of allowing a company to use your data for a useful service in return is an acceptable one. I find this to be a reasonable stance, but I took my growing interest in internet privacy as a chance to learn about how I can take control of my data.\nInitially, I lurked on forums like /r/privacy to learn what I could do to avoid big-tech\u0026rsquo;s watchful eye. There were numerous comments along the lines of: \u0026ldquo;The only way to be in control of your data is to self-host your services.\u0026rdquo; I had no idea what this meant! Hard to believe that less than a year later, I learned to use (and love) Linux as my primary OS, and have happily replaced Google Photos, Google Drive and other services with my own self-hosted alternatives. Self-hosting, I have since learned, is when you run useful programs from your own computer. By doing so, you have complete knowledge of where and how your data is stored and how it is being used. It has the additional effect of being a bottomless time sink.\nTo begin, I needed an always-on computer to run these useful programs. I began with a humble Raspberry Pi.\nFigure 1: My humble Raspberry Pi and its hard drive. This dude currently tirelessly runs the excellent Adguard Home and downloads a backup of my data every night.\nThese are tiny, but capable computers that are great for fiddling with. The projects people develop for these are amazing and diverse. With RPi in hand, I began with the ambitious project of replacing Google Drive with Nextcloud. After much frustration with a bare metal installation, I found the NextcloudPi project. Surprisingly, it went pretty okay! At first, I was intimidated by Linux defaults, but over time I grew to appreciate, and indeed, prefer Linux as an operating system. My decision to use Linux over Windows/MacOS is because it is free and open source software (FOSS). This is a topic for a different post, but I think using FOSS when possible is a moral imperative of sorts. I used Nextcloud strictly from my home for a few months, without the ability to connect to it from the internet, to test the self-hosting waters. My first true cloud replacement spun up once I decided to access this lil\u0026rsquo; guy from the internet. To do so, I purchased a domain (not the one this site is hosted on) and pointed it to the IP of my house. I forwarded the appropriate ports of my router to the RPi.\nThis is when the real exploration began. I was able to access my files and images using Nextcloud, but the photo viewing service left something to be desired. No problem, why not spin up an instance of Photoprism? I use RSS feeds to keep on top of the latest science in the journals relevant to my field using Feedly. Why not host my own RSS feed aggregator so I can subscribe to as many feeds as I desire?\nThis cycle continued, and I accrued many cool applications, but in the back of my mind I worried about opening up my home network to the internet. I also struggled to run some programs because the RPi uses the arm64 architecture, and most services are written with amd64 in mind. These two forces eventually convinced me to purchase a server where I could manage all of my services remotely. Some would say that not owning the hardware that is running your own services is not \u0026ldquo;true\u0026rdquo; self-hosting. I think this is needlessly exclusive. Let everyone self host, dangit! Someday, when I have more stable internet and a more permanent home, I hope to host everything from my own home, but until then, I\u0026rsquo;m extremely pleased with my current stack. And that is where I am now. I happily host numerous services on my virtual private server that entirely replace Google Photos, Google Drive and GitHub for me. Even better, there are specialized services that fill a need I never realized I had. What\u0026rsquo;s more, if I ever want to spin up a new service, all I have to do is add it to my to docker-compose file and it will be up within minutes. What a world!\nI thought about making this into a \u0026ldquo;guide\u0026rdquo; style post. I nixed that idea because, quite frankly, I feel like I don\u0026rsquo;t know what I\u0026rsquo;m doing. I am really happy with my setup, but I don\u0026rsquo;t feel like I have the authority to tell people how to administer their own services. If you are interested, allow me to point you toward the guide that really got me rolling: Ultimate Traefik Docker Compose Guide.\nFor those of you wondering what I am currently hosting, check out my current list at the link and let me know what you think!\n","permalink":"https://www.zacharybillman.com/posts/my-selfhosting-journey/","summary":"\u003cp\u003eMy interest in self-hosting began in my with my interests in internet privacy. Plastered all over the internet are stories about how much Google, Facebook and Amazon know about you. I deleted my Facebook account years ago, and I\u0026rsquo;m too paranoid to go back to the site because there\u0026rsquo;s \u003ca href=\"https://www.reddit.com/r/privacy/comments/6nmjfh/facebook_account_fully_recovered_3_years_after/\"\u003ea real possibility that Facebook has cached my account, ready to spin it back up\u003c/a\u003e in case I try to login again. The ads served to me were too accurate for my liking.\n\u003cspan class=\"sidenote-number\"\u003e\u003csmall class=\"sidenote\"\u003e\nThis is despite almost never clicking on them!\n\u003c/small\u003e\u003c/span\u003e\nI have become convinced of the idea that, if you are not paying for the product, you are the product. From this assumption, it follows that anywhere I trust with my data that I am not paying for (like Google Drive, Google Photos, Dropbox, Facebook, Twitter) is using my data to earn money. We know that \u003ca href=\"https://www.theverge.com/2020/11/11/21559930/google-train-ai-photos-image-labelling-app-android-update\"\u003eGoogle uses the labels you add to Photos to train it\u0026rsquo;s AI\u003c/a\u003e, and \u003ca href=\"https://ai.facebook.com/blog/seer-the-start-of-a-more-powerful-flexible-and-accessible-era-for-computer-vision/\"\u003eFacebook uses (at least) Instagram photos to train it\u0026rsquo;s AI\u003c/a\u003e. For some, the value proposition of allowing a company to use your data for a useful service in return is an acceptable one. I find this to be a reasonable stance, but I took my growing interest in internet privacy as a chance to learn about how I can take control of my data.\u003c/p\u003e","title":"My selfhosting journey."},{"content":"N.B.: I hope to add screenshots for each of these eventually. For now, I hope links to each services\u0026rsquo; website will suffice.\nSeafile\nThis is a great tool for managing files. I moved to this from Nextcloud because I am of the philosophy that I would prefer services that do one thing excellently instead of many things well. Nextcloud is an incredible Office365 replacement, but I found myself using a fraction of what it was capable of providing. Enter Seafile. It is cloud file syncing with a robust encryption implementation, just what the doctor ordered.\nPhotoprism\nNextcloud\u0026rsquo;s implementation of photo management was a bit clumsy for my tastes, so I began on a hunt for a more feature complete option. I was very lucky to stumble upon Photoprism early on in my self hosting journey. I am a proud supporter of this project. It brings a ton to the table, and doesn\u0026rsquo;t leave me missing Google Photos one bit. It is also actively developed. For instance, as of 2022-07-02, there was a recent update that improved scrolling a ton, which was one of my remaining quibbles with it\u0026rsquo;s functionality. Some people complain that it doesn\u0026rsquo;t scale up for libraries of 10,000+ photos, but my 2000 photo library works swimmingly. On my phone, I use the Folder Sync app to automatically send any pictures I take on my phone to the Photoprism imports folder. Within 15 minutes of snapping a photo, it is there on my Photoprism instance. I highly recommend giving it a go.\nMealie\nI have to admit that the name leaves something to be desired. Fortunately, the service itself doesn\u0026rsquo;t fall short. Mealie is a recipe management application. It is able to parse your favorite recipe websites to create immortalized versions of the recipe. This helps fight detestable link rot that plagues the internet. It allows you to edit ingredient amounts, make comments about what you would change next time, and plan out your weekly meals. It helps that it is beautiful and intuitive to use. If only I could get my partner to use it\u0026hellip; I want to go on the record here and say that I think it is sensible that she doesn\u0026rsquo;t trust my self hosted services that much. In the early days of my self hosting journey, let\u0026rsquo;s just say that the up-time of my services were extremely finicky. I like to think they are more permanent now, especially because I am hosting everything on a VPS, but I certainly cannot compete with the stability of Google and Amazon. (Or pretty much any other paid service for that matter.) \u0026#x1f609;\nGitea\nGitea is a community managed, lightweight code hosting solution written in Go. I use it to manage my data analysis (using Private repos) and even host the source code for this very website! Using Gitea has given me the surface level introduction to the behemoth that is git. Fortunately, that is all I need. Once I have removed any sensitive data (like passwords, etc.) I will make my docker-compose file public. The docker-compose file is where I determine which services I pick to host, and how to configure them to my liking. Hopefully someone will find this useful.\nSyncthing\nIf I could only tell someone to self host a single service, I would have to pick Syncthing. It is a continuous file synchronization program, which means it keeps a specific file or folder the same between any device running Syncthing. I use it to keep my password database and my org-mode notes Now org-mode might be the biggest rabbithole of them all, and definitely the topic for another blog post. I use it to manage my TODO list, my lab notebook, my shopping lists, write this blog, and maintain my Zettelkasten note database. It is an immensely powerful tool. up to date between all of my devices. With Syncthing, all of my data is stored on my own devices and encrypted in transit.\nFreshRSS\nI keep up to date on the science in my field by subscribing to relevant RSS feeds. Yet another topic to write a post about. This really changed the game for my ability to keep on top of the latest research. 2022-07-14 Update: post complete! Check it out here. FreshRSS replaced Feedly for me, as I ran up against the number of feeds I could subscribe to on a free account. Also, when self hosting, I can save as many articles as my heart desires (even if I will never look at them again \u0026#x1f635; ).\nWallabag\nRemember Pocket for Firefox? (Yes, I know it still exists, okay?) Give Wallabag a spin, it is great for storing articles you want to read later. I set up FreshRSS to save articles to my Wallabag instance to keep for later.\nChangeDetection\nNow this is a fun one! ChangeDetection.io is a service that loads a webpage and checks to see if something has changed since the last time. This might not sound useful at first, but I recently used this to check for when a hot item for my new coffee roasting hobby was back in stock. I got an email the other day to let me know it was in stock. Pretty cool!\nHugo\nHugo is the static site generator I use to make this here blog! I was amazed at how much more response my site was using Hugo compare to when I paid a company to host a WordPress site. I\u0026rsquo;m sure WordPress could be fast, but I just wanted a barebones, pure html experience, and Hugo made it easy.\nCommento++\nYou may have noticed that I have some pretty snazzy comments sections on my site. I initially used Disqus, which you may recognize from a ton of sites around the internet, but didn\u0026rsquo;t like how it would serve ads through my comments section, and provided sign-ins using Google/Facebook/Twitter. I wanted to serve the simplest comments section I could, that still gave me the ability to migrate the comments to wherever I decide to keep my server. Go ahead and use the anonymous comment button, fill in your name, and you are off to the races.\nAuthelia\nThere are a few services I host that I really want to lock down. For these services, Authelia is great. It puts up a \u0026ldquo;Enter the 6 digit code on your phone\u0026rdquo; style 2 factor authentication in front of the services I choose. Or, if you follow the guide here, you can have it send you a DUO push, just like you are one of the big hitters out there. I feel much more secure with Authelia in front of Adminer, Traefik, and Portainer.\nBoring stuff that allows everything else to work!\nPostgreSQL database MariaDB database Traefik reverse proxy Umami privacy respecting site analytics Portainer for docker container management Redis in-memory data store Adminer database management traefik-socket-proxy to prevent pesky backdoors to my server! ","permalink":"https://www.zacharybillman.com/posts/zpb-current-selfhosted/","summary":"\u003cp\u003e\u003cem\u003eN.B.: I hope to add screenshots for each of these eventually. For now, I hope links to each services\u0026rsquo; website will suffice.\u003c/em\u003e\u003c/p\u003e\n\u003col\u003e\n\u003cli\u003e\n\u003cp\u003e\u003ca href=\"https://www.seafile.com/en/home/\"\u003eSeafile\u003c/a\u003e\u003c/p\u003e\n\u003cp\u003eThis is a great tool for managing files. I moved to this from Nextcloud because I am of the philosophy that I would prefer services that do one thing excellently instead of many things well. Nextcloud is an incredible Office365 replacement, but I found myself using a fraction of what it was capable of providing. Enter Seafile. It is cloud file syncing with a robust encryption implementation, just what the doctor ordered.\u003c/p\u003e","title":"What I'm currently selfhosting."},{"content":"My partner and I took a trip to the Mason Farm Biological Reserve the other day, and what a glorious day it was. This year, I\u0026rsquo;ve been quite busy in the lab, and missed a lot of the early spring warbler season, so I was very excited by the opportunity to check out the old stomping grounds.\nI brought the camera with me despite the fact we were going to be there around midday when the birds are much less active. I\u0026rsquo;m glad I did, because I got the best look at a common yellowthroat I\u0026rsquo;ve ever had. Normally these guys are flighty, staying close to the ground in small brush or tall grasses, but this one was putting on a proper show for the mating season. Even when you get a glimpse of one, it is usually just that, as they have jumped away before you can pull out the camera, taunting you with their iconic call. I was very pleased to capture a few choice shots of the bird. Hopefully there are more to come. While we were out, I also got a nice picture of a hermit thrush and a king snake.\nThese images have been compressed quite a bit for a lighter internet footprint. These have all been resized to 25% of their original size. If you would like the full sized images, let me know and I will send you a link!\n","permalink":"https://www.zacharybillman.com/posts/the-uncommon-yellowthroat/","summary":"\u003cp\u003eMy partner and I took a trip to the \u003ca href=\"https://ncbg.unc.edu/visit/mason-farm-biological-reserve/\"\u003eMason Farm Biological Reserve\u003c/a\u003e the other day, and what a glorious day it was. This year, I\u0026rsquo;ve been quite busy in the lab, and missed a lot of the early spring warbler season, so I was very excited by the opportunity to check out the old stomping grounds.\u003c/p\u003e\n\u003cp\u003eI brought the camera with me despite the fact we were going to be there around midday when the birds are much less active. I\u0026rsquo;m glad I did, because I got the best look at a common yellowthroat I\u0026rsquo;ve ever had.\n\u003cspan class=\"sidenote-number\"\u003e\u003csmall class=\"sidenote\"\u003e\nNormally these guys are flighty, staying close to the ground in small brush or tall grasses, but this one was putting on a proper show for the mating season. Even when you get a glimpse of one, it is usually just that, as they have jumped away before you can pull out the camera, taunting you with their \u003ca href=\"https://ebird.org/species/comyel#Modal-playlist\"\u003eiconic call\u003c/a\u003e.\n\u003c/small\u003e\u003c/span\u003e\nI was very pleased to capture a few choice shots of the bird. Hopefully there are more to come. While we were out, I also got a nice picture of a hermit thrush and a king snake.\u003c/p\u003e","title":"The (un)common yellowthroat."}]
\ No newline at end of file
+[{"content":"Welcome to my site! My name is Zachary Billman. I\u0026rsquo;m an MD-PhD student at UNC Chapel Hill in Ed Miao\u0026rsquo;s lab. The curious reader may be thinking: \u0026ldquo;But Zach, Ed Miao\u0026rsquo;s lab is at Duke now! What does that make you?\u0026rdquo; What an astute question! I am a card-carrying UNC Microbiology and Immunology student who happens to have all of their research take place at Duke. This move was quite a trial, especially when compounded with the onset of the pandemic. I suspect my research timeline suffered, though this is an extremely minor inconvenience compared to the tragedy the pandemic caused. This makes for very interesting basketball viewing parties with my Duke friends!\nMy research and scientific interests. I am broadly interested in innate immunology. I am in the 4th year of my PhD studying the host-pathogen interaction between the intracellular fungus Histoplasma capsulatum and macrophages. There are many unstudied curiosities regarding the innate immune response to Histoplasma spp. and other intracellular fungi that I think are quite interesting. Stay tuned, hopefully there is a major breakthrough to report here someday.\nHobbies I may write about. Besides my science, I am interested in birding, baking sourdough bread (I swear I began years before the pandemic, though hearing of people baking bread brings me joy no matter when they first began!), board games, roasting coffee, and self-hosting free and open source software. Over the course of the pandemic, I have learned how to maintain a basic suite of services on a server I rent that have replaced my need for Google Photos and Google Drive. I\u0026rsquo;m hoping to be able to move away from these platforms entirely soon. I think they provide a great service, but at a substantial cost to privacy. Hopefully more to be said about my thoughts on FOSS soon! I also transitioned my old, (and quite frankly, embarrassingly slow) managed WordPress site with this lean, static site made in Hugo that I host myself. Now that I have mangled together some CSS to get my precious sidenotes up and running again, I\u0026rsquo;m ready to begin putting some ideas to paper. I love marginalia. I\u0026rsquo;m not sure if this is unique to me, but I seem to get caught up in parenthetical / tangential thoughts very often, and I think using an Edward Tufte-esque sidenote is a great way for me to communicate in this way without distracting the reader too much. It seems marginalia such as this have been used throughout history, so perhaps it is normal, but most people can keep their thoughts focused better than me. The implementation I use is inspired by the Tufte CSS project and largely taken from this incredibly helpful post found at scripter.co. I\u0026rsquo;m quite proud of my progress in administering my server and self-hosting useful services.\nThe future of this site. On this site I plan to post updates about my journey through med school, grad school, and self-hosting I would like to share with the world. I have been helped immensely by many others\u0026rsquo; advice and I hope to impart similar tips to others someday. I suspect most posts will be about much lighter fare, like whatever hobbies tickle my fancy at the time.\n","permalink":"https://www.zacharybillman.com/posts/about-me/","summary":"\u003ch2 id=\"welcome-to-my-site\"\u003eWelcome to my site!\u003c/h2\u003e\n\u003cp\u003eMy name is Zachary Billman. I\u0026rsquo;m an MD-PhD student at UNC Chapel Hill in Ed Miao\u0026rsquo;s lab. The curious reader may be thinking: \u0026ldquo;But Zach, Ed Miao\u0026rsquo;s lab is at Duke now! What does that make you?\u0026rdquo; What an astute question! I am a card-carrying UNC Microbiology and Immunology student who happens to have all of their research take place at Duke.\n\u003cspan class=\"sidenote-number\"\u003e\u003csmall class=\"sidenote\"\u003e\nThis move was quite a trial, especially when compounded with the onset of the pandemic. I suspect my research timeline suffered, though this is an extremely minor inconvenience compared to the tragedy the pandemic caused.\n\u003c/small\u003e\u003c/span\u003e\nThis makes for very interesting basketball viewing parties with my Duke friends!\u003c/p\u003e","title":"About me. 👋"},{"content":"It\u0026rsquo;s over. My third year of medical school is officially behind me. I managed to get in a grand total of zero blog posts during grad school, so here\u0026rsquo;s to a new year with hopefully some more thoughts being shared. I have a lot to reflect on from the past year. It was wonderful. I wish everyone could experience what I did this past year. I think it goes without saying:\nI loved the third year of med school, but I do not want to do it again.\nA year of change. In the days leading up to my return to med school, I thought \u0026ldquo;Oh no, I really enjoy doing science, do I really have to go to med school?\u0026rdquo;. I also remember at the end of Step 1 and the first two years of med school thinking, \u0026ldquo;Oh no, I really enjoy med school, do I really have to do science again?\u0026rdquo;. I think I have a welcome problem of enjoying what I\u0026rsquo;m doing. The third year of med school is a shift. After years of memorizing and examinations, the doors to the promised land are finally opened. I have experienced nothing like it before It feels intentionally unsettling. You are thrown into the clinic with a modicum of guidance so you aren\u0026rsquo;t totally caught off guard, but you are thrown out to the wolves. I don\u0026rsquo;t mean this as a criticism of the system, it feels necessary. Third year medical students—commonly shorted to MS3s—have just one year to experience a broad swath of medicine and pick a specialty. So you had better be ready to dive in.\nTotal immersion I came to terms with my new reality quickly. Gone were the days of hitting the snooze button and going home when I pleased. I am now beholden to other people\u0026rsquo;s schedules. This came back relatively naturally. Maybe not hitting snooze. A regrettable personal failing of mine. I was, however, immediately faced with a new reality in the patient room. Patients come to the doctor for a number of reasons, but often seek relief. To get to the core of what ails them, they will tell you everything. I was not prepared for how vulnerable patients would be with me. I am not sure if this ever will feel natural. I hope it never does. I was told many stories of experiences living with scary diagnoses, and not knowing what to do with it. Family histories of all sorts. Personal details that were sometimes (oftentimes?) off the wall. I see all of these specifics as flailing, grasping at sand hoping that something could explain their pain. Sometimes it could. Usually it did not. But since I was in a white coat, I was privileged to hear it.\nI think my years spent in the lab have prepared me to face some of the challenges set before me. At the very least, having a few more years under my belt helped me approach the year with a bit of maturity. This seems to have paid off. I guess my recommendation is to simply get old before going to med school. Returning to studying The hospital is how I spent the majority of my time, but a new reality for me was also going back to daily studying. There is a strange dichotomy in medicine of \u0026ldquo;Oh, it doesn\u0026rsquo;t really matter\u0026rdquo; and \u0026ldquo;If you don\u0026rsquo;t get this class/score/grade then you won\u0026rsquo;t be able to be the kind of doctor you want to be, so you had better get your act together.\u0026rdquo; Simultaneously there are no expectations and immense responsibility for the looming specter of Step 2. I\u0026rsquo;m glad that studying regularly came back easily enough. I was concerned I would experience a studying whiplash. I\u0026rsquo;m glad it never came. I did UWorld and Anki nearly every day for a full year and felt alright.\nBecoming invisible I quickly learned I needed to change my understanding of my contribution to the team. Exiting grad school, people understood that they could come to me for help. I was a resource, a seasoned veteran of the lab. If someone needed an experiment done, I could do it, and be trusted to do it. In med school as a third year, I was nothing. A fly on the wall; a worm beneath the feet of the real doctors. In science, I felt like I was treated as a peer with even my committee members with multiple R01s. Even if I didn\u0026rsquo;t understand the science perfectly, I could contribute some different perspective. In medicine, sometimes not being recognized at all by my attendings was the best outcome. Which happened regularly. My role, was not as a contributor—as it was in science—it was simply to get in the reps. Once I understood that the expectations of me were below the ground, I understood that everything I did in third year was for myself. This is taken at face value by the team at times. I would spend 30 minutes working on a presentation, pre-rounding, the works, and at the end of my part, the intern would nod, then turn to the senior resident and say \u0026ldquo;I was thinking that we\u0026hellip;\u0026rdquo; without thinking of my work. This is perhaps a bit of cognitive restructuring, but recognizing this is what gave me the freedom to embed myself in the hospital flow, without a single worry about the outcome. Simply doing my best was the best thing I could do. Obviously. But this was not apparent to me at first. I needed more quality repetitions to develop good habits in the future. And also experience as much of medicine as possible to find what I want to do with my life. This permission allowed me to approach specialties I do not care about with the awe and respect they deserve.\nA year of wonder. Med school prepares you for the standardized tests. I think this is generally useful. The tests on aggregate are reasonable and evaluate your ability to think through common clinical scenarios. There will always be oddball questions that come out of left field, but I let these flow over me. No need to perseverate on the small stuff. The time for that can come later.\nWhat I didn\u0026rsquo;t realize is how much of the \u0026ldquo;classic\u0026rdquo; material we are fed in the first couple years of med school would come to the forefront. The \u0026ldquo;sandpaper rash\u0026rdquo; of scarlet fever really does feel like sandpaper. Nikolsky\u0026rsquo;s sign actually works. Tripoding for epiglottitis gets the physicians worked up. Don\u0026rsquo;t forget about von Willebrand\u0026rsquo;s disease when someone seems to be bleeding a bit too much. TB is out there, watch for hemoptosis. Night sweats, unintended weight loss, is cancer until proven otherwise. And yes, it really can be lupus.\nIn general, facing the unknown with a sense of earnestness was the way I felt best able to respect those who gathered and passed down the medical knowledge I am privileged to learn today. Sometimes, my excitement to see aspects of medicine would rouse a curious response from the residents. I project here, but I felt a sense of surprise, like that of a doting parent seeing their child experience something new, after forgetting the astonishment they once felt.\nEarnestness is next to med studentlyness.\nPerhaps what I\u0026rsquo;m getting at here is that I found it important to bask in the privilege of seeing the pathology I encountered in med school, and to remind the residents of this sensation. I felt childish at times—and perhaps overanimated—but I found this excitement was to my and my resident\u0026rsquo;s benefit.\nMy surgery rotation overflowed with examples of wonder of medicine. Partially because of the team I worked with, and the rest because of the undeniable coolness of surgery. The OR is a cool place. The orderliness and chaos ebb. The spans of steady, industrious work are interrupted with staccato notes of bedlam. The anatomy I learned in class was ever present, but the surgeons bemoaned \u0026ldquo;normal anatomic variation\u0026rdquo;.\nI was struck with wonder at the sight of human anatomy as it unfolded before me. What I was able to experience in the OR felt like the culmination of centuries of human curiosity. There is an ancientness to medicine that I catch flashes of—I could perform the physical exam on humans hundred of millions of years ago and interrogate the same pathologies as I do in the hospital today—and viewing the exposed anatomy is a pressure-bagged infusion of this collective wonder. To gaze upon the peristalsing of the small intestine, or steady beating of the heart is a sight to behold, indeed.\nA year of shame. It weighs upon me the circumstances that resulted in these transcendent experiences. Not one patient was in the hospital without reason. What to make of these patients with horrible pathology? I still feel unsettled about how the cause of their pain sparked wonder. How dare I gain, merely by the circumstance of having their care managed at UNC, Which, as a tertiary care center, layers on more complexity. Many patients end up at UNC because they have no where else they can go for help. And this signs them up for med students? For shame. from the very essence of their malady? I do not know what to do with my discomfort, but I think it is best that I dwell in it. With this, I respect the people before me in the hospital and recognize their humanity.\nBut I often complained of what I say here I was lucky to do. I find myself resentful of my future schedule; when was I supposed to learn that I will be working 13 hour days, 6 days a week for the rest of my life? And what of having a family? Medicine by necessity requires sacrifice. I happened to sign up for sacrifices years before I recognized how profound they were. How might I balance this dread and with the joy of practicing medicine? And why do I seem more concerned about this than others? Am I not grateful enough? Am I not capable of the sacrifices that others seem to offer so effortlessly? I don\u0026rsquo;t necessarily think this to be true, but these questions erode at my will to pursue medicine.\nPerhaps most shameful of all is how my understanding of the patient-provider interaction evolved over the year. It began as an exploration of an open book, a tabula rasa that held within it a diagnosis and how to best intervene. On my first day in the outpatient clinic, it was clear that this is not the case. My preceptor had only 20 minutes for me to ① interview the patient and perform the physical exam, ② present with a plan, ③ return to the room and do everything again, ④ write orders, educate, and get the patient out of the door. It simply is not amenable to the free form, personable, curious interview I hoped to perform. By the end of the year, I had optimized how I asked questions to keep patients from going off the rails. When prerounding in medicine, I was there to extract information and not much else. Small talk had to go, there was no time. I like to chat, so this came at a loss of who I think I am. I am not sure how to do this well, while still feeling like Zachary. And from what I gather from the interns, that may just come later in my career. I found myself questioning, \u0026ldquo;Is this the \u0026lsquo;patient interaction\u0026rsquo; that has been mythologized throughout my training?\u0026rdquo; The carrot at the end of the stick dangled before me with a \u0026ldquo;You are so lucky to be able to do this, so you had better not complain of any abuse that comes your way.\u0026rdquo; It wasn\u0026rsquo;t a genuine interaction as much as me leading the patient along to tell me what I wanted to know. Of course, I used open ended questions, but only open enough. Leave the door a bit too open and next thing you know, you are talking about their dog\u0026rsquo;s breeder while you constantly stare at your watch, imagining what your attending will say when you return. I feel like I am alone in missing the core human element that funnels sprightly youths into medicine. Or worse, finding it a façade.\nThe shame extends beyond the hospital. One aspect of my life that has changed most dramatically is the sheer amount of time I felt I needed to dedicate to medicine, whether at the hospital or at home. I spent all day basking in the wonder of medicine, then I would come home and study for hours. I relied on my partner for keeping our household together more than ever, because I spent all day—all year, rather—in a state of discovery. Her life was largely the same, with the normal challenges of being a scientist, with the added bonus of getting less help from me. The shame built over the year. Again, how dare I?\nA year of glad. This has been an undeniable year of growth and joy, with these quibbles. It is clear that I was happier than I was during grad school. I know this from within myself, and reinforced by my wife\u0026rsquo;s comments on my mood. The pace of the day, and immediacy of problem solving were a welcome change.\nI recall, during the very first days preparing for med school during xTAP, having to do a simulated patient encounter complete with patient presentation to an attending physician. We were told about this encounter days in advance. And yet, I dreaded it. And near the last day of my final rotation, I did 8 of these in a row without breaking a sweat. Progress!\nI think, in a word, what I\u0026rsquo;ve experienced in the third year of med school is gratitude. Gratitude to be privileged to learn what I am learning. Gratitude for the experiences in my life that brought me here. Gratitude for the support from my wife. Gratitude to be involved in people\u0026rsquo;s lives when they are fragile. Ever since reading Braiding Sweetgrass I think one could call me \u0026ldquo;gratitude-pilled\u0026rdquo;. I also selfishly enjoyed the gratitude from patients as I put on my best doctor performance. In reflection on the year, I have spent time thinking of a phrase that I heard a number of times throughout med school from residents, \u0026ldquo;The worst day of residency is better than the best day of med school.\u0026rdquo; I find this hard to believe. This year has been magical. It is hard to imagine a year filled with more wonder and joy of caring for those in need. I will have to rely on the experience of those who have walked this path and trust that the rest of my training has plenty of magic to spare.\n","permalink":"https://www.zacharybillman.com/posts/ms3-year-is-magical/","summary":"\u003ch2 id=\"it-s-over-dot\"\u003eIt\u0026rsquo;s over.\u003c/h2\u003e\n\u003cp\u003eMy third year of medical school is officially behind me. I managed to get in a grand total of \u003cem\u003ezero\u003c/em\u003e blog posts during grad school, so here\u0026rsquo;s to a new year with hopefully some more thoughts being shared. I have a lot to reflect on from the past year. It was wonderful. I wish everyone could experience what I did this past year. I think it goes without saying:\u003c/p\u003e","title":"The third year of medical school is magical."},{"content":"I, like many others, picked up a new hobby during the pandemic. Other people\u0026rsquo;s hobbies may bring them joy. This could be for many reasons. There is the joy of creating something from scratch. You can revel in your thriftiness. You can embrace the pride when you recognize that your creation is on par (or better!) than what you can buy. I feel like these are embodied in the sourdough craze that caught fire early on in COVID. Dare I say that I did this before it was cool? \u0026#x1f60e; I baked two loaves of bread almost every weekend through med school. Maybe I should bring that back, it\u0026rsquo;s been a while since I brought out the ole\u0026rsquo; starter. My pandemic hobby is similar, but different in that it often feels like a chore, costs more money, and often turns out worse than what I can buy. Of course, I am talking about how I\u0026rsquo;ve started roasting my own coffee at home.\nI\u0026rsquo;m not sure where this idea was planted into my brain. I don\u0026rsquo;t think I know anyone who roasts their own beans, and I certainly didn\u0026rsquo;t know how. I didn\u0026rsquo;t even drink coffee regularly until after college! I guess that extra time on the computer sent me down a rabbithole I have yet to emerge from.\nFirst, I want to preface the following with a disclaimer: This is not a detailed guide about how to roast your own coffee. If you are interested, I recommend checking out the How To Roast Your Own Coffee guide at Sweet Maria\u0026rsquo;s as a starting point. There is also the /r/roasting subreddit if that is your cup of tea. My only warning is there will be a lot of smoke. Roast your coffee outside, for Pete\u0026rsquo;s sake!\nIt all started with a trusty popcorn popper. There are a few things you want when you roast coffee:\nAir hot enough to roast coffee Remove the chaff from the beans Turns out that a classic popcorn popper fits the bill, as long as it has an upwards airflow and doesn\u0026rsquo;t let the chaff fall into the heating element. There is a bit of a cult following for the West Bend Poppery 2 model, but that one seemed a bit pricey, so I settled for a very capable popper from Nostalgia.\nFigure 1: I got a good bit of mileage out of my popcorn popper. If you are interested in roasting your own coffee I would give it a whirl.\nThings were simple back then. I still bought most of the coffee I drank, but I roasted enough to enjoy some freshly roasted coffee as an occasional treat. I ordered 10 pounds of green beans from Sweet Maria\u0026rsquo;s and life was good.\nThen I became a bit of a coffee snob.\nI could only roast 100 grams of coffee at a time in the popcorn popper, which is only enough for one pot of coffee in the morning for me. So it was time to upgrade.\nI bought the SR800 fluid bed roaster, which upped my roasting capacity and gave me finer control on temperature and airflow. Suffice to say my roasts improved a lot! At this point, I would consider my coffee good enough to sell at a farmer\u0026rsquo;s market to break even.\nIf you ever find yourself on a coffee roasting forum and bring up the SR800, someone is bound to bring up the famous RazzoRoasting extension tube. If you look for advice for how to use the SR800, I swear it\u0026rsquo;s assumed that you have this very specific accessory. \u0026hellip;And so I bought one.\nDon\u0026rsquo;t worry, that is the extent of all of my coffee spending (for now). I am a very satisfied coffee roaster now. Check out this quick series of images going from the green beans to a nearly finished product! I can spend about 45 minutes and go from nothing to nearly 2 pounds of roasted beans, enough for about a week and a half of coffee. Not bad! The only downside is that now I feel like I need to buy coffee from local roasters to get my fix. There are certainly crueler fates.\nAs a sign off, I will share something that surprised me about coffee roasting. When I roast coffee, the most important cue to determine if the coffee is roasted is the sound. That\u0026rsquo;s right, not the color, not the smell, but the sound. When heating up a coffee bean, the water trapped inside eventually bursts out of the bean in a rapid expansion. This is called \u0026ldquo;first crack\u0026rdquo;, and indicates that the coffee is roasted enough to be drinkable. The expansion also releases the chaff from the bean. If you continue heating up the bean, you will eventually reach \u0026ldquo;second crack\u0026rdquo;. I think a solid medium roast is taken out just before second crack, so I try to take my coffee out to this point and it hasn\u0026rsquo;t proved me wrong yet.\nHappy coffee-ing! \u0026#x2615;\n","permalink":"https://www.zacharybillman.com/posts/roasting-coffee-at-home/","summary":"\u003cp\u003eI, like many others, picked up a new hobby during the pandemic. Other people\u0026rsquo;s hobbies may bring them joy. This could be for many reasons. There is the joy of creating something from scratch. You can revel in your thriftiness. You can embrace the pride when you recognize that your creation is on par (or better!) than what you can buy. I feel like these are embodied in the sourdough craze that caught fire early on in COVID.\n\u003cspan class=\"sidenote-number\"\u003e\u003csmall class=\"sidenote\"\u003e\nDare I say that I did this before it was cool? \u0026#x1f60e; I baked two loaves of bread almost every weekend through med school. Maybe I should bring that back, it\u0026rsquo;s been a while since I brought out the ole\u0026rsquo; starter.\n\u003c/small\u003e\u003c/span\u003e\nMy pandemic hobby is similar, but different in that it often feels like a chore, costs more money, and often turns out worse than what I can buy. Of course, I am talking about how I\u0026rsquo;ve started roasting my own coffee at home.\u003c/p\u003e","title":"Roasting coffee at home. ☕"},{"content":"It is an age-old question: how can one keep up with the continuous output of science? I remember at the beginning of my PhD struggling to figure out how anyone found out when a new paper came out. \u0026#x1f635; Did they sit on nature.com and spam the refresh button? Did they know when each journal released their latest issue?\nBehold the power of RSS! Most websites have a page that contains information about each subpage in a computer-readable format called RSS (Really Simple Syndication). Mine has one right here! These pages can be parsed by a number of RSS feed aggregators. The way these pages are set up make it such that they add any new information hosted at that domain. This is useful in the science world because you can find the RSS feed of a given journal, subscribe to it, then have every new article published online be delivered right to you.\nThere are a plethora of RSS feed aggregators you can pick from manage your feeds. I have previously used Feedly and Inoreader, which are great free solutions, but have moved on to selfhosting my own instance of FreshRSS.\nAfter making an account at your friendly local RSS feed aggregator, you can add whatever feeds your heart desires. To find a journal\u0026rsquo;s rss feed, I often just search \u0026ldquo;$JOURNAL_NAME rss feed\u0026rdquo; and poke around until I find something that looks right. Most of the aggregators will test the feed out first to make sure that you are trying to add a legitimate one. Here are a few of the heavy hitters to get you started:\nhttp://feeds.nature.com/nature/rss/current https://www.science.org/rss/express.xml https://www.cell.com/cell/inpress.rss Nothing like a constant stream of Cell, Science, and Nature to make your project feel like a real winner, eh?\nHere is what my own site looks like.\nFigure 1: My current FreshRSS setup. On the left I have my feeds separated into folders. In the middle you can see the titles of papers that appear in my feed.\nAnd after I hit J to move to the first item in the feed.\nFigure 2: With a title selected, you can see the abstract and authors.\nAfter collecting all of your desired RSS feeds, you cannot forego your responsibility of actually reading them! Most RSS feed aggregators have shortcuts to move through titles quickly (Typically J to move on to the next one and K to move up.) They always seem to use vi keybindings. A bunch of computer nerds have really cornered the keybinding market. I have let them take over my computing life. Each morning when I get into the lab, I quickly set up something, then head to my desk to hit J until the counter reaches zero.\nBut what about my very specific field? You can subscribe to all of the journals you want, but that doesn\u0026rsquo;t make the papers with your specific interests pop out. Fortunately, the NIH has this exact circumstance in mind.\nWhen you make a new search on PubMed you might notice the \u0026ldquo;Create RSS\u0026rdquo; button. Give it a click, then you will have a personal link you can add to your favorite RSS feed aggregator.\nFigure 3: Somehow I never noticed this button until I needed it.\nThis changed the game for me for keeping up with papers. Unfortunately, it doesn\u0026rsquo;t solve the problem of library management, or actually getting around to reading the papers you care about. I will leave library management as an exercise for the interested reader. Here\u0026rsquo;s a tip, the best solution uses the Zotero citation manager. Bonus points for using Zotfile for renaming your PDFs and Better BibTex for Zotero. \u0026#x1f609; I hope this helps you get your eyeballs on that science you crave. If you have solved the problem of accruing papers to read faster than you read them, let me know.\n","permalink":"https://www.zacharybillman.com/posts/rss-feeds-to-find-science-papers/","summary":"\u003cp\u003eIt is an age-old question: how can one keep up with the continuous output of science? I remember at the beginning of my PhD struggling to figure out how anyone found out when a new paper came out. \u0026#x1f635; Did they sit on nature.com and spam the refresh button? Did they know when each journal released their latest issue?\u003c/p\u003e\n\u003ch2 id=\"behold-the-power-of-rss\"\u003eBehold the power of RSS!\u003c/h2\u003e\n\u003cp\u003eMost websites have a page that contains information about each subpage in a computer-readable format called RSS (Really Simple Syndication). \u003ca href=\"https://zacharybillman.com/index.xml\"\u003eMine has one right here!\u003c/a\u003e These pages can be parsed by a number of RSS feed aggregators. The way these pages are set up make it such that they add any new information hosted at that domain. This is useful in the science world because you can find the RSS feed of a given journal, subscribe to it, then have every new article published online be delivered right to you.\u003c/p\u003e","title":"Using RSS feeds to keep on top of science."},{"content":"My interest in self-hosting began in my with my interests in internet privacy. Plastered all over the internet are stories about how much Google, Facebook and Amazon know about you. I deleted my Facebook account years ago, and I\u0026rsquo;m too paranoid to go back to the site because there\u0026rsquo;s a real possibility that Facebook has cached my account, ready to spin it back up in case I try to login again. The ads served to me were too accurate for my liking. This is despite almost never clicking on them! I have become convinced of the idea that, if you are not paying for the product, you are the product. From this assumption, it follows that anywhere I trust with my data that I am not paying for (like Google Drive, Google Photos, Dropbox, Facebook, Twitter) is using my data to earn money. We know that Google uses the labels you add to Photos to train it\u0026rsquo;s AI, and Facebook uses (at least) Instagram photos to train it\u0026rsquo;s AI. For some, the value proposition of allowing a company to use your data for a useful service in return is an acceptable one. I find this to be a reasonable stance, but I took my growing interest in internet privacy as a chance to learn about how I can take control of my data.\nInitially, I lurked on forums like /r/privacy to learn what I could do to avoid big-tech\u0026rsquo;s watchful eye. There were numerous comments along the lines of: \u0026ldquo;The only way to be in control of your data is to self-host your services.\u0026rdquo; I had no idea what this meant! Hard to believe that less than a year later, I learned to use (and love) Linux as my primary OS, and have happily replaced Google Photos, Google Drive and other services with my own self-hosted alternatives. Self-hosting, I have since learned, is when you run useful programs from your own computer. By doing so, you have complete knowledge of where and how your data is stored and how it is being used. It has the additional effect of being a bottomless time sink.\nTo begin, I needed an always-on computer to run these useful programs. I began with a humble Raspberry Pi.\nFigure 1: My humble Raspberry Pi and its hard drive. This dude currently tirelessly runs the excellent Adguard Home and downloads a backup of my data every night.\nThese are tiny, but capable computers that are great for fiddling with. The projects people develop for these are amazing and diverse. With RPi in hand, I began with the ambitious project of replacing Google Drive with Nextcloud. After much frustration with a bare metal installation, I found the NextcloudPi project. Surprisingly, it went pretty okay! At first, I was intimidated by Linux defaults, but over time I grew to appreciate, and indeed, prefer Linux as an operating system. My decision to use Linux over Windows/MacOS is because it is free and open source software (FOSS). This is a topic for a different post, but I think using FOSS when possible is a moral imperative of sorts. I used Nextcloud strictly from my home for a few months, without the ability to connect to it from the internet, to test the self-hosting waters. My first true cloud replacement spun up once I decided to access this lil\u0026rsquo; guy from the internet. To do so, I purchased a domain (not the one this site is hosted on) and pointed it to the IP of my house. I forwarded the appropriate ports of my router to the RPi.\nThis is when the real exploration began. I was able to access my files and images using Nextcloud, but the photo viewing service left something to be desired. No problem, why not spin up an instance of Photoprism? I use RSS feeds to keep on top of the latest science in the journals relevant to my field using Feedly. Why not host my own RSS feed aggregator so I can subscribe to as many feeds as I desire?\nThis cycle continued, and I accrued many cool applications, but in the back of my mind I worried about opening up my home network to the internet. I also struggled to run some programs because the RPi uses the arm64 architecture, and most services are written with amd64 in mind. These two forces eventually convinced me to purchase a server where I could manage all of my services remotely. Some would say that not owning the hardware that is running your own services is not \u0026ldquo;true\u0026rdquo; self-hosting. I think this is needlessly exclusive. Let everyone self host, dangit! Someday, when I have more stable internet and a more permanent home, I hope to host everything from my own home, but until then, I\u0026rsquo;m extremely pleased with my current stack. And that is where I am now. I happily host numerous services on my virtual private server that entirely replace Google Photos, Google Drive and GitHub for me. Even better, there are specialized services that fill a need I never realized I had. What\u0026rsquo;s more, if I ever want to spin up a new service, all I have to do is add it to my to docker-compose file and it will be up within minutes. What a world!\nI thought about making this into a \u0026ldquo;guide\u0026rdquo; style post. I nixed that idea because, quite frankly, I feel like I don\u0026rsquo;t know what I\u0026rsquo;m doing. I am really happy with my setup, but I don\u0026rsquo;t feel like I have the authority to tell people how to administer their own services. If you are interested, allow me to point you toward the guide that really got me rolling: Ultimate Traefik Docker Compose Guide.\nFor those of you wondering what I am currently hosting, check out my current list at the link and let me know what you think!\n","permalink":"https://www.zacharybillman.com/posts/my-selfhosting-journey/","summary":"\u003cp\u003eMy interest in self-hosting began in my with my interests in internet privacy. Plastered all over the internet are stories about how much Google, Facebook and Amazon know about you. I deleted my Facebook account years ago, and I\u0026rsquo;m too paranoid to go back to the site because there\u0026rsquo;s \u003ca href=\"https://www.reddit.com/r/privacy/comments/6nmjfh/facebook_account_fully_recovered_3_years_after/\"\u003ea real possibility that Facebook has cached my account, ready to spin it back up\u003c/a\u003e in case I try to login again. The ads served to me were too accurate for my liking.\n\u003cspan class=\"sidenote-number\"\u003e\u003csmall class=\"sidenote\"\u003e\nThis is despite almost never clicking on them!\n\u003c/small\u003e\u003c/span\u003e\nI have become convinced of the idea that, if you are not paying for the product, you are the product. From this assumption, it follows that anywhere I trust with my data that I am not paying for (like Google Drive, Google Photos, Dropbox, Facebook, Twitter) is using my data to earn money. We know that \u003ca href=\"https://www.theverge.com/2020/11/11/21559930/google-train-ai-photos-image-labelling-app-android-update\"\u003eGoogle uses the labels you add to Photos to train it\u0026rsquo;s AI\u003c/a\u003e, and \u003ca href=\"https://ai.facebook.com/blog/seer-the-start-of-a-more-powerful-flexible-and-accessible-era-for-computer-vision/\"\u003eFacebook uses (at least) Instagram photos to train it\u0026rsquo;s AI\u003c/a\u003e. For some, the value proposition of allowing a company to use your data for a useful service in return is an acceptable one. I find this to be a reasonable stance, but I took my growing interest in internet privacy as a chance to learn about how I can take control of my data.\u003c/p\u003e","title":"My selfhosting journey."},{"content":"N.B.: I hope to add screenshots for each of these eventually. For now, I hope links to each services\u0026rsquo; website will suffice.\nSeafile\nThis is a great tool for managing files. I moved to this from Nextcloud because I am of the philosophy that I would prefer services that do one thing excellently instead of many things well. Nextcloud is an incredible Office365 replacement, but I found myself using a fraction of what it was capable of providing. Enter Seafile. It is cloud file syncing with a robust encryption implementation, just what the doctor ordered.\nPhotoprism\nNextcloud\u0026rsquo;s implementation of photo management was a bit clumsy for my tastes, so I began on a hunt for a more feature complete option. I was very lucky to stumble upon Photoprism early on in my self hosting journey. I am a proud supporter of this project. It brings a ton to the table, and doesn\u0026rsquo;t leave me missing Google Photos one bit. It is also actively developed. For instance, as of 2022-07-02, there was a recent update that improved scrolling a ton, which was one of my remaining quibbles with it\u0026rsquo;s functionality. Some people complain that it doesn\u0026rsquo;t scale up for libraries of 10,000+ photos, but my 2000 photo library works swimmingly. On my phone, I use the Folder Sync app to automatically send any pictures I take on my phone to the Photoprism imports folder. Within 15 minutes of snapping a photo, it is there on my Photoprism instance. I highly recommend giving it a go.\nMealie\nI have to admit that the name leaves something to be desired. Fortunately, the service itself doesn\u0026rsquo;t fall short. Mealie is a recipe management application. It is able to parse your favorite recipe websites to create immortalized versions of the recipe. This helps fight detestable link rot that plagues the internet. It allows you to edit ingredient amounts, make comments about what you would change next time, and plan out your weekly meals. It helps that it is beautiful and intuitive to use. If only I could get my partner to use it\u0026hellip; I want to go on the record here and say that I think it is sensible that she doesn\u0026rsquo;t trust my self hosted services that much. In the early days of my self hosting journey, let\u0026rsquo;s just say that the up-time of my services were extremely finicky. I like to think they are more permanent now, especially because I am hosting everything on a VPS, but I certainly cannot compete with the stability of Google and Amazon. (Or pretty much any other paid service for that matter.) \u0026#x1f609;\nGitea\nGitea is a community managed, lightweight code hosting solution written in Go. I use it to manage my data analysis (using Private repos) and even host the source code for this very website! Using Gitea has given me the surface level introduction to the behemoth that is git. Fortunately, that is all I need. Once I have removed any sensitive data (like passwords, etc.) I will make my docker-compose file public. The docker-compose file is where I determine which services I pick to host, and how to configure them to my liking. Hopefully someone will find this useful.\nSyncthing\nIf I could only tell someone to self host a single service, I would have to pick Syncthing. It is a continuous file synchronization program, which means it keeps a specific file or folder the same between any device running Syncthing. I use it to keep my password database and my org-mode notes Now org-mode might be the biggest rabbithole of them all, and definitely the topic for another blog post. I use it to manage my TODO list, my lab notebook, my shopping lists, write this blog, and maintain my Zettelkasten note database. It is an immensely powerful tool. up to date between all of my devices. With Syncthing, all of my data is stored on my own devices and encrypted in transit.\nFreshRSS\nI keep up to date on the science in my field by subscribing to relevant RSS feeds. Yet another topic to write a post about. This really changed the game for my ability to keep on top of the latest research. 2022-07-14 Update: post complete! Check it out here. FreshRSS replaced Feedly for me, as I ran up against the number of feeds I could subscribe to on a free account. Also, when self hosting, I can save as many articles as my heart desires (even if I will never look at them again \u0026#x1f635; ).\nWallabag\nRemember Pocket for Firefox? (Yes, I know it still exists, okay?) Give Wallabag a spin, it is great for storing articles you want to read later. I set up FreshRSS to save articles to my Wallabag instance to keep for later.\nChangeDetection\nNow this is a fun one! ChangeDetection.io is a service that loads a webpage and checks to see if something has changed since the last time. This might not sound useful at first, but I recently used this to check for when a hot item for my new coffee roasting hobby was back in stock. I got an email the other day to let me know it was in stock. Pretty cool!\nHugo\nHugo is the static site generator I use to make this here blog! I was amazed at how much more response my site was using Hugo compare to when I paid a company to host a WordPress site. I\u0026rsquo;m sure WordPress could be fast, but I just wanted a barebones, pure html experience, and Hugo made it easy.\nCommento++\nYou may have noticed that I have some pretty snazzy comments sections on my site. I initially used Disqus, which you may recognize from a ton of sites around the internet, but didn\u0026rsquo;t like how it would serve ads through my comments section, and provided sign-ins using Google/Facebook/Twitter. I wanted to serve the simplest comments section I could, that still gave me the ability to migrate the comments to wherever I decide to keep my server. Go ahead and use the anonymous comment button, fill in your name, and you are off to the races.\nAuthelia\nThere are a few services I host that I really want to lock down. For these services, Authelia is great. It puts up a \u0026ldquo;Enter the 6 digit code on your phone\u0026rdquo; style 2 factor authentication in front of the services I choose. Or, if you follow the guide here, you can have it send you a DUO push, just like you are one of the big hitters out there. I feel much more secure with Authelia in front of Adminer, Traefik, and Portainer.\nBoring stuff that allows everything else to work!\nPostgreSQL database MariaDB database Traefik reverse proxy Umami privacy respecting site analytics Portainer for docker container management Redis in-memory data store Adminer database management traefik-socket-proxy to prevent pesky backdoors to my server! ","permalink":"https://www.zacharybillman.com/posts/zpb-current-selfhosted/","summary":"\u003cp\u003e\u003cem\u003eN.B.: I hope to add screenshots for each of these eventually. For now, I hope links to each services\u0026rsquo; website will suffice.\u003c/em\u003e\u003c/p\u003e\n\u003col\u003e\n\u003cli\u003e\n\u003cp\u003e\u003ca href=\"https://www.seafile.com/en/home/\"\u003eSeafile\u003c/a\u003e\u003c/p\u003e\n\u003cp\u003eThis is a great tool for managing files. I moved to this from Nextcloud because I am of the philosophy that I would prefer services that do one thing excellently instead of many things well. Nextcloud is an incredible Office365 replacement, but I found myself using a fraction of what it was capable of providing. Enter Seafile. It is cloud file syncing with a robust encryption implementation, just what the doctor ordered.\u003c/p\u003e","title":"What I'm currently selfhosting."},{"content":"My partner and I took a trip to the Mason Farm Biological Reserve the other day, and what a glorious day it was. This year, I\u0026rsquo;ve been quite busy in the lab, and missed a lot of the early spring warbler season, so I was very excited by the opportunity to check out the old stomping grounds.\nI brought the camera with me despite the fact we were going to be there around midday when the birds are much less active. I\u0026rsquo;m glad I did, because I got the best look at a common yellowthroat I\u0026rsquo;ve ever had. Normally these guys are flighty, staying close to the ground in small brush or tall grasses, but this one was putting on a proper show for the mating season. Even when you get a glimpse of one, it is usually just that, as they have jumped away before you can pull out the camera, taunting you with their iconic call. I was very pleased to capture a few choice shots of the bird. Hopefully there are more to come. While we were out, I also got a nice picture of a hermit thrush and a king snake.\nThese images have been compressed quite a bit for a lighter internet footprint. These have all been resized to 25% of their original size. If you would like the full sized images, let me know and I will send you a link!\n","permalink":"https://www.zacharybillman.com/posts/the-uncommon-yellowthroat/","summary":"\u003cp\u003eMy partner and I took a trip to the \u003ca href=\"https://ncbg.unc.edu/visit/mason-farm-biological-reserve/\"\u003eMason Farm Biological Reserve\u003c/a\u003e the other day, and what a glorious day it was. This year, I\u0026rsquo;ve been quite busy in the lab, and missed a lot of the early spring warbler season, so I was very excited by the opportunity to check out the old stomping grounds.\u003c/p\u003e\n\u003cp\u003eI brought the camera with me despite the fact we were going to be there around midday when the birds are much less active. I\u0026rsquo;m glad I did, because I got the best look at a common yellowthroat I\u0026rsquo;ve ever had.\n\u003cspan class=\"sidenote-number\"\u003e\u003csmall class=\"sidenote\"\u003e\nNormally these guys are flighty, staying close to the ground in small brush or tall grasses, but this one was putting on a proper show for the mating season. Even when you get a glimpse of one, it is usually just that, as they have jumped away before you can pull out the camera, taunting you with their \u003ca href=\"https://ebird.org/species/comyel#Modal-playlist\"\u003eiconic call\u003c/a\u003e.\n\u003c/small\u003e\u003c/span\u003e\nI was very pleased to capture a few choice shots of the bird. Hopefully there are more to come. While we were out, I also got a nice picture of a hermit thrush and a king snake.\u003c/p\u003e","title":"The (un)common yellowthroat."},{"content":"Welcome to my site! ATTACH My name is Zachary Billman. I\u0026rsquo;m a UNC MD-PhD student in my 4th year of med school applying to pathology residency programs. I completed my PhD in Ed Miao\u0026rsquo;s lab. The curious reader may be thinking: \u0026ldquo;But Zach, Dr. Miao\u0026rsquo;s lab is at Duke, how did that come about?\u0026rdquo; What an astute question! Ed\u0026rsquo;s lab moved from UNC to Duke in early 2020, and I followed him down the street. My PhD was awarded by the UNC department of Microbiology and Immunology, but it just so happens that (nearly) all of my research took place at Duke. This move was quite a trial, especially when compounded with the onset of the pandemic. I suspect my research timeline suffered, though this is an extremely minor inconvenience compared to the tragedy the pandemic caused. This makes for very interesting basketball viewing parties with my Duke friends!\nMaybe having a diagram will make my training timeline make a bit more sense.\ntimeline.svg\nMy research and scientific interests. I am broadly interested in innate immunology. I spent most of my time in graduate school studying the host-pathogen interaction between the intracellular fungus Histoplasma capsulatum and macrophages. There are many unstudied curiosities regarding the innate immune response to Histoplasma spp. and other intracellular fungi that I think are quite interesting. I also spent a considerable time thinking about the evolution of proteins involved in the programmed cell death pathway called pyroptosis.\nHobbies I may write about. Besides my science, I am interested in birding, baking sourdough bread (I swear I began years before the pandemic, though hearing of people baking bread brings me joy no matter when they first began!), board games, roasting coffee, and self-hosting free and open source software. Over the course of the pandemic, I have learned how to maintain a basic suite of services spread between a server I rent and a computer at home that have replaced my need for Google Photos and Google Drive. I\u0026rsquo;m hoping to be able to move away from these platforms entirely soon. I think they provide a great service, but at a substantial cost to privacy. Hopefully more to be said about my thoughts on FOSS soon! I also transitioned my old, (and quite frankly, embarrassingly slow) managed WordPress site with this lean, static site made in Hugo that I host myself. Now that I have mangled together some CSS to get my precious sidenotes up and running again, I\u0026rsquo;m ready to begin putting some ideas to paper. I love marginalia (the word to describe these notes on the side of this webpage). I\u0026rsquo;m not sure if this is unique to me, but I seem to get caught up in parenthetical / tangential thoughts very often, and I think using an Edward Tufte-esque sidenote is a great way for me to communicate in this way without distracting the reader too much. It seems marginalia such as this have been used throughout history, so perhaps it is normal, but most people can keep their thoughts focused better than me. The implementation I use is inspired by the Tufte CSS project and largely taken from this incredibly helpful post found at scripter.co. I\u0026rsquo;m quite proud of my progress in administering my server and self-hosting useful services.\nThe future of this site. On this site I plan to post updates about my journey through med school, grad school, and self-hosting I would like to share with the world. I have been helped immensely by many others\u0026rsquo; advice and I hope to impart similar tips to others someday. I suspect most posts will be about much lighter fare, like whatever hobbies tickle my fancy at the time.\n","permalink":"https://www.zacharybillman.com/posts/about-me/about-me/","summary":"\u003ch2 id=\"welcome-to-my-site\"\u003eWelcome to my site! \u003cspan class=\"tag\"\u003e\u003cspan class=\"ATTACH\"\u003eATTACH\u003c/span\u003e\u003c/span\u003e\u003c/h2\u003e\n\u003cp\u003eMy name is Zachary Billman. I\u0026rsquo;m a UNC MD-PhD student in my 4th year of med school applying to pathology residency programs. I completed my PhD in Ed Miao\u0026rsquo;s lab. The curious reader may be thinking: \u0026ldquo;But Zach, Dr. Miao\u0026rsquo;s lab is at Duke, how did that come about?\u0026rdquo; What an astute question! Ed\u0026rsquo;s lab moved from UNC to Duke in early 2020, and I followed him down the street. My PhD was awarded by the UNC department of Microbiology and Immunology, but it just so happens that (nearly) all of my research took place at Duke.\n\u003cspan class=\"sidenote-number\"\u003e\u003csmall class=\"sidenote\"\u003e\nThis move was quite a trial, especially when compounded with the onset of the pandemic. I suspect my research timeline suffered, though this is an extremely minor inconvenience compared to the tragedy the pandemic caused.\n\u003c/small\u003e\u003c/span\u003e\nThis makes for very interesting basketball viewing parties with my Duke friends!\u003c/p\u003e","title":"About me. 👋"},{"content":"Welcome to my site! My name is Zachary Billman. I\u0026rsquo;m an MD-PhD student at UNC Chapel Hill in Ed Miao\u0026rsquo;s lab. The curious reader may be thinking: \u0026ldquo;But Zach, Ed Miao\u0026rsquo;s lab is at Duke now! What does that make you?\u0026rdquo; What an astute question! I am a card-carrying UNC Microbiology and Immunology student who happens to have all of their research take place at Duke. This move was quite a trial, especially when compounded with the onset of the pandemic. I suspect my research timeline suffered, though this is an extremely minor inconvenience compared to the tragedy the pandemic caused. This makes for very interesting basketball viewing parties with my Duke friends!\nMy research and scientific interests. I am broadly interested in innate immunology. I am in the 4th year of my PhD studying the host-pathogen interaction between the intracellular fungus Histoplasma capsulatum and macrophages. There are many unstudied curiosities regarding the innate immune response to Histoplasma spp. and other intracellular fungi that I think are quite interesting. Stay tuned, hopefully there is a major breakthrough to report here someday.\nHobbies I may write about. Besides my science, I am interested in birding, baking sourdough bread (I swear I began years before the pandemic, though hearing of people baking bread brings me joy no matter when they first began!), board games, roasting coffee, and self-hosting free and open source software. Over the course of the pandemic, I have learned how to maintain a basic suite of services on a server I rent that have replaced my need for Google Photos and Google Drive. I\u0026rsquo;m hoping to be able to move away from these platforms entirely soon. I think they provide a great service, but at a substantial cost to privacy. Hopefully more to be said about my thoughts on FOSS soon! I also transitioned my old, (and quite frankly, embarrassingly slow) managed WordPress site with this lean, static site made in Hugo that I host myself. Now that I have mangled together some CSS to get my precious sidenotes up and running again, I\u0026rsquo;m ready to begin putting some ideas to paper. I love marginalia. I\u0026rsquo;m not sure if this is unique to me, but I seem to get caught up in parenthetical / tangential thoughts very often, and I think using an Edward Tufte-esque sidenote is a great way for me to communicate in this way without distracting the reader too much. It seems marginalia such as this have been used throughout history, so perhaps it is normal, but most people can keep their thoughts focused better than me. The implementation I use is inspired by the Tufte CSS project and largely taken from this incredibly helpful post found at scripter.co. I\u0026rsquo;m quite proud of my progress in administering my server and self-hosting useful services.\nThe future of this site. On this site I plan to post updates about my journey through med school, grad school, and self-hosting I would like to share with the world. I have been helped immensely by many others\u0026rsquo; advice and I hope to impart similar tips to others someday. I suspect most posts will be about much lighter fare, like whatever hobbies tickle my fancy at the time.\n","permalink":"https://www.zacharybillman.com/posts/about-me/","summary":"\u003ch2 id=\"welcome-to-my-site\"\u003eWelcome to my site!\u003c/h2\u003e\n\u003cp\u003eMy name is Zachary Billman. I\u0026rsquo;m an MD-PhD student at UNC Chapel Hill in Ed Miao\u0026rsquo;s lab. The curious reader may be thinking: \u0026ldquo;But Zach, Ed Miao\u0026rsquo;s lab is at Duke now! What does that make you?\u0026rdquo; What an astute question! I am a card-carrying UNC Microbiology and Immunology student who happens to have all of their research take place at Duke.\n\u003cspan class=\"sidenote-number\"\u003e\u003csmall class=\"sidenote\"\u003e\nThis move was quite a trial, especially when compounded with the onset of the pandemic. I suspect my research timeline suffered, though this is an extremely minor inconvenience compared to the tragedy the pandemic caused.\n\u003c/small\u003e\u003c/span\u003e\nThis makes for very interesting basketball viewing parties with my Duke friends!\u003c/p\u003e","title":"About me. 👋"},{"content":"It\u0026rsquo;s over. My third year of medical school is officially behind me. I managed to get in a grand total of zero blog posts during grad school, so here\u0026rsquo;s to a new year with hopefully some more thoughts being shared. I have a lot to reflect on from the past year. It was wonderful. I wish everyone could experience what I did this past year. I think it goes without saying:\nI loved the third year of med school, but I do not want to do it again.\nA year of change. In the days leading up to my return to med school, I thought \u0026ldquo;Oh no, I really enjoy doing science, do I really have to go to med school?\u0026rdquo;. I also remember at the end of Step 1 and the first two years of med school thinking, \u0026ldquo;Oh no, I really enjoy med school, do I really have to do science again?\u0026rdquo;. I think I have a welcome problem of enjoying what I\u0026rsquo;m doing. The third year of med school is a shift. After years of memorizing and examinations, the doors to the promised land are finally opened. I have experienced nothing like it before It feels intentionally unsettling. You are thrown into the clinic with a modicum of guidance so you aren\u0026rsquo;t totally caught off guard, but you are thrown out to the wolves. I don\u0026rsquo;t mean this as a criticism of the system, it feels necessary. Third year medical students—commonly shorted to MS3s—have just one year to experience a broad swath of medicine and pick a specialty. So you had better be ready to dive in.\nTotal immersion I came to terms with my new reality quickly. Gone were the days of hitting the snooze button and going home when I pleased. I am now beholden to other people\u0026rsquo;s schedules. This came back relatively naturally. Maybe not hitting snooze. A regrettable personal failing of mine. I was, however, immediately faced with a new reality in the patient room. Patients come to the doctor for a number of reasons, but often seek relief. To get to the core of what ails them, they will tell you everything. I was not prepared for how vulnerable patients would be with me. I am not sure if this ever will feel natural. I hope it never does. I was told many stories of experiences living with scary diagnoses, and not knowing what to do with it. Family histories of all sorts. Personal details that were sometimes (oftentimes?) off the wall. I see all of these specifics as flailing, grasping at sand hoping that something could explain their pain. Sometimes it could. Usually it did not. But since I was in a white coat, I was privileged to hear it.\nI think my years spent in the lab have prepared me to face some of the challenges set before me. At the very least, having a few more years under my belt helped me approach the year with a bit of maturity. This seems to have paid off. I guess my recommendation is to simply get old before going to med school. Returning to studying The hospital is how I spent the majority of my time, but a new reality for me was also going back to daily studying. There is a strange dichotomy in medicine of \u0026ldquo;Oh, it doesn\u0026rsquo;t really matter\u0026rdquo; and \u0026ldquo;If you don\u0026rsquo;t get this class/score/grade then you won\u0026rsquo;t be able to be the kind of doctor you want to be, so you had better get your act together.\u0026rdquo; Simultaneously there are no expectations and immense responsibility for the looming specter of Step 2. I\u0026rsquo;m glad that studying regularly came back easily enough. I was concerned I would experience a studying whiplash. I\u0026rsquo;m glad it never came. I did UWorld and Anki nearly every day for a full year and felt alright.\nBecoming invisible I quickly learned I needed to change my understanding of my contribution to the team. Exiting grad school, people understood that they could come to me for help. I was a resource, a seasoned veteran of the lab. If someone needed an experiment done, I could do it, and be trusted to do it. In med school as a third year, I was nothing. A fly on the wall; a worm beneath the feet of the real doctors. In science, I felt like I was treated as a peer with even my committee members with multiple R01s. Even if I didn\u0026rsquo;t understand the science perfectly, I could contribute some different perspective. In medicine, sometimes not being recognized at all by my attendings was the best outcome. Which happened regularly. My role, was not as a contributor—as it was in science—it was simply to get in the reps. Once I understood that the expectations of me were below the ground, I understood that everything I did in third year was for myself. This is taken at face value by the team at times. I would spend 30 minutes working on a presentation, pre-rounding, the works, and at the end of my part, the intern would nod, then turn to the senior resident and say \u0026ldquo;I was thinking that we\u0026hellip;\u0026rdquo; without thinking of my work. This is perhaps a bit of cognitive restructuring, but recognizing this is what gave me the freedom to embed myself in the hospital flow, without a single worry about the outcome. Simply doing my best was the best thing I could do. Obviously. But this was not apparent to me at first. I needed more quality repetitions to develop good habits in the future. And also experience as much of medicine as possible to find what I want to do with my life. This permission allowed me to approach specialties I do not care about with the awe and respect they deserve.\nA year of wonder. Med school prepares you for the standardized tests. I think this is generally useful. The tests on aggregate are reasonable and evaluate your ability to think through common clinical scenarios. There will always be oddball questions that come out of left field, but I let these flow over me. No need to perseverate on the small stuff. The time for that can come later.\nWhat I didn\u0026rsquo;t realize is how much of the \u0026ldquo;classic\u0026rdquo; material we are fed in the first couple years of med school would come to the forefront. The \u0026ldquo;sandpaper rash\u0026rdquo; of scarlet fever really does feel like sandpaper. Nikolsky\u0026rsquo;s sign actually works. Tripoding for epiglottitis gets the physicians worked up. Don\u0026rsquo;t forget about von Willebrand\u0026rsquo;s disease when someone seems to be bleeding a bit too much. TB is out there, watch for hemoptosis. Night sweats, unintended weight loss, is cancer until proven otherwise. And yes, it really can be lupus.\nIn general, facing the unknown with a sense of earnestness was the way I felt best able to respect those who gathered and passed down the medical knowledge I am privileged to learn today. Sometimes, my excitement to see aspects of medicine would rouse a curious response from the residents. I project here, but I felt a sense of surprise, like that of a doting parent seeing their child experience something new, after forgetting the astonishment they once felt.\nEarnestness is next to med studentlyness.\nPerhaps what I\u0026rsquo;m getting at here is that I found it important to bask in the privilege of seeing the pathology I encountered in med school, and to remind the residents of this sensation. I felt childish at times—and perhaps overanimated—but I found this excitement was to my and my resident\u0026rsquo;s benefit.\nMy surgery rotation overflowed with examples of wonder of medicine. Partially because of the team I worked with, and the rest because of the undeniable coolness of surgery. The OR is a cool place. The orderliness and chaos ebb. The spans of steady, industrious work are interrupted with staccato notes of bedlam. The anatomy I learned in class was ever present, but the surgeons bemoaned \u0026ldquo;normal anatomic variation\u0026rdquo;.\nI was struck with wonder at the sight of human anatomy as it unfolded before me. What I was able to experience in the OR felt like the culmination of centuries of human curiosity. There is an ancientness to medicine that I catch flashes of—I could perform the physical exam on humans hundred of millions of years ago and interrogate the same pathologies as I do in the hospital today—and viewing the exposed anatomy is a pressure-bagged infusion of this collective wonder. To gaze upon the peristalsing of the small intestine, or steady beating of the heart is a sight to behold, indeed.\nA year of shame. It weighs upon me the circumstances that resulted in these transcendent experiences. Not one patient was in the hospital without reason. What to make of these patients with horrible pathology? I still feel unsettled about how the cause of their pain sparked wonder. How dare I gain, merely by the circumstance of having their care managed at UNC, Which, as a tertiary care center, layers on more complexity. Many patients end up at UNC because they have no where else they can go for help. And this signs them up for med students? For shame. from the very essence of their malady? I do not know what to do with my discomfort, but I think it is best that I dwell in it. With this, I respect the people before me in the hospital and recognize their humanity.\nBut I often complained of what I say here I was lucky to do. I find myself resentful of my future schedule; when was I supposed to learn that I will be working 13 hour days, 6 days a week for the rest of my life? And what of having a family? Medicine by necessity requires sacrifice. I happened to sign up for sacrifices years before I recognized how profound they were. How might I balance this dread and with the joy of practicing medicine? And why do I seem more concerned about this than others? Am I not grateful enough? Am I not capable of the sacrifices that others seem to offer so effortlessly? I don\u0026rsquo;t necessarily think this to be true, but these questions erode at my will to pursue medicine.\nPerhaps most shameful of all is how my understanding of the patient-provider interaction evolved over the year. It began as an exploration of an open book, a tabula rasa that held within it a diagnosis and how to best intervene. On my first day in the outpatient clinic, it was clear that this is not the case. My preceptor had only 20 minutes for me to ① interview the patient and perform the physical exam, ② present with a plan, ③ return to the room and do everything again, ④ write orders, educate, and get the patient out of the door. It simply is not amenable to the free form, personable, curious interview I hoped to perform. By the end of the year, I had optimized how I asked questions to keep patients from going off the rails. When prerounding in medicine, I was there to extract information and not much else. Small talk had to go, there was no time. I like to chat, so this came at a loss of who I think I am. I am not sure how to do this well, while still feeling like Zachary. And from what I gather from the interns, that may just come later in my career. I found myself questioning, \u0026ldquo;Is this the \u0026lsquo;patient interaction\u0026rsquo; that has been mythologized throughout my training?\u0026rdquo; The carrot at the end of the stick dangled before me with a \u0026ldquo;You are so lucky to be able to do this, so you had better not complain of any abuse that comes your way.\u0026rdquo; It wasn\u0026rsquo;t a genuine interaction as much as me leading the patient along to tell me what I wanted to know. Of course, I used open ended questions, but only open enough. Leave the door a bit too open and next thing you know, you are talking about their dog\u0026rsquo;s breeder while you constantly stare at your watch, imagining what your attending will say when you return. I feel like I am alone in missing the core human element that funnels sprightly youths into medicine. Or worse, finding it a façade.\nThe shame extends beyond the hospital. One aspect of my life that has changed most dramatically is the sheer amount of time I felt I needed to dedicate to medicine, whether at the hospital or at home. I spent all day basking in the wonder of medicine, then I would come home and study for hours. I relied on my partner for keeping our household together more than ever, because I spent all day—all year, rather—in a state of discovery. Her life was largely the same, with the normal challenges of being a scientist, with the added bonus of getting less help from me. The shame built over the year. Again, how dare I?\nA year of glad. This has been an undeniable year of growth and joy, with these quibbles. It is clear that I was happier than I was during grad school. I know this from within myself, and reinforced by my wife\u0026rsquo;s comments on my mood. The pace of the day, and immediacy of problem solving were a welcome change.\nI recall, during the very first days preparing for med school during xTAP, having to do a simulated patient encounter complete with patient presentation to an attending physician. We were told about this encounter days in advance. And yet, I dreaded it. And near the last day of my final rotation, I did 8 of these in a row without breaking a sweat. Progress!\nI think, in a word, what I\u0026rsquo;ve experienced in the third year of med school is gratitude. Gratitude to be privileged to learn what I am learning. Gratitude for the experiences in my life that brought me here. Gratitude for the support from my wife. Gratitude to be involved in people\u0026rsquo;s lives when they are fragile. Ever since reading Braiding Sweetgrass I think one could call me \u0026ldquo;gratitude-pilled\u0026rdquo;. I also selfishly enjoyed the gratitude from patients as I put on my best doctor performance. In reflection on the year, I have spent time thinking of a phrase that I heard a number of times throughout med school from residents, \u0026ldquo;The worst day of residency is better than the best day of med school.\u0026rdquo; I find this hard to believe. This year has been magical. It is hard to imagine a year filled with more wonder and joy of caring for those in need. I will have to rely on the experience of those who have walked this path and trust that the rest of my training has plenty of magic to spare.\n","permalink":"https://www.zacharybillman.com/posts/ms3-year-is-magical/","summary":"\u003ch2 id=\"it-s-over-dot\"\u003eIt\u0026rsquo;s over.\u003c/h2\u003e\n\u003cp\u003eMy third year of medical school is officially behind me. I managed to get in a grand total of \u003cem\u003ezero\u003c/em\u003e blog posts during grad school, so here\u0026rsquo;s to a new year with hopefully some more thoughts being shared. I have a lot to reflect on from the past year. It was wonderful. I wish everyone could experience what I did this past year. I think it goes without saying:\u003c/p\u003e","title":"The third year of medical school is magical."},{"content":"I, like many others, picked up a new hobby during the pandemic. Other people\u0026rsquo;s hobbies may bring them joy. This could be for many reasons. There is the joy of creating something from scratch. You can revel in your thriftiness. You can embrace the pride when you recognize that your creation is on par (or better!) than what you can buy. I feel like these are embodied in the sourdough craze that caught fire early on in COVID. Dare I say that I did this before it was cool? \u0026#x1f60e; I baked two loaves of bread almost every weekend through med school. Maybe I should bring that back, it\u0026rsquo;s been a while since I brought out the ole\u0026rsquo; starter. My pandemic hobby is similar, but different in that it often feels like a chore, costs more money, and often turns out worse than what I can buy. Of course, I am talking about how I\u0026rsquo;ve started roasting my own coffee at home.\nI\u0026rsquo;m not sure where this idea was planted into my brain. I don\u0026rsquo;t think I know anyone who roasts their own beans, and I certainly didn\u0026rsquo;t know how. I didn\u0026rsquo;t even drink coffee regularly until after college! I guess that extra time on the computer sent me down a rabbithole I have yet to emerge from.\nFirst, I want to preface the following with a disclaimer: This is not a detailed guide about how to roast your own coffee. If you are interested, I recommend checking out the How To Roast Your Own Coffee guide at Sweet Maria\u0026rsquo;s as a starting point. There is also the /r/roasting subreddit if that is your cup of tea. My only warning is there will be a lot of smoke. Roast your coffee outside, for Pete\u0026rsquo;s sake!\nIt all started with a trusty popcorn popper. There are a few things you want when you roast coffee:\nAir hot enough to roast coffee Remove the chaff from the beans Turns out that a classic popcorn popper fits the bill, as long as it has an upwards airflow and doesn\u0026rsquo;t let the chaff fall into the heating element. There is a bit of a cult following for the West Bend Poppery 2 model, but that one seemed a bit pricey, so I settled for a very capable popper from Nostalgia.\nFigure 1: I got a good bit of mileage out of my popcorn popper. If you are interested in roasting your own coffee I would give it a whirl.\nThings were simple back then. I still bought most of the coffee I drank, but I roasted enough to enjoy some freshly roasted coffee as an occasional treat. I ordered 10 pounds of green beans from Sweet Maria\u0026rsquo;s and life was good.\nThen I became a bit of a coffee snob.\nI could only roast 100 grams of coffee at a time in the popcorn popper, which is only enough for one pot of coffee in the morning for me. So it was time to upgrade.\nI bought the SR800 fluid bed roaster, which upped my roasting capacity and gave me finer control on temperature and airflow. Suffice to say my roasts improved a lot! At this point, I would consider my coffee good enough to sell at a farmer\u0026rsquo;s market to break even.\nIf you ever find yourself on a coffee roasting forum and bring up the SR800, someone is bound to bring up the famous RazzoRoasting extension tube. If you look for advice for how to use the SR800, I swear it\u0026rsquo;s assumed that you have this very specific accessory. \u0026hellip;And so I bought one.\nDon\u0026rsquo;t worry, that is the extent of all of my coffee spending (for now). I am a very satisfied coffee roaster now. Check out this quick series of images going from the green beans to a nearly finished product! I can spend about 45 minutes and go from nothing to nearly 2 pounds of roasted beans, enough for about a week and a half of coffee. Not bad! The only downside is that now I feel like I need to buy coffee from local roasters to get my fix. There are certainly crueler fates.\nAs a sign off, I will share something that surprised me about coffee roasting. When I roast coffee, the most important cue to determine if the coffee is roasted is the sound. That\u0026rsquo;s right, not the color, not the smell, but the sound. When heating up a coffee bean, the water trapped inside eventually bursts out of the bean in a rapid expansion. This is called \u0026ldquo;first crack\u0026rdquo;, and indicates that the coffee is roasted enough to be drinkable. The expansion also releases the chaff from the bean. If you continue heating up the bean, you will eventually reach \u0026ldquo;second crack\u0026rdquo;. I think a solid medium roast is taken out just before second crack, so I try to take my coffee out to this point and it hasn\u0026rsquo;t proved me wrong yet.\nHappy coffee-ing! \u0026#x2615;\n","permalink":"https://www.zacharybillman.com/posts/roasting-coffee-at-home/","summary":"\u003cp\u003eI, like many others, picked up a new hobby during the pandemic. Other people\u0026rsquo;s hobbies may bring them joy. This could be for many reasons. There is the joy of creating something from scratch. You can revel in your thriftiness. You can embrace the pride when you recognize that your creation is on par (or better!) than what you can buy. I feel like these are embodied in the sourdough craze that caught fire early on in COVID.\n\u003cspan class=\"sidenote-number\"\u003e\u003csmall class=\"sidenote\"\u003e\nDare I say that I did this before it was cool? \u0026#x1f60e; I baked two loaves of bread almost every weekend through med school. Maybe I should bring that back, it\u0026rsquo;s been a while since I brought out the ole\u0026rsquo; starter.\n\u003c/small\u003e\u003c/span\u003e\nMy pandemic hobby is similar, but different in that it often feels like a chore, costs more money, and often turns out worse than what I can buy. Of course, I am talking about how I\u0026rsquo;ve started roasting my own coffee at home.\u003c/p\u003e","title":"Roasting coffee at home. ☕"},{"content":"It is an age-old question: how can one keep up with the continuous output of science? I remember at the beginning of my PhD struggling to figure out how anyone found out when a new paper came out. \u0026#x1f635; Did they sit on nature.com and spam the refresh button? Did they know when each journal released their latest issue?\nBehold the power of RSS! Most websites have a page that contains information about each subpage in a computer-readable format called RSS (Really Simple Syndication). Mine has one right here! These pages can be parsed by a number of RSS feed aggregators. The way these pages are set up make it such that they add any new information hosted at that domain. This is useful in the science world because you can find the RSS feed of a given journal, subscribe to it, then have every new article published online be delivered right to you.\nThere are a plethora of RSS feed aggregators you can pick from manage your feeds. I have previously used Feedly and Inoreader, which are great free solutions, but have moved on to selfhosting my own instance of FreshRSS.\nAfter making an account at your friendly local RSS feed aggregator, you can add whatever feeds your heart desires. To find a journal\u0026rsquo;s rss feed, I often just search \u0026ldquo;$JOURNAL_NAME rss feed\u0026rdquo; and poke around until I find something that looks right. Most of the aggregators will test the feed out first to make sure that you are trying to add a legitimate one. Here are a few of the heavy hitters to get you started:\nhttp://feeds.nature.com/nature/rss/current https://www.science.org/rss/express.xml https://www.cell.com/cell/inpress.rss Nothing like a constant stream of Cell, Science, and Nature to make your project feel like a real winner, eh?\nHere is what my own site looks like.\nFigure 1: My current FreshRSS setup. On the left I have my feeds separated into folders. In the middle you can see the titles of papers that appear in my feed.\nAnd after I hit J to move to the first item in the feed.\nFigure 2: With a title selected, you can see the abstract and authors.\nAfter collecting all of your desired RSS feeds, you cannot forego your responsibility of actually reading them! Most RSS feed aggregators have shortcuts to move through titles quickly (Typically J to move on to the next one and K to move up.) They always seem to use vi keybindings. A bunch of computer nerds have really cornered the keybinding market. I have let them take over my computing life. Each morning when I get into the lab, I quickly set up something, then head to my desk to hit J until the counter reaches zero.\nBut what about my very specific field? You can subscribe to all of the journals you want, but that doesn\u0026rsquo;t make the papers with your specific interests pop out. Fortunately, the NIH has this exact circumstance in mind.\nWhen you make a new search on PubMed you might notice the \u0026ldquo;Create RSS\u0026rdquo; button. Give it a click, then you will have a personal link you can add to your favorite RSS feed aggregator.\nFigure 3: Somehow I never noticed this button until I needed it.\nThis changed the game for me for keeping up with papers. Unfortunately, it doesn\u0026rsquo;t solve the problem of library management, or actually getting around to reading the papers you care about. I will leave library management as an exercise for the interested reader. Here\u0026rsquo;s a tip, the best solution uses the Zotero citation manager. Bonus points for using Zotfile for renaming your PDFs and Better BibTex for Zotero. \u0026#x1f609; I hope this helps you get your eyeballs on that science you crave. If you have solved the problem of accruing papers to read faster than you read them, let me know.\n","permalink":"https://www.zacharybillman.com/posts/rss-feeds-to-find-science-papers/","summary":"\u003cp\u003eIt is an age-old question: how can one keep up with the continuous output of science? I remember at the beginning of my PhD struggling to figure out how anyone found out when a new paper came out. \u0026#x1f635; Did they sit on nature.com and spam the refresh button? Did they know when each journal released their latest issue?\u003c/p\u003e\n\u003ch2 id=\"behold-the-power-of-rss\"\u003eBehold the power of RSS!\u003c/h2\u003e\n\u003cp\u003eMost websites have a page that contains information about each subpage in a computer-readable format called RSS (Really Simple Syndication). \u003ca href=\"https://zacharybillman.com/index.xml\"\u003eMine has one right here!\u003c/a\u003e These pages can be parsed by a number of RSS feed aggregators. The way these pages are set up make it such that they add any new information hosted at that domain. This is useful in the science world because you can find the RSS feed of a given journal, subscribe to it, then have every new article published online be delivered right to you.\u003c/p\u003e","title":"Using RSS feeds to keep on top of science."},{"content":"My interest in self-hosting began in my with my interests in internet privacy. Plastered all over the internet are stories about how much Google, Facebook and Amazon know about you. I deleted my Facebook account years ago, and I\u0026rsquo;m too paranoid to go back to the site because there\u0026rsquo;s a real possibility that Facebook has cached my account, ready to spin it back up in case I try to login again. The ads served to me were too accurate for my liking. This is despite almost never clicking on them! I have become convinced of the idea that, if you are not paying for the product, you are the product. From this assumption, it follows that anywhere I trust with my data that I am not paying for (like Google Drive, Google Photos, Dropbox, Facebook, Twitter) is using my data to earn money. We know that Google uses the labels you add to Photos to train it\u0026rsquo;s AI, and Facebook uses (at least) Instagram photos to train it\u0026rsquo;s AI. For some, the value proposition of allowing a company to use your data for a useful service in return is an acceptable one. I find this to be a reasonable stance, but I took my growing interest in internet privacy as a chance to learn about how I can take control of my data.\nInitially, I lurked on forums like /r/privacy to learn what I could do to avoid big-tech\u0026rsquo;s watchful eye. There were numerous comments along the lines of: \u0026ldquo;The only way to be in control of your data is to self-host your services.\u0026rdquo; I had no idea what this meant! Hard to believe that less than a year later, I learned to use (and love) Linux as my primary OS, and have happily replaced Google Photos, Google Drive and other services with my own self-hosted alternatives. Self-hosting, I have since learned, is when you run useful programs from your own computer. By doing so, you have complete knowledge of where and how your data is stored and how it is being used. It has the additional effect of being a bottomless time sink.\nTo begin, I needed an always-on computer to run these useful programs. I began with a humble Raspberry Pi.\nFigure 1: My humble Raspberry Pi and its hard drive. This dude currently tirelessly runs the excellent Adguard Home and downloads a backup of my data every night.\nThese are tiny, but capable computers that are great for fiddling with. The projects people develop for these are amazing and diverse. With RPi in hand, I began with the ambitious project of replacing Google Drive with Nextcloud. After much frustration with a bare metal installation, I found the NextcloudPi project. Surprisingly, it went pretty okay! At first, I was intimidated by Linux defaults, but over time I grew to appreciate, and indeed, prefer Linux as an operating system. My decision to use Linux over Windows/MacOS is because it is free and open source software (FOSS). This is a topic for a different post, but I think using FOSS when possible is a moral imperative of sorts. I used Nextcloud strictly from my home for a few months, without the ability to connect to it from the internet, to test the self-hosting waters. My first true cloud replacement spun up once I decided to access this lil\u0026rsquo; guy from the internet. To do so, I purchased a domain (not the one this site is hosted on) and pointed it to the IP of my house. I forwarded the appropriate ports of my router to the RPi.\nThis is when the real exploration began. I was able to access my files and images using Nextcloud, but the photo viewing service left something to be desired. No problem, why not spin up an instance of Photoprism? I use RSS feeds to keep on top of the latest science in the journals relevant to my field using Feedly. Why not host my own RSS feed aggregator so I can subscribe to as many feeds as I desire?\nThis cycle continued, and I accrued many cool applications, but in the back of my mind I worried about opening up my home network to the internet. I also struggled to run some programs because the RPi uses the arm64 architecture, and most services are written with amd64 in mind. These two forces eventually convinced me to purchase a server where I could manage all of my services remotely. Some would say that not owning the hardware that is running your own services is not \u0026ldquo;true\u0026rdquo; self-hosting. I think this is needlessly exclusive. Let everyone self host, dangit! Someday, when I have more stable internet and a more permanent home, I hope to host everything from my own home, but until then, I\u0026rsquo;m extremely pleased with my current stack. And that is where I am now. I happily host numerous services on my virtual private server that entirely replace Google Photos, Google Drive and GitHub for me. Even better, there are specialized services that fill a need I never realized I had. What\u0026rsquo;s more, if I ever want to spin up a new service, all I have to do is add it to my to docker-compose file and it will be up within minutes. What a world!\nI thought about making this into a \u0026ldquo;guide\u0026rdquo; style post. I nixed that idea because, quite frankly, I feel like I don\u0026rsquo;t know what I\u0026rsquo;m doing. I am really happy with my setup, but I don\u0026rsquo;t feel like I have the authority to tell people how to administer their own services. If you are interested, allow me to point you toward the guide that really got me rolling: Ultimate Traefik Docker Compose Guide.\nFor those of you wondering what I am currently hosting, check out my current list at the link and let me know what you think!\n","permalink":"https://www.zacharybillman.com/posts/my-selfhosting-journey/","summary":"\u003cp\u003eMy interest in self-hosting began in my with my interests in internet privacy. Plastered all over the internet are stories about how much Google, Facebook and Amazon know about you. I deleted my Facebook account years ago, and I\u0026rsquo;m too paranoid to go back to the site because there\u0026rsquo;s \u003ca href=\"https://www.reddit.com/r/privacy/comments/6nmjfh/facebook_account_fully_recovered_3_years_after/\"\u003ea real possibility that Facebook has cached my account, ready to spin it back up\u003c/a\u003e in case I try to login again. The ads served to me were too accurate for my liking.\n\u003cspan class=\"sidenote-number\"\u003e\u003csmall class=\"sidenote\"\u003e\nThis is despite almost never clicking on them!\n\u003c/small\u003e\u003c/span\u003e\nI have become convinced of the idea that, if you are not paying for the product, you are the product. From this assumption, it follows that anywhere I trust with my data that I am not paying for (like Google Drive, Google Photos, Dropbox, Facebook, Twitter) is using my data to earn money. We know that \u003ca href=\"https://www.theverge.com/2020/11/11/21559930/google-train-ai-photos-image-labelling-app-android-update\"\u003eGoogle uses the labels you add to Photos to train it\u0026rsquo;s AI\u003c/a\u003e, and \u003ca href=\"https://ai.facebook.com/blog/seer-the-start-of-a-more-powerful-flexible-and-accessible-era-for-computer-vision/\"\u003eFacebook uses (at least) Instagram photos to train it\u0026rsquo;s AI\u003c/a\u003e. For some, the value proposition of allowing a company to use your data for a useful service in return is an acceptable one. I find this to be a reasonable stance, but I took my growing interest in internet privacy as a chance to learn about how I can take control of my data.\u003c/p\u003e","title":"My selfhosting journey."},{"content":"N.B.: I hope to add screenshots for each of these eventually. For now, I hope links to each services\u0026rsquo; website will suffice.\nSeafile\nThis is a great tool for managing files. I moved to this from Nextcloud because I am of the philosophy that I would prefer services that do one thing excellently instead of many things well. Nextcloud is an incredible Office365 replacement, but I found myself using a fraction of what it was capable of providing. Enter Seafile. It is cloud file syncing with a robust encryption implementation, just what the doctor ordered.\nPhotoprism\nNextcloud\u0026rsquo;s implementation of photo management was a bit clumsy for my tastes, so I began on a hunt for a more feature complete option. I was very lucky to stumble upon Photoprism early on in my self hosting journey. I am a proud supporter of this project. It brings a ton to the table, and doesn\u0026rsquo;t leave me missing Google Photos one bit. It is also actively developed. For instance, as of 2022-07-02, there was a recent update that improved scrolling a ton, which was one of my remaining quibbles with it\u0026rsquo;s functionality. Some people complain that it doesn\u0026rsquo;t scale up for libraries of 10,000+ photos, but my 2000 photo library works swimmingly. On my phone, I use the Folder Sync app to automatically send any pictures I take on my phone to the Photoprism imports folder. Within 15 minutes of snapping a photo, it is there on my Photoprism instance. I highly recommend giving it a go.\nMealie\nI have to admit that the name leaves something to be desired. Fortunately, the service itself doesn\u0026rsquo;t fall short. Mealie is a recipe management application. It is able to parse your favorite recipe websites to create immortalized versions of the recipe. This helps fight detestable link rot that plagues the internet. It allows you to edit ingredient amounts, make comments about what you would change next time, and plan out your weekly meals. It helps that it is beautiful and intuitive to use. If only I could get my partner to use it\u0026hellip; I want to go on the record here and say that I think it is sensible that she doesn\u0026rsquo;t trust my self hosted services that much. In the early days of my self hosting journey, let\u0026rsquo;s just say that the up-time of my services were extremely finicky. I like to think they are more permanent now, especially because I am hosting everything on a VPS, but I certainly cannot compete with the stability of Google and Amazon. (Or pretty much any other paid service for that matter.) \u0026#x1f609;\nGitea\nGitea is a community managed, lightweight code hosting solution written in Go. I use it to manage my data analysis (using Private repos) and even host the source code for this very website! Using Gitea has given me the surface level introduction to the behemoth that is git. Fortunately, that is all I need. Once I have removed any sensitive data (like passwords, etc.) I will make my docker-compose file public. The docker-compose file is where I determine which services I pick to host, and how to configure them to my liking. Hopefully someone will find this useful.\nSyncthing\nIf I could only tell someone to self host a single service, I would have to pick Syncthing. It is a continuous file synchronization program, which means it keeps a specific file or folder the same between any device running Syncthing. I use it to keep my password database and my org-mode notes Now org-mode might be the biggest rabbithole of them all, and definitely the topic for another blog post. I use it to manage my TODO list, my lab notebook, my shopping lists, write this blog, and maintain my Zettelkasten note database. It is an immensely powerful tool. up to date between all of my devices. With Syncthing, all of my data is stored on my own devices and encrypted in transit.\nFreshRSS\nI keep up to date on the science in my field by subscribing to relevant RSS feeds. Yet another topic to write a post about. This really changed the game for my ability to keep on top of the latest research. 2022-07-14 Update: post complete! Check it out here. FreshRSS replaced Feedly for me, as I ran up against the number of feeds I could subscribe to on a free account. Also, when self hosting, I can save as many articles as my heart desires (even if I will never look at them again \u0026#x1f635; ).\nWallabag\nRemember Pocket for Firefox? (Yes, I know it still exists, okay?) Give Wallabag a spin, it is great for storing articles you want to read later. I set up FreshRSS to save articles to my Wallabag instance to keep for later.\nChangeDetection\nNow this is a fun one! ChangeDetection.io is a service that loads a webpage and checks to see if something has changed since the last time. This might not sound useful at first, but I recently used this to check for when a hot item for my new coffee roasting hobby was back in stock. I got an email the other day to let me know it was in stock. Pretty cool!\nHugo\nHugo is the static site generator I use to make this here blog! I was amazed at how much more response my site was using Hugo compare to when I paid a company to host a WordPress site. I\u0026rsquo;m sure WordPress could be fast, but I just wanted a barebones, pure html experience, and Hugo made it easy.\nCommento++\nYou may have noticed that I have some pretty snazzy comments sections on my site. I initially used Disqus, which you may recognize from a ton of sites around the internet, but didn\u0026rsquo;t like how it would serve ads through my comments section, and provided sign-ins using Google/Facebook/Twitter. I wanted to serve the simplest comments section I could, that still gave me the ability to migrate the comments to wherever I decide to keep my server. Go ahead and use the anonymous comment button, fill in your name, and you are off to the races.\nAuthelia\nThere are a few services I host that I really want to lock down. For these services, Authelia is great. It puts up a \u0026ldquo;Enter the 6 digit code on your phone\u0026rdquo; style 2 factor authentication in front of the services I choose. Or, if you follow the guide here, you can have it send you a DUO push, just like you are one of the big hitters out there. I feel much more secure with Authelia in front of Adminer, Traefik, and Portainer.\nBoring stuff that allows everything else to work!\nPostgreSQL database MariaDB database Traefik reverse proxy Umami privacy respecting site analytics Portainer for docker container management Redis in-memory data store Adminer database management traefik-socket-proxy to prevent pesky backdoors to my server! ","permalink":"https://www.zacharybillman.com/posts/zpb-current-selfhosted/","summary":"\u003cp\u003e\u003cem\u003eN.B.: I hope to add screenshots for each of these eventually. For now, I hope links to each services\u0026rsquo; website will suffice.\u003c/em\u003e\u003c/p\u003e\n\u003col\u003e\n\u003cli\u003e\n\u003cp\u003e\u003ca href=\"https://www.seafile.com/en/home/\"\u003eSeafile\u003c/a\u003e\u003c/p\u003e\n\u003cp\u003eThis is a great tool for managing files. I moved to this from Nextcloud because I am of the philosophy that I would prefer services that do one thing excellently instead of many things well. Nextcloud is an incredible Office365 replacement, but I found myself using a fraction of what it was capable of providing. Enter Seafile. It is cloud file syncing with a robust encryption implementation, just what the doctor ordered.\u003c/p\u003e","title":"What I'm currently selfhosting."},{"content":"My partner and I took a trip to the Mason Farm Biological Reserve the other day, and what a glorious day it was. This year, I\u0026rsquo;ve been quite busy in the lab, and missed a lot of the early spring warbler season, so I was very excited by the opportunity to check out the old stomping grounds.\nI brought the camera with me despite the fact we were going to be there around midday when the birds are much less active. I\u0026rsquo;m glad I did, because I got the best look at a common yellowthroat I\u0026rsquo;ve ever had. Normally these guys are flighty, staying close to the ground in small brush or tall grasses, but this one was putting on a proper show for the mating season. Even when you get a glimpse of one, it is usually just that, as they have jumped away before you can pull out the camera, taunting you with their iconic call. I was very pleased to capture a few choice shots of the bird. Hopefully there are more to come. While we were out, I also got a nice picture of a hermit thrush and a king snake.\nThese images have been compressed quite a bit for a lighter internet footprint. These have all been resized to 25% of their original size. If you would like the full sized images, let me know and I will send you a link!\n","permalink":"https://www.zacharybillman.com/posts/the-uncommon-yellowthroat/","summary":"\u003cp\u003eMy partner and I took a trip to the \u003ca href=\"https://ncbg.unc.edu/visit/mason-farm-biological-reserve/\"\u003eMason Farm Biological Reserve\u003c/a\u003e the other day, and what a glorious day it was. This year, I\u0026rsquo;ve been quite busy in the lab, and missed a lot of the early spring warbler season, so I was very excited by the opportunity to check out the old stomping grounds.\u003c/p\u003e\n\u003cp\u003eI brought the camera with me despite the fact we were going to be there around midday when the birds are much less active. I\u0026rsquo;m glad I did, because I got the best look at a common yellowthroat I\u0026rsquo;ve ever had.\n\u003cspan class=\"sidenote-number\"\u003e\u003csmall class=\"sidenote\"\u003e\nNormally these guys are flighty, staying close to the ground in small brush or tall grasses, but this one was putting on a proper show for the mating season. Even when you get a glimpse of one, it is usually just that, as they have jumped away before you can pull out the camera, taunting you with their \u003ca href=\"https://ebird.org/species/comyel#Modal-playlist\"\u003eiconic call\u003c/a\u003e.\n\u003c/small\u003e\u003c/span\u003e\nI was very pleased to capture a few choice shots of the bird. Hopefully there are more to come. While we were out, I also got a nice picture of a hermit thrush and a king snake.\u003c/p\u003e","title":"The (un)common yellowthroat."},{"content":"It\u0026rsquo;s over. My third year of medical school is officially behind me. I managed to get in a grand total of zero blog posts during grad school, so here\u0026rsquo;s to a new year with hopefully some more thoughts being shared. I have a lot to reflect on from the past year. It was wonderful. I wish everyone could experience what I did this past year. I think it goes without saying:\nI loved the third year of med school, but I do not want to do it again.\nA year of change. In the days leading up to my return to med school, I thought \u0026ldquo;Oh no, I really enjoy doing science, do I really have to go to med school?\u0026rdquo;. I also remember at the end of Step 1 and the first two years of med school thinking, \u0026ldquo;Oh no, I really enjoy med school, do I really have to do science again?\u0026rdquo;. I think I have a welcome problem of enjoying what I\u0026rsquo;m doing. The third year of med school is a shift. After years of memorizing and examinations, the doors to the promised land are finally opened. I have experienced nothing like it before It feels intentionally unsettling. You are thrown into the clinic with a modicum of guidance so you aren\u0026rsquo;t totally caught off guard, but you are thrown out to the wolves. I don\u0026rsquo;t mean this as a criticism of the system, it feels necessary. Third year medical students—commonly shorted to MS3s—have just one year to experience a broad swath of medicine and pick a specialty. So you had better be ready to dive in.\nTotal immersion I came to terms with my new reality quickly. Gone were the days of hitting the snooze button and going home when I pleased. I am now beholden to other people\u0026rsquo;s schedules. This came back relatively naturally. Maybe not hitting snooze. A regrettable personal failing of mine. I was, however, immediately faced with a new reality in the patient room. Patients come to the doctor for a number of reasons, but often seek relief. To get to the core of what ails them, they will tell you everything. I was not prepared for how vulnerable patients would be with me. I am not sure if this ever will feel natural. I hope it never does. I was told many stories of experiences living with scary diagnoses, and not knowing what to do with it. Family histories of all sorts. Personal details that were sometimes (oftentimes?) off the wall. I see all of these specifics as flailing, grasping at sand hoping that something could explain their pain. Sometimes it could. Usually it did not. But since I was in a white coat, I was privileged to hear it.\nI think my years spent in the lab have prepared me to face some of the challenges set before me. At the very least, having a few more years under my belt helped me approach the year with a bit of maturity. This seems to have paid off. I guess my recommendation is to simply get old before going to med school. Returning to studying The hospital is how I spent the majority of my time, but a new reality for me was also going back to daily studying. There is a strange dichotomy in medicine of \u0026ldquo;Oh, it doesn\u0026rsquo;t really matter\u0026rdquo; and \u0026ldquo;If you don\u0026rsquo;t get this class/score/grade then you won\u0026rsquo;t be able to be the kind of doctor you want to be, so you had better get your act together.\u0026rdquo; Simultaneously there are no expectations and immense responsibility for the looming specter of Step 2. I\u0026rsquo;m glad that studying regularly came back easily enough. I was concerned I would experience a studying whiplash. I\u0026rsquo;m glad it never came. I did UWorld and Anki nearly every day for a full year and felt alright.\nBecoming invisible I quickly learned I needed to change my understanding of my contribution to the team. Exiting grad school, people understood that they could come to me for help. I was a resource, a seasoned veteran of the lab. If someone needed an experiment done, I could do it, and be trusted to do it. In med school as a third year, I was nothing. A fly on the wall; a worm beneath the feet of the real doctors. In science, I felt like I was treated as a peer with even my committee members with multiple R01s. Even if I didn\u0026rsquo;t understand the science perfectly, I could contribute some different perspective. In medicine, sometimes not being recognized at all by my attendings was the best outcome. Which happened regularly. My role, was not as a contributor—as it was in science—it was simply to get in the reps. Once I understood that the expectations of me were below the ground, I understood that everything I did in third year was for myself. This is taken at face value by the team at times. I would spend 30 minutes working on a presentation, pre-rounding, the works, and at the end of my part, the intern would nod, then turn to the senior resident and say \u0026ldquo;I was thinking that we\u0026hellip;\u0026rdquo; without thinking of my work. This is perhaps a bit of cognitive restructuring, but recognizing this is what gave me the freedom to embed myself in the hospital flow, without a single worry about the outcome. Simply doing my best was the best thing I could do. Obviously. But this was not apparent to me at first. I needed more quality repetitions to develop good habits in the future. And also experience as much of medicine as possible to find what I want to do with my life. This permission allowed me to approach specialties I do not care about with the awe and respect they deserve.\nA year of wonder. Med school prepares you for the standardized tests. I think this is generally useful. The tests on aggregate are reasonable and evaluate your ability to think through common clinical scenarios. There will always be oddball questions that come out of left field, but I let these flow over me. No need to perseverate on the small stuff. The time for that can come later.\nWhat I didn\u0026rsquo;t realize is how much of the \u0026ldquo;classic\u0026rdquo; material we are fed in the first couple years of med school would come to the forefront. The \u0026ldquo;sandpaper rash\u0026rdquo; of scarlet fever really does feel like sandpaper. Nikolsky\u0026rsquo;s sign actually works. Tripoding for epiglottitis gets the physicians worked up. Don\u0026rsquo;t forget about von Willebrand\u0026rsquo;s disease when someone seems to be bleeding a bit too much. TB is out there, watch for hemoptosis. Night sweats, unintended weight loss, is cancer until proven otherwise. And yes, it really can be lupus.\nIn general, facing the unknown with a sense of earnestness was the way I felt best able to respect those who gathered and passed down the medical knowledge I am privileged to learn today. Sometimes, my excitement to see aspects of medicine would rouse a curious response from the residents. I project here, but I felt a sense of surprise, like that of a doting parent seeing their child experience something new, after forgetting the astonishment they once felt.\nEarnestness is next to med studentlyness.\nPerhaps what I\u0026rsquo;m getting at here is that I found it important to bask in the privilege of seeing the pathology I encountered in med school, and to remind the residents of this sensation. I felt childish at times—and perhaps overanimated—but I found this excitement was to my and my resident\u0026rsquo;s benefit.\nMy surgery rotation overflowed with examples of wonder of medicine. Partially because of the team I worked with, and the rest because of the undeniable coolness of surgery. The OR is a cool place. The orderliness and chaos ebb. The spans of steady, industrious work are interrupted with staccato notes of bedlam. The anatomy I learned in class was ever present, but the surgeons bemoaned \u0026ldquo;normal anatomic variation\u0026rdquo;.\nI was struck with wonder at the sight of human anatomy as it unfolded before me. What I was able to experience in the OR felt like the culmination of centuries of human curiosity. There is an ancientness to medicine that I catch flashes of—I could perform the physical exam on humans hundred of millions of years ago and interrogate the same pathologies as I do in the hospital today—and viewing the exposed anatomy is a pressure-bagged infusion of this collective wonder. To gaze upon the peristalsing of the small intestine, or steady beating of the heart is a sight to behold, indeed.\nA year of shame. It weighs upon me the circumstances that resulted in these transcendent experiences. Not one patient was in the hospital without reason. What to make of these patients with horrible pathology? I still feel unsettled about how the cause of their pain sparked wonder. How dare I gain, merely by the circumstance of having their care managed at UNC, Which, as a tertiary care center, layers on more complexity. Many patients end up at UNC because they have no where else they can go for help. And this signs them up for med students? For shame. from the very essence of their malady? I do not know what to do with my discomfort, but I think it is best that I dwell in it. With this, I respect the people before me in the hospital and recognize their humanity.\nBut I often complained of what I say here I was lucky to do. I find myself resentful of my future schedule; when was I supposed to learn that I will be working 13 hour days, 6 days a week for the rest of my life? And what of having a family? Medicine by necessity requires sacrifice. I happened to sign up for sacrifices years before I recognized how profound they were. How might I balance this dread and with the joy of practicing medicine? And why do I seem more concerned about this than others? Am I not grateful enough? Am I not capable of the sacrifices that others seem to offer so effortlessly? I don\u0026rsquo;t necessarily think this to be true, but these questions erode at my will to pursue medicine.\nPerhaps most shameful of all is how my understanding of the patient-provider interaction evolved over the year. It began as an exploration of an open book, a tabula rasa that held within it a diagnosis and how to best intervene. On my first day in the outpatient clinic, it was clear that this is not the case. My preceptor had only 20 minutes for me to ① interview the patient and perform the physical exam, ② present with a plan, ③ return to the room and do everything again, ④ write orders, educate, and get the patient out of the door. It simply is not amenable to the free form, personable, curious interview I hoped to perform. By the end of the year, I had optimized how I asked questions to keep patients from going off the rails. When prerounding in medicine, I was there to extract information and not much else. Small talk had to go, there was no time. I like to chat, so this came at a loss of who I think I am. I am not sure how to do this well, while still feeling like Zachary. And from what I gather from the interns, that may just come later in my career. I found myself questioning, \u0026ldquo;Is this the \u0026lsquo;patient interaction\u0026rsquo; that has been mythologized throughout my training?\u0026rdquo; The carrot at the end of the stick dangled before me with a \u0026ldquo;You are so lucky to be able to do this, so you had better not complain of any abuse that comes your way.\u0026rdquo; It wasn\u0026rsquo;t a genuine interaction as much as me leading the patient along to tell me what I wanted to know. Of course, I used open ended questions, but only open enough. Leave the door a bit too open and next thing you know, you are talking about their dog\u0026rsquo;s breeder while you constantly stare at your watch, imagining what your attending will say when you return. I feel like I am alone in missing the core human element that funnels sprightly youths into medicine. Or worse, finding it a façade.\nThe shame extends beyond the hospital. One aspect of my life that has changed most dramatically is the sheer amount of time I felt I needed to dedicate to medicine, whether at the hospital or at home. I spent all day basking in the wonder of medicine, then I would come home and study for hours. I relied on my partner for keeping our household together more than ever, because I spent all day—all year, rather—in a state of discovery. Her life was largely the same, with the normal challenges of being a scientist, with the added bonus of getting less help from me. The shame built over the year. Again, how dare I?\nA year of glad. This has been an undeniable year of growth and joy, with these quibbles. It is clear that I was happier than I was during grad school. I know this from within myself, and reinforced by my wife\u0026rsquo;s comments on my mood. The pace of the day, and immediacy of problem solving were a welcome change.\nI recall, during the very first days preparing for med school during xTAP, having to do a simulated patient encounter complete with patient presentation to an attending physician. We were told about this encounter days in advance. And yet, I dreaded it. And near the last day of my final rotation, I did 8 of these in a row without breaking a sweat. Progress!\nI think, in a word, what I\u0026rsquo;ve experienced in the third year of med school is gratitude. Gratitude to be privileged to learn what I am learning. Gratitude for the experiences in my life that brought me here. Gratitude for the support from my wife. Gratitude to be involved in people\u0026rsquo;s lives when they are fragile. Ever since reading Braiding Sweetgrass I think one could call me \u0026ldquo;gratitude-pilled\u0026rdquo;. I also selfishly enjoyed the gratitude from patients as I put on my best doctor performance. In reflection on the year, I have spent time thinking of a phrase that I heard a number of times throughout med school from residents, \u0026ldquo;The worst day of residency is better than the best day of med school.\u0026rdquo; I find this hard to believe. This year has been magical. It is hard to imagine a year filled with more wonder and joy of caring for those in need. I will have to rely on the experience of those who have walked this path and trust that the rest of my training has plenty of magic to spare.\n","permalink":"https://www.zacharybillman.com/posts/ms3-year-is-magical/","summary":"\u003ch2 id=\"it-s-over-dot\"\u003eIt\u0026rsquo;s over.\u003c/h2\u003e\n\u003cp\u003eMy third year of medical school is officially behind me. I managed to get in a grand total of \u003cem\u003ezero\u003c/em\u003e blog posts during grad school, so here\u0026rsquo;s to a new year with hopefully some more thoughts being shared. I have a lot to reflect on from the past year. It was wonderful. I wish everyone could experience what I did this past year. I think it goes without saying:\u003c/p\u003e","title":"The third year of medical school is magical."},{"content":"I, like many others, picked up a new hobby during the pandemic. Other people\u0026rsquo;s hobbies may bring them joy. This could be for many reasons. There is the joy of creating something from scratch. You can revel in your thriftiness. You can embrace the pride when you recognize that your creation is on par (or better!) than what you can buy. I feel like these are embodied in the sourdough craze that caught fire early on in COVID. Dare I say that I did this before it was cool? \u0026#x1f60e; I baked two loaves of bread almost every weekend through med school. Maybe I should bring that back, it\u0026rsquo;s been a while since I brought out the ole\u0026rsquo; starter. My pandemic hobby is similar, but different in that it often feels like a chore, costs more money, and often turns out worse than what I can buy. Of course, I am talking about how I\u0026rsquo;ve started roasting my own coffee at home.\nI\u0026rsquo;m not sure where this idea was planted into my brain. I don\u0026rsquo;t think I know anyone who roasts their own beans, and I certainly didn\u0026rsquo;t know how. I didn\u0026rsquo;t even drink coffee regularly until after college! I guess that extra time on the computer sent me down a rabbithole I have yet to emerge from.\nFirst, I want to preface the following with a disclaimer: This is not a detailed guide about how to roast your own coffee. If you are interested, I recommend checking out the How To Roast Your Own Coffee guide at Sweet Maria\u0026rsquo;s as a starting point. There is also the /r/roasting subreddit if that is your cup of tea. My only warning is there will be a lot of smoke. Roast your coffee outside, for Pete\u0026rsquo;s sake!\nIt all started with a trusty popcorn popper. There are a few things you want when you roast coffee:\nAir hot enough to roast coffee Remove the chaff from the beans Turns out that a classic popcorn popper fits the bill, as long as it has an upwards airflow and doesn\u0026rsquo;t let the chaff fall into the heating element. There is a bit of a cult following for the West Bend Poppery 2 model, but that one seemed a bit pricey, so I settled for a very capable popper from Nostalgia.\nFigure 1: I got a good bit of mileage out of my popcorn popper. If you are interested in roasting your own coffee I would give it a whirl.\nThings were simple back then. I still bought most of the coffee I drank, but I roasted enough to enjoy some freshly roasted coffee as an occasional treat. I ordered 10 pounds of green beans from Sweet Maria\u0026rsquo;s and life was good.\nThen I became a bit of a coffee snob.\nI could only roast 100 grams of coffee at a time in the popcorn popper, which is only enough for one pot of coffee in the morning for me. So it was time to upgrade.\nI bought the SR800 fluid bed roaster, which upped my roasting capacity and gave me finer control on temperature and airflow. Suffice to say my roasts improved a lot! At this point, I would consider my coffee good enough to sell at a farmer\u0026rsquo;s market to break even.\nIf you ever find yourself on a coffee roasting forum and bring up the SR800, someone is bound to bring up the famous RazzoRoasting extension tube. If you look for advice for how to use the SR800, I swear it\u0026rsquo;s assumed that you have this very specific accessory. \u0026hellip;And so I bought one.\nDon\u0026rsquo;t worry, that is the extent of all of my coffee spending (for now). I am a very satisfied coffee roaster now. Check out this quick series of images going from the green beans to a nearly finished product! I can spend about 45 minutes and go from nothing to nearly 2 pounds of roasted beans, enough for about a week and a half of coffee. Not bad! The only downside is that now I feel like I need to buy coffee from local roasters to get my fix. There are certainly crueler fates.\nAs a sign off, I will share something that surprised me about coffee roasting. When I roast coffee, the most important cue to determine if the coffee is roasted is the sound. That\u0026rsquo;s right, not the color, not the smell, but the sound. When heating up a coffee bean, the water trapped inside eventually bursts out of the bean in a rapid expansion. This is called \u0026ldquo;first crack\u0026rdquo;, and indicates that the coffee is roasted enough to be drinkable. The expansion also releases the chaff from the bean. If you continue heating up the bean, you will eventually reach \u0026ldquo;second crack\u0026rdquo;. I think a solid medium roast is taken out just before second crack, so I try to take my coffee out to this point and it hasn\u0026rsquo;t proved me wrong yet.\nHappy coffee-ing! \u0026#x2615;\n","permalink":"https://www.zacharybillman.com/posts/roasting-coffee-at-home/","summary":"\u003cp\u003eI, like many others, picked up a new hobby during the pandemic. Other people\u0026rsquo;s hobbies may bring them joy. This could be for many reasons. There is the joy of creating something from scratch. You can revel in your thriftiness. You can embrace the pride when you recognize that your creation is on par (or better!) than what you can buy. I feel like these are embodied in the sourdough craze that caught fire early on in COVID.\n\u003cspan class=\"sidenote-number\"\u003e\u003csmall class=\"sidenote\"\u003e\nDare I say that I did this before it was cool? \u0026#x1f60e; I baked two loaves of bread almost every weekend through med school. Maybe I should bring that back, it\u0026rsquo;s been a while since I brought out the ole\u0026rsquo; starter.\n\u003c/small\u003e\u003c/span\u003e\nMy pandemic hobby is similar, but different in that it often feels like a chore, costs more money, and often turns out worse than what I can buy. Of course, I am talking about how I\u0026rsquo;ve started roasting my own coffee at home.\u003c/p\u003e","title":"Roasting coffee at home. ☕"},{"content":"It is an age-old question: how can one keep up with the continuous output of science? I remember at the beginning of my PhD struggling to figure out how anyone found out when a new paper came out. \u0026#x1f635; Did they sit on nature.com and spam the refresh button? Did they know when each journal released their latest issue?\nBehold the power of RSS! Most websites have a page that contains information about each subpage in a computer-readable format called RSS (Really Simple Syndication). Mine has one right here! These pages can be parsed by a number of RSS feed aggregators. The way these pages are set up make it such that they add any new information hosted at that domain. This is useful in the science world because you can find the RSS feed of a given journal, subscribe to it, then have every new article published online be delivered right to you.\nThere are a plethora of RSS feed aggregators you can pick from manage your feeds. I have previously used Feedly and Inoreader, which are great free solutions, but have moved on to selfhosting my own instance of FreshRSS.\nAfter making an account at your friendly local RSS feed aggregator, you can add whatever feeds your heart desires. To find a journal\u0026rsquo;s rss feed, I often just search \u0026ldquo;$JOURNAL_NAME rss feed\u0026rdquo; and poke around until I find something that looks right. Most of the aggregators will test the feed out first to make sure that you are trying to add a legitimate one. Here are a few of the heavy hitters to get you started:\nhttp://feeds.nature.com/nature/rss/current https://www.science.org/rss/express.xml https://www.cell.com/cell/inpress.rss Nothing like a constant stream of Cell, Science, and Nature to make your project feel like a real winner, eh?\nHere is what my own site looks like.\nFigure 1: My current FreshRSS setup. On the left I have my feeds separated into folders. In the middle you can see the titles of papers that appear in my feed.\nAnd after I hit J to move to the first item in the feed.\nFigure 2: With a title selected, you can see the abstract and authors.\nAfter collecting all of your desired RSS feeds, you cannot forego your responsibility of actually reading them! Most RSS feed aggregators have shortcuts to move through titles quickly (Typically J to move on to the next one and K to move up.) They always seem to use vi keybindings. A bunch of computer nerds have really cornered the keybinding market. I have let them take over my computing life. Each morning when I get into the lab, I quickly set up something, then head to my desk to hit J until the counter reaches zero.\nBut what about my very specific field? You can subscribe to all of the journals you want, but that doesn\u0026rsquo;t make the papers with your specific interests pop out. Fortunately, the NIH has this exact circumstance in mind.\nWhen you make a new search on PubMed you might notice the \u0026ldquo;Create RSS\u0026rdquo; button. Give it a click, then you will have a personal link you can add to your favorite RSS feed aggregator.\nFigure 3: Somehow I never noticed this button until I needed it.\nThis changed the game for me for keeping up with papers. Unfortunately, it doesn\u0026rsquo;t solve the problem of library management, or actually getting around to reading the papers you care about. I will leave library management as an exercise for the interested reader. Here\u0026rsquo;s a tip, the best solution uses the Zotero citation manager. Bonus points for using Zotfile for renaming your PDFs and Better BibTex for Zotero. \u0026#x1f609; I hope this helps you get your eyeballs on that science you crave. If you have solved the problem of accruing papers to read faster than you read them, let me know.\n","permalink":"https://www.zacharybillman.com/posts/rss-feeds-to-find-science-papers/","summary":"\u003cp\u003eIt is an age-old question: how can one keep up with the continuous output of science? I remember at the beginning of my PhD struggling to figure out how anyone found out when a new paper came out. \u0026#x1f635; Did they sit on nature.com and spam the refresh button? Did they know when each journal released their latest issue?\u003c/p\u003e\n\u003ch2 id=\"behold-the-power-of-rss\"\u003eBehold the power of RSS!\u003c/h2\u003e\n\u003cp\u003eMost websites have a page that contains information about each subpage in a computer-readable format called RSS (Really Simple Syndication). \u003ca href=\"https://zacharybillman.com/index.xml\"\u003eMine has one right here!\u003c/a\u003e These pages can be parsed by a number of RSS feed aggregators. The way these pages are set up make it such that they add any new information hosted at that domain. This is useful in the science world because you can find the RSS feed of a given journal, subscribe to it, then have every new article published online be delivered right to you.\u003c/p\u003e","title":"Using RSS feeds to keep on top of science."},{"content":"My interest in self-hosting began in my with my interests in internet privacy. Plastered all over the internet are stories about how much Google, Facebook and Amazon know about you. I deleted my Facebook account years ago, and I\u0026rsquo;m too paranoid to go back to the site because there\u0026rsquo;s a real possibility that Facebook has cached my account, ready to spin it back up in case I try to login again. The ads served to me were too accurate for my liking. This is despite almost never clicking on them! I have become convinced of the idea that, if you are not paying for the product, you are the product. From this assumption, it follows that anywhere I trust with my data that I am not paying for (like Google Drive, Google Photos, Dropbox, Facebook, Twitter) is using my data to earn money. We know that Google uses the labels you add to Photos to train it\u0026rsquo;s AI, and Facebook uses (at least) Instagram photos to train it\u0026rsquo;s AI. For some, the value proposition of allowing a company to use your data for a useful service in return is an acceptable one. I find this to be a reasonable stance, but I took my growing interest in internet privacy as a chance to learn about how I can take control of my data.\nInitially, I lurked on forums like /r/privacy to learn what I could do to avoid big-tech\u0026rsquo;s watchful eye. There were numerous comments along the lines of: \u0026ldquo;The only way to be in control of your data is to self-host your services.\u0026rdquo; I had no idea what this meant! Hard to believe that less than a year later, I learned to use (and love) Linux as my primary OS, and have happily replaced Google Photos, Google Drive and other services with my own self-hosted alternatives. Self-hosting, I have since learned, is when you run useful programs from your own computer. By doing so, you have complete knowledge of where and how your data is stored and how it is being used. It has the additional effect of being a bottomless time sink.\nTo begin, I needed an always-on computer to run these useful programs. I began with a humble Raspberry Pi.\nFigure 1: My humble Raspberry Pi and its hard drive. This dude currently tirelessly runs the excellent Adguard Home and downloads a backup of my data every night.\nThese are tiny, but capable computers that are great for fiddling with. The projects people develop for these are amazing and diverse. With RPi in hand, I began with the ambitious project of replacing Google Drive with Nextcloud. After much frustration with a bare metal installation, I found the NextcloudPi project. Surprisingly, it went pretty okay! At first, I was intimidated by Linux defaults, but over time I grew to appreciate, and indeed, prefer Linux as an operating system. My decision to use Linux over Windows/MacOS is because it is free and open source software (FOSS). This is a topic for a different post, but I think using FOSS when possible is a moral imperative of sorts. I used Nextcloud strictly from my home for a few months, without the ability to connect to it from the internet, to test the self-hosting waters. My first true cloud replacement spun up once I decided to access this lil\u0026rsquo; guy from the internet. To do so, I purchased a domain (not the one this site is hosted on) and pointed it to the IP of my house. I forwarded the appropriate ports of my router to the RPi.\nThis is when the real exploration began. I was able to access my files and images using Nextcloud, but the photo viewing service left something to be desired. No problem, why not spin up an instance of Photoprism? I use RSS feeds to keep on top of the latest science in the journals relevant to my field using Feedly. Why not host my own RSS feed aggregator so I can subscribe to as many feeds as I desire?\nThis cycle continued, and I accrued many cool applications, but in the back of my mind I worried about opening up my home network to the internet. I also struggled to run some programs because the RPi uses the arm64 architecture, and most services are written with amd64 in mind. These two forces eventually convinced me to purchase a server where I could manage all of my services remotely. Some would say that not owning the hardware that is running your own services is not \u0026ldquo;true\u0026rdquo; self-hosting. I think this is needlessly exclusive. Let everyone self host, dangit! Someday, when I have more stable internet and a more permanent home, I hope to host everything from my own home, but until then, I\u0026rsquo;m extremely pleased with my current stack. And that is where I am now. I happily host numerous services on my virtual private server that entirely replace Google Photos, Google Drive and GitHub for me. Even better, there are specialized services that fill a need I never realized I had. What\u0026rsquo;s more, if I ever want to spin up a new service, all I have to do is add it to my to docker-compose file and it will be up within minutes. What a world!\nI thought about making this into a \u0026ldquo;guide\u0026rdquo; style post. I nixed that idea because, quite frankly, I feel like I don\u0026rsquo;t know what I\u0026rsquo;m doing. I am really happy with my setup, but I don\u0026rsquo;t feel like I have the authority to tell people how to administer their own services. If you are interested, allow me to point you toward the guide that really got me rolling: Ultimate Traefik Docker Compose Guide.\nFor those of you wondering what I am currently hosting, check out my current list at the link and let me know what you think!\n","permalink":"https://www.zacharybillman.com/posts/my-selfhosting-journey/","summary":"\u003cp\u003eMy interest in self-hosting began in my with my interests in internet privacy. Plastered all over the internet are stories about how much Google, Facebook and Amazon know about you. I deleted my Facebook account years ago, and I\u0026rsquo;m too paranoid to go back to the site because there\u0026rsquo;s \u003ca href=\"https://www.reddit.com/r/privacy/comments/6nmjfh/facebook_account_fully_recovered_3_years_after/\"\u003ea real possibility that Facebook has cached my account, ready to spin it back up\u003c/a\u003e in case I try to login again. The ads served to me were too accurate for my liking.\n\u003cspan class=\"sidenote-number\"\u003e\u003csmall class=\"sidenote\"\u003e\nThis is despite almost never clicking on them!\n\u003c/small\u003e\u003c/span\u003e\nI have become convinced of the idea that, if you are not paying for the product, you are the product. From this assumption, it follows that anywhere I trust with my data that I am not paying for (like Google Drive, Google Photos, Dropbox, Facebook, Twitter) is using my data to earn money. We know that \u003ca href=\"https://www.theverge.com/2020/11/11/21559930/google-train-ai-photos-image-labelling-app-android-update\"\u003eGoogle uses the labels you add to Photos to train it\u0026rsquo;s AI\u003c/a\u003e, and \u003ca href=\"https://ai.facebook.com/blog/seer-the-start-of-a-more-powerful-flexible-and-accessible-era-for-computer-vision/\"\u003eFacebook uses (at least) Instagram photos to train it\u0026rsquo;s AI\u003c/a\u003e. For some, the value proposition of allowing a company to use your data for a useful service in return is an acceptable one. I find this to be a reasonable stance, but I took my growing interest in internet privacy as a chance to learn about how I can take control of my data.\u003c/p\u003e","title":"My selfhosting journey."},{"content":"N.B.: I hope to add screenshots for each of these eventually. For now, I hope links to each services\u0026rsquo; website will suffice.\nSeafile\nThis is a great tool for managing files. I moved to this from Nextcloud because I am of the philosophy that I would prefer services that do one thing excellently instead of many things well. Nextcloud is an incredible Office365 replacement, but I found myself using a fraction of what it was capable of providing. Enter Seafile. It is cloud file syncing with a robust encryption implementation, just what the doctor ordered.\nPhotoprism\nNextcloud\u0026rsquo;s implementation of photo management was a bit clumsy for my tastes, so I began on a hunt for a more feature complete option. I was very lucky to stumble upon Photoprism early on in my self hosting journey. I am a proud supporter of this project. It brings a ton to the table, and doesn\u0026rsquo;t leave me missing Google Photos one bit. It is also actively developed. For instance, as of 2022-07-02, there was a recent update that improved scrolling a ton, which was one of my remaining quibbles with it\u0026rsquo;s functionality. Some people complain that it doesn\u0026rsquo;t scale up for libraries of 10,000+ photos, but my 2000 photo library works swimmingly. On my phone, I use the Folder Sync app to automatically send any pictures I take on my phone to the Photoprism imports folder. Within 15 minutes of snapping a photo, it is there on my Photoprism instance. I highly recommend giving it a go.\nMealie\nI have to admit that the name leaves something to be desired. Fortunately, the service itself doesn\u0026rsquo;t fall short. Mealie is a recipe management application. It is able to parse your favorite recipe websites to create immortalized versions of the recipe. This helps fight detestable link rot that plagues the internet. It allows you to edit ingredient amounts, make comments about what you would change next time, and plan out your weekly meals. It helps that it is beautiful and intuitive to use. If only I could get my partner to use it\u0026hellip; I want to go on the record here and say that I think it is sensible that she doesn\u0026rsquo;t trust my self hosted services that much. In the early days of my self hosting journey, let\u0026rsquo;s just say that the up-time of my services were extremely finicky. I like to think they are more permanent now, especially because I am hosting everything on a VPS, but I certainly cannot compete with the stability of Google and Amazon. (Or pretty much any other paid service for that matter.) \u0026#x1f609;\nGitea\nGitea is a community managed, lightweight code hosting solution written in Go. I use it to manage my data analysis (using Private repos) and even host the source code for this very website! Using Gitea has given me the surface level introduction to the behemoth that is git. Fortunately, that is all I need. Once I have removed any sensitive data (like passwords, etc.) I will make my docker-compose file public. The docker-compose file is where I determine which services I pick to host, and how to configure them to my liking. Hopefully someone will find this useful.\nSyncthing\nIf I could only tell someone to self host a single service, I would have to pick Syncthing. It is a continuous file synchronization program, which means it keeps a specific file or folder the same between any device running Syncthing. I use it to keep my password database and my org-mode notes Now org-mode might be the biggest rabbithole of them all, and definitely the topic for another blog post. I use it to manage my TODO list, my lab notebook, my shopping lists, write this blog, and maintain my Zettelkasten note database. It is an immensely powerful tool. up to date between all of my devices. With Syncthing, all of my data is stored on my own devices and encrypted in transit.\nFreshRSS\nI keep up to date on the science in my field by subscribing to relevant RSS feeds. Yet another topic to write a post about. This really changed the game for my ability to keep on top of the latest research. 2022-07-14 Update: post complete! Check it out here. FreshRSS replaced Feedly for me, as I ran up against the number of feeds I could subscribe to on a free account. Also, when self hosting, I can save as many articles as my heart desires (even if I will never look at them again \u0026#x1f635; ).\nWallabag\nRemember Pocket for Firefox? (Yes, I know it still exists, okay?) Give Wallabag a spin, it is great for storing articles you want to read later. I set up FreshRSS to save articles to my Wallabag instance to keep for later.\nChangeDetection\nNow this is a fun one! ChangeDetection.io is a service that loads a webpage and checks to see if something has changed since the last time. This might not sound useful at first, but I recently used this to check for when a hot item for my new coffee roasting hobby was back in stock. I got an email the other day to let me know it was in stock. Pretty cool!\nHugo\nHugo is the static site generator I use to make this here blog! I was amazed at how much more response my site was using Hugo compare to when I paid a company to host a WordPress site. I\u0026rsquo;m sure WordPress could be fast, but I just wanted a barebones, pure html experience, and Hugo made it easy.\nCommento++\nYou may have noticed that I have some pretty snazzy comments sections on my site. I initially used Disqus, which you may recognize from a ton of sites around the internet, but didn\u0026rsquo;t like how it would serve ads through my comments section, and provided sign-ins using Google/Facebook/Twitter. I wanted to serve the simplest comments section I could, that still gave me the ability to migrate the comments to wherever I decide to keep my server. Go ahead and use the anonymous comment button, fill in your name, and you are off to the races.\nAuthelia\nThere are a few services I host that I really want to lock down. For these services, Authelia is great. It puts up a \u0026ldquo;Enter the 6 digit code on your phone\u0026rdquo; style 2 factor authentication in front of the services I choose. Or, if you follow the guide here, you can have it send you a DUO push, just like you are one of the big hitters out there. I feel much more secure with Authelia in front of Adminer, Traefik, and Portainer.\nBoring stuff that allows everything else to work!\nPostgreSQL database MariaDB database Traefik reverse proxy Umami privacy respecting site analytics Portainer for docker container management Redis in-memory data store Adminer database management traefik-socket-proxy to prevent pesky backdoors to my server! ","permalink":"https://www.zacharybillman.com/posts/zpb-current-selfhosted/","summary":"\u003cp\u003e\u003cem\u003eN.B.: I hope to add screenshots for each of these eventually. For now, I hope links to each services\u0026rsquo; website will suffice.\u003c/em\u003e\u003c/p\u003e\n\u003col\u003e\n\u003cli\u003e\n\u003cp\u003e\u003ca href=\"https://www.seafile.com/en/home/\"\u003eSeafile\u003c/a\u003e\u003c/p\u003e\n\u003cp\u003eThis is a great tool for managing files. I moved to this from Nextcloud because I am of the philosophy that I would prefer services that do one thing excellently instead of many things well. Nextcloud is an incredible Office365 replacement, but I found myself using a fraction of what it was capable of providing. Enter Seafile. It is cloud file syncing with a robust encryption implementation, just what the doctor ordered.\u003c/p\u003e","title":"What I'm currently selfhosting."},{"content":"My partner and I took a trip to the Mason Farm Biological Reserve the other day, and what a glorious day it was. This year, I\u0026rsquo;ve been quite busy in the lab, and missed a lot of the early spring warbler season, so I was very excited by the opportunity to check out the old stomping grounds.\nI brought the camera with me despite the fact we were going to be there around midday when the birds are much less active. I\u0026rsquo;m glad I did, because I got the best look at a common yellowthroat I\u0026rsquo;ve ever had. Normally these guys are flighty, staying close to the ground in small brush or tall grasses, but this one was putting on a proper show for the mating season. Even when you get a glimpse of one, it is usually just that, as they have jumped away before you can pull out the camera, taunting you with their iconic call. I was very pleased to capture a few choice shots of the bird. Hopefully there are more to come. While we were out, I also got a nice picture of a hermit thrush and a king snake.\nThese images have been compressed quite a bit for a lighter internet footprint. These have all been resized to 25% of their original size. If you would like the full sized images, let me know and I will send you a link!\n","permalink":"https://www.zacharybillman.com/posts/the-uncommon-yellowthroat/","summary":"\u003cp\u003eMy partner and I took a trip to the \u003ca href=\"https://ncbg.unc.edu/visit/mason-farm-biological-reserve/\"\u003eMason Farm Biological Reserve\u003c/a\u003e the other day, and what a glorious day it was. This year, I\u0026rsquo;ve been quite busy in the lab, and missed a lot of the early spring warbler season, so I was very excited by the opportunity to check out the old stomping grounds.\u003c/p\u003e\n\u003cp\u003eI brought the camera with me despite the fact we were going to be there around midday when the birds are much less active. I\u0026rsquo;m glad I did, because I got the best look at a common yellowthroat I\u0026rsquo;ve ever had.\n\u003cspan class=\"sidenote-number\"\u003e\u003csmall class=\"sidenote\"\u003e\nNormally these guys are flighty, staying close to the ground in small brush or tall grasses, but this one was putting on a proper show for the mating season. Even when you get a glimpse of one, it is usually just that, as they have jumped away before you can pull out the camera, taunting you with their \u003ca href=\"https://ebird.org/species/comyel#Modal-playlist\"\u003eiconic call\u003c/a\u003e.\n\u003c/small\u003e\u003c/span\u003e\nI was very pleased to capture a few choice shots of the bird. Hopefully there are more to come. While we were out, I also got a nice picture of a hermit thrush and a king snake.\u003c/p\u003e","title":"The (un)common yellowthroat."},{"content":"Welcome to my site! My name is Zachary Billman. I\u0026rsquo;m a UNC MD-PhD student in my 4th year of med school applying to pathology residency programs. I completed my PhD in Ed Miao\u0026rsquo;s lab. The curious reader may be thinking: \u0026ldquo;But Zach, Dr. Miao\u0026rsquo;s lab is at Duke, how did that come about?\u0026rdquo; What an astute question! Ed\u0026rsquo;s lab moved from UNC to Duke in early 2020, and I followed him down the street. My PhD was awarded by the UNC department of Microbiology and Immunology, but it just so happens that (nearly) all of my research took place at Duke. This move was quite a trial, especially when compounded with the onset of the pandemic. I suspect my research timeline suffered, though this is an extremely minor inconvenience compared to the tragedy the pandemic caused. This makes for very interesting basketball viewing parties with my Duke friends!\nMaybe having a diagram will make my training timeline make a bit more sense.\ntimeline.png\nMy research and scientific interests. I am broadly interested in innate immunology. I spent most of my time in graduate school studying the host-pathogen interaction between the intracellular fungus Histoplasma capsulatum and macrophages. There are many unstudied curiosities regarding the innate immune response to Histoplasma spp. and other intracellular fungi that I think are quite interesting. I also spent a considerable time thinking about the evolution of proteins involved in the programmed cell death pathway called pyroptosis.\nHobbies I may write about. Besides my science, I am interested in birding, baking sourdough bread (I swear I began years before the pandemic, though hearing of people baking bread brings me joy no matter when they first began!), board games, roasting coffee, and self-hosting free and open source software. Over the course of the pandemic, I have learned how to maintain a basic suite of services spread between a server I rent and a computer at home that have replaced my need for Google Photos and Google Drive. I\u0026rsquo;m hoping to be able to move away from these platforms entirely soon. I think they provide a great service, but at a substantial cost to privacy. Hopefully more to be said about my thoughts on FOSS soon! I also transitioned my old, (and quite frankly, embarrassingly slow) managed WordPress site with this lean, static site made in Hugo that I host myself. Now that I have mangled together some CSS to get my precious sidenotes up and running again, I\u0026rsquo;m ready to begin putting some ideas to paper. I love marginalia (the word to describe these notes on the side of this webpage). I\u0026rsquo;m not sure if this is unique to me, but I seem to get caught up in parenthetical / tangential thoughts very often, and I think using an Edward Tufte-esque sidenote is a great way for me to communicate in this way without distracting the reader too much. It seems marginalia such as this have been used throughout history, so perhaps it is normal, but most people can keep their thoughts focused better than me. The implementation I use is inspired by the Tufte CSS project and largely taken from this incredibly helpful post found at scripter.co. I\u0026rsquo;m quite proud of my progress in administering my server and self-hosting useful services.\nThe future of this site. On this site I plan to post updates about my journey through med school, grad school, and self-hosting I would like to share with the world. I have been helped immensely by many others\u0026rsquo; advice and I hope to impart similar tips to others someday. I suspect most posts will be about much lighter fare, like whatever hobbies tickle my fancy at the time.\n","permalink":"https://www.zacharybillman.com/posts/about-me/","summary":"\u003ch2 id=\"welcome-to-my-site\"\u003eWelcome to my site!\u003c/h2\u003e\n\u003cp\u003eMy name is Zachary Billman. I\u0026rsquo;m a UNC MD-PhD student in my 4th year of med school applying to pathology residency programs. I completed my PhD in Ed Miao\u0026rsquo;s lab. The curious reader may be thinking: \u0026ldquo;But Zach, Dr. Miao\u0026rsquo;s lab is at Duke, how did that come about?\u0026rdquo; What an astute question! Ed\u0026rsquo;s lab moved from UNC to Duke in early 2020, and I followed him down the street. My PhD was awarded by the UNC department of Microbiology and Immunology, but it just so happens that (nearly) all of my research took place at Duke.\n\u003cspan class=\"sidenote-number\"\u003e\u003csmall class=\"sidenote\"\u003e\nThis move was quite a trial, especially when compounded with the onset of the pandemic. I suspect my research timeline suffered, though this is an extremely minor inconvenience compared to the tragedy the pandemic caused.\n\u003c/small\u003e\u003c/span\u003e\nThis makes for very interesting basketball viewing parties with my Duke friends!\u003c/p\u003e","title":"About me. 👋"},{"content":"It\u0026rsquo;s over. My third year of medical school is officially behind me. I managed to get in a grand total of zero blog posts during grad school, so here\u0026rsquo;s to a new year with hopefully some more thoughts being shared. I have a lot to reflect on from the past year. It was wonderful. I wish everyone could experience what I did this past year. I think it goes without saying:\nI loved the third year of med school, but I do not want to do it again.\nA year of change. In the days leading up to my return to med school, I thought \u0026ldquo;Oh no, I really enjoy doing science, do I really have to go to med school?\u0026rdquo;. I also remember at the end of Step 1 and the first two years of med school thinking, \u0026ldquo;Oh no, I really enjoy med school, do I really have to do science again?\u0026rdquo;. I think I have a welcome problem of enjoying what I\u0026rsquo;m doing. The third year of med school is a shift. After years of memorizing and examinations, the doors to the promised land are finally opened. I have experienced nothing like it before It feels intentionally unsettling. You are thrown into the clinic with a modicum of guidance so you aren\u0026rsquo;t totally caught off guard, but you are thrown out to the wolves. I don\u0026rsquo;t mean this as a criticism of the system, it feels necessary. Third year medical students—commonly shorted to MS3s—have just one year to experience a broad swath of medicine and pick a specialty. So you had better be ready to dive in.\nTotal immersion I came to terms with my new reality quickly. Gone were the days of hitting the snooze button and going home when I pleased. I am now beholden to other people\u0026rsquo;s schedules. This came back relatively naturally. Maybe not hitting snooze. A regrettable personal failing of mine. I was, however, immediately faced with a new reality in the patient room. Patients come to the doctor for a number of reasons, but often seek relief. To get to the core of what ails them, they will tell you everything. I was not prepared for how vulnerable patients would be with me. I am not sure if this ever will feel natural. I hope it never does. I was told many stories of experiences living with scary diagnoses, and not knowing what to do with it. Family histories of all sorts. Personal details that were sometimes (oftentimes?) off the wall. I see all of these specifics as flailing, grasping at sand hoping that something could explain their pain. Sometimes it could. Usually it did not. But since I was in a white coat, I was privileged to hear it.\nI think my years spent in the lab have prepared me to face some of the challenges set before me. At the very least, having a few more years under my belt helped me approach the year with a bit of maturity. This seems to have paid off. I guess my recommendation is to simply get old before going to med school. Returning to studying The hospital is how I spent the majority of my time, but a new reality for me was also going back to daily studying. There is a strange dichotomy in medicine of \u0026ldquo;Oh, it doesn\u0026rsquo;t really matter\u0026rdquo; and \u0026ldquo;If you don\u0026rsquo;t get this class/score/grade then you won\u0026rsquo;t be able to be the kind of doctor you want to be, so you had better get your act together.\u0026rdquo; Simultaneously there are no expectations and immense responsibility for the looming specter of Step 2. I\u0026rsquo;m glad that studying regularly came back easily enough. I was concerned I would experience a studying whiplash. I\u0026rsquo;m glad it never came. I did UWorld and Anki nearly every day for a full year and felt alright.\nBecoming invisible I quickly learned I needed to change my understanding of my contribution to the team. Exiting grad school, people understood that they could come to me for help. I was a resource, a seasoned veteran of the lab. If someone needed an experiment done, I could do it, and be trusted to do it. In med school as a third year, I was nothing. A fly on the wall; a worm beneath the feet of the real doctors. In science, I felt like I was treated as a peer with even my committee members with multiple R01s. Even if I didn\u0026rsquo;t understand the science perfectly, I could contribute some different perspective. In medicine, sometimes not being recognized at all by my attendings was the best outcome. Which happened regularly. My role, was not as a contributor—as it was in science—it was simply to get in the reps. Once I understood that the expectations of me were below the ground, I understood that everything I did in third year was for myself. This is taken at face value by the team at times. I would spend 30 minutes working on a presentation, pre-rounding, the works, and at the end of my part, the intern would nod, then turn to the senior resident and say \u0026ldquo;I was thinking that we\u0026hellip;\u0026rdquo; without thinking of my work. This is perhaps a bit of cognitive restructuring, but recognizing this is what gave me the freedom to embed myself in the hospital flow, without a single worry about the outcome. Simply doing my best was the best thing I could do. Obviously. But this was not apparent to me at first. I needed more quality repetitions to develop good habits in the future. And also experience as much of medicine as possible to find what I want to do with my life. This permission allowed me to approach specialties I do not care about with the awe and respect they deserve.\nA year of wonder. Med school prepares you for the standardized tests. I think this is generally useful. The tests on aggregate are reasonable and evaluate your ability to think through common clinical scenarios. There will always be oddball questions that come out of left field, but I let these flow over me. No need to perseverate on the small stuff. The time for that can come later.\nWhat I didn\u0026rsquo;t realize is how much of the \u0026ldquo;classic\u0026rdquo; material we are fed in the first couple years of med school would come to the forefront. The \u0026ldquo;sandpaper rash\u0026rdquo; of scarlet fever really does feel like sandpaper. Nikolsky\u0026rsquo;s sign actually works. Tripoding for epiglottitis gets the physicians worked up. Don\u0026rsquo;t forget about von Willebrand\u0026rsquo;s disease when someone seems to be bleeding a bit too much. TB is out there, watch for hemoptosis. Night sweats, unintended weight loss, is cancer until proven otherwise. And yes, it really can be lupus.\nIn general, facing the unknown with a sense of earnestness was the way I felt best able to respect those who gathered and passed down the medical knowledge I am privileged to learn today. Sometimes, my excitement to see aspects of medicine would rouse a curious response from the residents. I project here, but I felt a sense of surprise, like that of a doting parent seeing their child experience something new, after forgetting the astonishment they once felt.\nEarnestness is next to med studentlyness.\nPerhaps what I\u0026rsquo;m getting at here is that I found it important to bask in the privilege of seeing the pathology I encountered in med school, and to remind the residents of this sensation. I felt childish at times—and perhaps overanimated—but I found this excitement was to my and my resident\u0026rsquo;s benefit.\nMy surgery rotation overflowed with examples of wonder of medicine. Partially because of the team I worked with, and the rest because of the undeniable coolness of surgery. The OR is a cool place. The orderliness and chaos ebb. The spans of steady, industrious work are interrupted with staccato notes of bedlam. The anatomy I learned in class was ever present, but the surgeons bemoaned \u0026ldquo;normal anatomic variation\u0026rdquo;.\nI was struck with wonder at the sight of human anatomy as it unfolded before me. What I was able to experience in the OR felt like the culmination of centuries of human curiosity. There is an ancientness to medicine that I catch flashes of—I could perform the physical exam on humans hundred of millions of years ago and interrogate the same pathologies as I do in the hospital today—and viewing the exposed anatomy is a pressure-bagged infusion of this collective wonder. To gaze upon the peristalsing of the small intestine, or steady beating of the heart is a sight to behold, indeed.\nA year of shame. It weighs upon me the circumstances that resulted in these transcendent experiences. Not one patient was in the hospital without reason. What to make of these patients with horrible pathology? I still feel unsettled about how the cause of their pain sparked wonder. How dare I gain, merely by the circumstance of having their care managed at UNC, Which, as a tertiary care center, layers on more complexity. Many patients end up at UNC because they have no where else they can go for help. And this signs them up for med students? For shame. from the very essence of their malady? I do not know what to do with my discomfort, but I think it is best that I dwell in it. With this, I respect the people before me in the hospital and recognize their humanity.\nBut I often complained of what I say here I was lucky to do. I find myself resentful of my future schedule; when was I supposed to learn that I will be working 13 hour days, 6 days a week for the rest of my life? And what of having a family? Medicine by necessity requires sacrifice. I happened to sign up for sacrifices years before I recognized how profound they were. How might I balance this dread and with the joy of practicing medicine? And why do I seem more concerned about this than others? Am I not grateful enough? Am I not capable of the sacrifices that others seem to offer so effortlessly? I don\u0026rsquo;t necessarily think this to be true, but these questions erode at my will to pursue medicine.\nPerhaps most shameful of all is how my understanding of the patient-provider interaction evolved over the year. It began as an exploration of an open book, a tabula rasa that held within it a diagnosis and how to best intervene. On my first day in the outpatient clinic, it was clear that this is not the case. My preceptor had only 20 minutes for me to ① interview the patient and perform the physical exam, ② present with a plan, ③ return to the room and do everything again, ④ write orders, educate, and get the patient out of the door. It simply is not amenable to the free form, personable, curious interview I hoped to perform. By the end of the year, I had optimized how I asked questions to keep patients from going off the rails. When prerounding in medicine, I was there to extract information and not much else. Small talk had to go, there was no time. I like to chat, so this came at a loss of who I think I am. I am not sure how to do this well, while still feeling like Zachary. And from what I gather from the interns, that may just come later in my career. I found myself questioning, \u0026ldquo;Is this the \u0026lsquo;patient interaction\u0026rsquo; that has been mythologized throughout my training?\u0026rdquo; The carrot at the end of the stick dangled before me with a \u0026ldquo;You are so lucky to be able to do this, so you had better not complain of any abuse that comes your way.\u0026rdquo; It wasn\u0026rsquo;t a genuine interaction as much as me leading the patient along to tell me what I wanted to know. Of course, I used open ended questions, but only open enough. Leave the door a bit too open and next thing you know, you are talking about their dog\u0026rsquo;s breeder while you constantly stare at your watch, imagining what your attending will say when you return. I feel like I am alone in missing the core human element that funnels sprightly youths into medicine. Or worse, finding it a façade.\nThe shame extends beyond the hospital. One aspect of my life that has changed most dramatically is the sheer amount of time I felt I needed to dedicate to medicine, whether at the hospital or at home. I spent all day basking in the wonder of medicine, then I would come home and study for hours. I relied on my partner for keeping our household together more than ever, because I spent all day—all year, rather—in a state of discovery. Her life was largely the same, with the normal challenges of being a scientist, with the added bonus of getting less help from me. The shame built over the year. Again, how dare I?\nA year of glad. This has been an undeniable year of growth and joy, with these quibbles. It is clear that I was happier than I was during grad school. I know this from within myself, and reinforced by my wife\u0026rsquo;s comments on my mood. The pace of the day, and immediacy of problem solving were a welcome change.\nI recall, during the very first days preparing for med school during xTAP, having to do a simulated patient encounter complete with patient presentation to an attending physician. We were told about this encounter days in advance. And yet, I dreaded it. And near the last day of my final rotation, I did 8 of these in a row without breaking a sweat. Progress!\nI think, in a word, what I\u0026rsquo;ve experienced in the third year of med school is gratitude. Gratitude to be privileged to learn what I am learning. Gratitude for the experiences in my life that brought me here. Gratitude for the support from my wife. Gratitude to be involved in people\u0026rsquo;s lives when they are fragile. Ever since reading Braiding Sweetgrass I think one could call me \u0026ldquo;gratitude-pilled\u0026rdquo;. I also selfishly enjoyed the gratitude from patients as I put on my best doctor performance. In reflection on the year, I have spent time thinking of a phrase that I heard a number of times throughout med school from residents, \u0026ldquo;The worst day of residency is better than the best day of med school.\u0026rdquo; I find this hard to believe. This year has been magical. It is hard to imagine a year filled with more wonder and joy of caring for those in need. I will have to rely on the experience of those who have walked this path and trust that the rest of my training has plenty of magic to spare.\n","permalink":"https://www.zacharybillman.com/posts/ms3-year-is-magical/","summary":"\u003ch2 id=\"it-s-over-dot\"\u003eIt\u0026rsquo;s over.\u003c/h2\u003e\n\u003cp\u003eMy third year of medical school is officially behind me. I managed to get in a grand total of \u003cem\u003ezero\u003c/em\u003e blog posts during grad school, so here\u0026rsquo;s to a new year with hopefully some more thoughts being shared. I have a lot to reflect on from the past year. It was wonderful. I wish everyone could experience what I did this past year. I think it goes without saying:\u003c/p\u003e","title":"The third year of medical school is magical."},{"content":"I, like many others, picked up a new hobby during the pandemic. Other people\u0026rsquo;s hobbies may bring them joy. This could be for many reasons. There is the joy of creating something from scratch. You can revel in your thriftiness. You can embrace the pride when you recognize that your creation is on par (or better!) than what you can buy. I feel like these are embodied in the sourdough craze that caught fire early on in COVID. Dare I say that I did this before it was cool? \u0026#x1f60e; I baked two loaves of bread almost every weekend through med school. Maybe I should bring that back, it\u0026rsquo;s been a while since I brought out the ole\u0026rsquo; starter. My pandemic hobby is similar, but different in that it often feels like a chore, costs more money, and often turns out worse than what I can buy. Of course, I am talking about how I\u0026rsquo;ve started roasting my own coffee at home.\nI\u0026rsquo;m not sure where this idea was planted into my brain. I don\u0026rsquo;t think I know anyone who roasts their own beans, and I certainly didn\u0026rsquo;t know how. I didn\u0026rsquo;t even drink coffee regularly until after college! I guess that extra time on the computer sent me down a rabbithole I have yet to emerge from.\nFirst, I want to preface the following with a disclaimer: This is not a detailed guide about how to roast your own coffee. If you are interested, I recommend checking out the How To Roast Your Own Coffee guide at Sweet Maria\u0026rsquo;s as a starting point. There is also the /r/roasting subreddit if that is your cup of tea. My only warning is there will be a lot of smoke. Roast your coffee outside, for Pete\u0026rsquo;s sake!\nIt all started with a trusty popcorn popper. There are a few things you want when you roast coffee:\nAir hot enough to roast coffee Remove the chaff from the beans Turns out that a classic popcorn popper fits the bill, as long as it has an upwards airflow and doesn\u0026rsquo;t let the chaff fall into the heating element. There is a bit of a cult following for the West Bend Poppery 2 model, but that one seemed a bit pricey, so I settled for a very capable popper from Nostalgia.\nFigure 1: I got a good bit of mileage out of my popcorn popper. If you are interested in roasting your own coffee I would give it a whirl.\nThings were simple back then. I still bought most of the coffee I drank, but I roasted enough to enjoy some freshly roasted coffee as an occasional treat. I ordered 10 pounds of green beans from Sweet Maria\u0026rsquo;s and life was good.\nThen I became a bit of a coffee snob.\nI could only roast 100 grams of coffee at a time in the popcorn popper, which is only enough for one pot of coffee in the morning for me. So it was time to upgrade.\nI bought the SR800 fluid bed roaster, which upped my roasting capacity and gave me finer control on temperature and airflow. Suffice to say my roasts improved a lot! At this point, I would consider my coffee good enough to sell at a farmer\u0026rsquo;s market to break even.\nIf you ever find yourself on a coffee roasting forum and bring up the SR800, someone is bound to bring up the famous RazzoRoasting extension tube. If you look for advice for how to use the SR800, I swear it\u0026rsquo;s assumed that you have this very specific accessory. \u0026hellip;And so I bought one.\nDon\u0026rsquo;t worry, that is the extent of all of my coffee spending (for now). I am a very satisfied coffee roaster now. Check out this quick series of images going from the green beans to a nearly finished product! I can spend about 45 minutes and go from nothing to nearly 2 pounds of roasted beans, enough for about a week and a half of coffee. Not bad! The only downside is that now I feel like I need to buy coffee from local roasters to get my fix. There are certainly crueler fates.\nAs a sign off, I will share something that surprised me about coffee roasting. When I roast coffee, the most important cue to determine if the coffee is roasted is the sound. That\u0026rsquo;s right, not the color, not the smell, but the sound. When heating up a coffee bean, the water trapped inside eventually bursts out of the bean in a rapid expansion. This is called \u0026ldquo;first crack\u0026rdquo;, and indicates that the coffee is roasted enough to be drinkable. The expansion also releases the chaff from the bean. If you continue heating up the bean, you will eventually reach \u0026ldquo;second crack\u0026rdquo;. I think a solid medium roast is taken out just before second crack, so I try to take my coffee out to this point and it hasn\u0026rsquo;t proved me wrong yet.\nHappy coffee-ing! \u0026#x2615;\n","permalink":"https://www.zacharybillman.com/posts/roasting-coffee-at-home/","summary":"\u003cp\u003eI, like many others, picked up a new hobby during the pandemic. Other people\u0026rsquo;s hobbies may bring them joy. This could be for many reasons. There is the joy of creating something from scratch. You can revel in your thriftiness. You can embrace the pride when you recognize that your creation is on par (or better!) than what you can buy. I feel like these are embodied in the sourdough craze that caught fire early on in COVID.\n\u003cspan class=\"sidenote-number\"\u003e\u003csmall class=\"sidenote\"\u003e\nDare I say that I did this before it was cool? \u0026#x1f60e; I baked two loaves of bread almost every weekend through med school. Maybe I should bring that back, it\u0026rsquo;s been a while since I brought out the ole\u0026rsquo; starter.\n\u003c/small\u003e\u003c/span\u003e\nMy pandemic hobby is similar, but different in that it often feels like a chore, costs more money, and often turns out worse than what I can buy. Of course, I am talking about how I\u0026rsquo;ve started roasting my own coffee at home.\u003c/p\u003e","title":"Roasting coffee at home. ☕"},{"content":"It is an age-old question: how can one keep up with the continuous output of science? I remember at the beginning of my PhD struggling to figure out how anyone found out when a new paper came out. \u0026#x1f635; Did they sit on nature.com and spam the refresh button? Did they know when each journal released their latest issue?\nBehold the power of RSS! Most websites have a page that contains information about each subpage in a computer-readable format called RSS (Really Simple Syndication). Mine has one right here! These pages can be parsed by a number of RSS feed aggregators. The way these pages are set up make it such that they add any new information hosted at that domain. This is useful in the science world because you can find the RSS feed of a given journal, subscribe to it, then have every new article published online be delivered right to you.\nThere are a plethora of RSS feed aggregators you can pick from manage your feeds. I have previously used Feedly and Inoreader, which are great free solutions, but have moved on to selfhosting my own instance of FreshRSS.\nAfter making an account at your friendly local RSS feed aggregator, you can add whatever feeds your heart desires. To find a journal\u0026rsquo;s rss feed, I often just search \u0026ldquo;$JOURNAL_NAME rss feed\u0026rdquo; and poke around until I find something that looks right. Most of the aggregators will test the feed out first to make sure that you are trying to add a legitimate one. Here are a few of the heavy hitters to get you started:\nhttp://feeds.nature.com/nature/rss/current https://www.science.org/rss/express.xml https://www.cell.com/cell/inpress.rss Nothing like a constant stream of Cell, Science, and Nature to make your project feel like a real winner, eh?\nHere is what my own site looks like.\nFigure 1: My current FreshRSS setup. On the left I have my feeds separated into folders. In the middle you can see the titles of papers that appear in my feed.\nAnd after I hit J to move to the first item in the feed.\nFigure 2: With a title selected, you can see the abstract and authors.\nAfter collecting all of your desired RSS feeds, you cannot forego your responsibility of actually reading them! Most RSS feed aggregators have shortcuts to move through titles quickly (Typically J to move on to the next one and K to move up.) They always seem to use vi keybindings. A bunch of computer nerds have really cornered the keybinding market. I have let them take over my computing life. Each morning when I get into the lab, I quickly set up something, then head to my desk to hit J until the counter reaches zero.\nBut what about my very specific field? You can subscribe to all of the journals you want, but that doesn\u0026rsquo;t make the papers with your specific interests pop out. Fortunately, the NIH has this exact circumstance in mind.\nWhen you make a new search on PubMed you might notice the \u0026ldquo;Create RSS\u0026rdquo; button. Give it a click, then you will have a personal link you can add to your favorite RSS feed aggregator.\nFigure 3: Somehow I never noticed this button until I needed it.\nThis changed the game for me for keeping up with papers. Unfortunately, it doesn\u0026rsquo;t solve the problem of library management, or actually getting around to reading the papers you care about. I will leave library management as an exercise for the interested reader. Here\u0026rsquo;s a tip, the best solution uses the Zotero citation manager. Bonus points for using Zotfile for renaming your PDFs and Better BibTex for Zotero. \u0026#x1f609; I hope this helps you get your eyeballs on that science you crave. If you have solved the problem of accruing papers to read faster than you read them, let me know.\n","permalink":"https://www.zacharybillman.com/posts/rss-feeds-to-find-science-papers/","summary":"\u003cp\u003eIt is an age-old question: how can one keep up with the continuous output of science? I remember at the beginning of my PhD struggling to figure out how anyone found out when a new paper came out. \u0026#x1f635; Did they sit on nature.com and spam the refresh button? Did they know when each journal released their latest issue?\u003c/p\u003e\n\u003ch2 id=\"behold-the-power-of-rss\"\u003eBehold the power of RSS!\u003c/h2\u003e\n\u003cp\u003eMost websites have a page that contains information about each subpage in a computer-readable format called RSS (Really Simple Syndication). \u003ca href=\"https://zacharybillman.com/index.xml\"\u003eMine has one right here!\u003c/a\u003e These pages can be parsed by a number of RSS feed aggregators. The way these pages are set up make it such that they add any new information hosted at that domain. This is useful in the science world because you can find the RSS feed of a given journal, subscribe to it, then have every new article published online be delivered right to you.\u003c/p\u003e","title":"Using RSS feeds to keep on top of science."},{"content":"My interest in self-hosting began in my with my interests in internet privacy. Plastered all over the internet are stories about how much Google, Facebook and Amazon know about you. I deleted my Facebook account years ago, and I\u0026rsquo;m too paranoid to go back to the site because there\u0026rsquo;s a real possibility that Facebook has cached my account, ready to spin it back up in case I try to login again. The ads served to me were too accurate for my liking. This is despite almost never clicking on them! I have become convinced of the idea that, if you are not paying for the product, you are the product. From this assumption, it follows that anywhere I trust with my data that I am not paying for (like Google Drive, Google Photos, Dropbox, Facebook, Twitter) is using my data to earn money. We know that Google uses the labels you add to Photos to train it\u0026rsquo;s AI, and Facebook uses (at least) Instagram photos to train it\u0026rsquo;s AI. For some, the value proposition of allowing a company to use your data for a useful service in return is an acceptable one. I find this to be a reasonable stance, but I took my growing interest in internet privacy as a chance to learn about how I can take control of my data.\nInitially, I lurked on forums like /r/privacy to learn what I could do to avoid big-tech\u0026rsquo;s watchful eye. There were numerous comments along the lines of: \u0026ldquo;The only way to be in control of your data is to self-host your services.\u0026rdquo; I had no idea what this meant! Hard to believe that less than a year later, I learned to use (and love) Linux as my primary OS, and have happily replaced Google Photos, Google Drive and other services with my own self-hosted alternatives. Self-hosting, I have since learned, is when you run useful programs from your own computer. By doing so, you have complete knowledge of where and how your data is stored and how it is being used. It has the additional effect of being a bottomless time sink.\nTo begin, I needed an always-on computer to run these useful programs. I began with a humble Raspberry Pi.\nFigure 1: My humble Raspberry Pi and its hard drive. This dude currently tirelessly runs the excellent Adguard Home and downloads a backup of my data every night.\nThese are tiny, but capable computers that are great for fiddling with. The projects people develop for these are amazing and diverse. With RPi in hand, I began with the ambitious project of replacing Google Drive with Nextcloud. After much frustration with a bare metal installation, I found the NextcloudPi project. Surprisingly, it went pretty okay! At first, I was intimidated by Linux defaults, but over time I grew to appreciate, and indeed, prefer Linux as an operating system. My decision to use Linux over Windows/MacOS is because it is free and open source software (FOSS). This is a topic for a different post, but I think using FOSS when possible is a moral imperative of sorts. I used Nextcloud strictly from my home for a few months, without the ability to connect to it from the internet, to test the self-hosting waters. My first true cloud replacement spun up once I decided to access this lil\u0026rsquo; guy from the internet. To do so, I purchased a domain (not the one this site is hosted on) and pointed it to the IP of my house. I forwarded the appropriate ports of my router to the RPi.\nThis is when the real exploration began. I was able to access my files and images using Nextcloud, but the photo viewing service left something to be desired. No problem, why not spin up an instance of Photoprism? I use RSS feeds to keep on top of the latest science in the journals relevant to my field using Feedly. Why not host my own RSS feed aggregator so I can subscribe to as many feeds as I desire?\nThis cycle continued, and I accrued many cool applications, but in the back of my mind I worried about opening up my home network to the internet. I also struggled to run some programs because the RPi uses the arm64 architecture, and most services are written with amd64 in mind. These two forces eventually convinced me to purchase a server where I could manage all of my services remotely. Some would say that not owning the hardware that is running your own services is not \u0026ldquo;true\u0026rdquo; self-hosting. I think this is needlessly exclusive. Let everyone self host, dangit! Someday, when I have more stable internet and a more permanent home, I hope to host everything from my own home, but until then, I\u0026rsquo;m extremely pleased with my current stack. And that is where I am now. I happily host numerous services on my virtual private server that entirely replace Google Photos, Google Drive and GitHub for me. Even better, there are specialized services that fill a need I never realized I had. What\u0026rsquo;s more, if I ever want to spin up a new service, all I have to do is add it to my to docker-compose file and it will be up within minutes. What a world!\nI thought about making this into a \u0026ldquo;guide\u0026rdquo; style post. I nixed that idea because, quite frankly, I feel like I don\u0026rsquo;t know what I\u0026rsquo;m doing. I am really happy with my setup, but I don\u0026rsquo;t feel like I have the authority to tell people how to administer their own services. If you are interested, allow me to point you toward the guide that really got me rolling: Ultimate Traefik Docker Compose Guide.\nFor those of you wondering what I am currently hosting, check out my current list at the link and let me know what you think!\n","permalink":"https://www.zacharybillman.com/posts/my-selfhosting-journey/","summary":"\u003cp\u003eMy interest in self-hosting began in my with my interests in internet privacy. Plastered all over the internet are stories about how much Google, Facebook and Amazon know about you. I deleted my Facebook account years ago, and I\u0026rsquo;m too paranoid to go back to the site because there\u0026rsquo;s \u003ca href=\"https://www.reddit.com/r/privacy/comments/6nmjfh/facebook_account_fully_recovered_3_years_after/\"\u003ea real possibility that Facebook has cached my account, ready to spin it back up\u003c/a\u003e in case I try to login again. The ads served to me were too accurate for my liking.\n\u003cspan class=\"sidenote-number\"\u003e\u003csmall class=\"sidenote\"\u003e\nThis is despite almost never clicking on them!\n\u003c/small\u003e\u003c/span\u003e\nI have become convinced of the idea that, if you are not paying for the product, you are the product. From this assumption, it follows that anywhere I trust with my data that I am not paying for (like Google Drive, Google Photos, Dropbox, Facebook, Twitter) is using my data to earn money. We know that \u003ca href=\"https://www.theverge.com/2020/11/11/21559930/google-train-ai-photos-image-labelling-app-android-update\"\u003eGoogle uses the labels you add to Photos to train it\u0026rsquo;s AI\u003c/a\u003e, and \u003ca href=\"https://ai.facebook.com/blog/seer-the-start-of-a-more-powerful-flexible-and-accessible-era-for-computer-vision/\"\u003eFacebook uses (at least) Instagram photos to train it\u0026rsquo;s AI\u003c/a\u003e. For some, the value proposition of allowing a company to use your data for a useful service in return is an acceptable one. I find this to be a reasonable stance, but I took my growing interest in internet privacy as a chance to learn about how I can take control of my data.\u003c/p\u003e","title":"My selfhosting journey."},{"content":"N.B.: I hope to add screenshots for each of these eventually. For now, I hope links to each services\u0026rsquo; website will suffice.\nSeafile\nThis is a great tool for managing files. I moved to this from Nextcloud because I am of the philosophy that I would prefer services that do one thing excellently instead of many things well. Nextcloud is an incredible Office365 replacement, but I found myself using a fraction of what it was capable of providing. Enter Seafile. It is cloud file syncing with a robust encryption implementation, just what the doctor ordered.\nPhotoprism\nNextcloud\u0026rsquo;s implementation of photo management was a bit clumsy for my tastes, so I began on a hunt for a more feature complete option. I was very lucky to stumble upon Photoprism early on in my self hosting journey. I am a proud supporter of this project. It brings a ton to the table, and doesn\u0026rsquo;t leave me missing Google Photos one bit. It is also actively developed. For instance, as of 2022-07-02, there was a recent update that improved scrolling a ton, which was one of my remaining quibbles with it\u0026rsquo;s functionality. Some people complain that it doesn\u0026rsquo;t scale up for libraries of 10,000+ photos, but my 2000 photo library works swimmingly. On my phone, I use the Folder Sync app to automatically send any pictures I take on my phone to the Photoprism imports folder. Within 15 minutes of snapping a photo, it is there on my Photoprism instance. I highly recommend giving it a go.\nMealie\nI have to admit that the name leaves something to be desired. Fortunately, the service itself doesn\u0026rsquo;t fall short. Mealie is a recipe management application. It is able to parse your favorite recipe websites to create immortalized versions of the recipe. This helps fight detestable link rot that plagues the internet. It allows you to edit ingredient amounts, make comments about what you would change next time, and plan out your weekly meals. It helps that it is beautiful and intuitive to use. If only I could get my partner to use it\u0026hellip; I want to go on the record here and say that I think it is sensible that she doesn\u0026rsquo;t trust my self hosted services that much. In the early days of my self hosting journey, let\u0026rsquo;s just say that the up-time of my services were extremely finicky. I like to think they are more permanent now, especially because I am hosting everything on a VPS, but I certainly cannot compete with the stability of Google and Amazon. (Or pretty much any other paid service for that matter.) \u0026#x1f609;\nGitea\nGitea is a community managed, lightweight code hosting solution written in Go. I use it to manage my data analysis (using Private repos) and even host the source code for this very website! Using Gitea has given me the surface level introduction to the behemoth that is git. Fortunately, that is all I need. Once I have removed any sensitive data (like passwords, etc.) I will make my docker-compose file public. The docker-compose file is where I determine which services I pick to host, and how to configure them to my liking. Hopefully someone will find this useful.\nSyncthing\nIf I could only tell someone to self host a single service, I would have to pick Syncthing. It is a continuous file synchronization program, which means it keeps a specific file or folder the same between any device running Syncthing. I use it to keep my password database and my org-mode notes Now org-mode might be the biggest rabbithole of them all, and definitely the topic for another blog post. I use it to manage my TODO list, my lab notebook, my shopping lists, write this blog, and maintain my Zettelkasten note database. It is an immensely powerful tool. up to date between all of my devices. With Syncthing, all of my data is stored on my own devices and encrypted in transit.\nFreshRSS\nI keep up to date on the science in my field by subscribing to relevant RSS feeds. Yet another topic to write a post about. This really changed the game for my ability to keep on top of the latest research. 2022-07-14 Update: post complete! Check it out here. FreshRSS replaced Feedly for me, as I ran up against the number of feeds I could subscribe to on a free account. Also, when self hosting, I can save as many articles as my heart desires (even if I will never look at them again \u0026#x1f635; ).\nWallabag\nRemember Pocket for Firefox? (Yes, I know it still exists, okay?) Give Wallabag a spin, it is great for storing articles you want to read later. I set up FreshRSS to save articles to my Wallabag instance to keep for later.\nChangeDetection\nNow this is a fun one! ChangeDetection.io is a service that loads a webpage and checks to see if something has changed since the last time. This might not sound useful at first, but I recently used this to check for when a hot item for my new coffee roasting hobby was back in stock. I got an email the other day to let me know it was in stock. Pretty cool!\nHugo\nHugo is the static site generator I use to make this here blog! I was amazed at how much more response my site was using Hugo compare to when I paid a company to host a WordPress site. I\u0026rsquo;m sure WordPress could be fast, but I just wanted a barebones, pure html experience, and Hugo made it easy.\nCommento++\nYou may have noticed that I have some pretty snazzy comments sections on my site. I initially used Disqus, which you may recognize from a ton of sites around the internet, but didn\u0026rsquo;t like how it would serve ads through my comments section, and provided sign-ins using Google/Facebook/Twitter. I wanted to serve the simplest comments section I could, that still gave me the ability to migrate the comments to wherever I decide to keep my server. Go ahead and use the anonymous comment button, fill in your name, and you are off to the races.\nAuthelia\nThere are a few services I host that I really want to lock down. For these services, Authelia is great. It puts up a \u0026ldquo;Enter the 6 digit code on your phone\u0026rdquo; style 2 factor authentication in front of the services I choose. Or, if you follow the guide here, you can have it send you a DUO push, just like you are one of the big hitters out there. I feel much more secure with Authelia in front of Adminer, Traefik, and Portainer.\nBoring stuff that allows everything else to work!\nPostgreSQL database MariaDB database Traefik reverse proxy Umami privacy respecting site analytics Portainer for docker container management Redis in-memory data store Adminer database management traefik-socket-proxy to prevent pesky backdoors to my server! ","permalink":"https://www.zacharybillman.com/posts/zpb-current-selfhosted/","summary":"\u003cp\u003e\u003cem\u003eN.B.: I hope to add screenshots for each of these eventually. For now, I hope links to each services\u0026rsquo; website will suffice.\u003c/em\u003e\u003c/p\u003e\n\u003col\u003e\n\u003cli\u003e\n\u003cp\u003e\u003ca href=\"https://www.seafile.com/en/home/\"\u003eSeafile\u003c/a\u003e\u003c/p\u003e\n\u003cp\u003eThis is a great tool for managing files. I moved to this from Nextcloud because I am of the philosophy that I would prefer services that do one thing excellently instead of many things well. Nextcloud is an incredible Office365 replacement, but I found myself using a fraction of what it was capable of providing. Enter Seafile. It is cloud file syncing with a robust encryption implementation, just what the doctor ordered.\u003c/p\u003e","title":"What I'm currently selfhosting."},{"content":"My partner and I took a trip to the Mason Farm Biological Reserve the other day, and what a glorious day it was. This year, I\u0026rsquo;ve been quite busy in the lab, and missed a lot of the early spring warbler season, so I was very excited by the opportunity to check out the old stomping grounds.\nI brought the camera with me despite the fact we were going to be there around midday when the birds are much less active. I\u0026rsquo;m glad I did, because I got the best look at a common yellowthroat I\u0026rsquo;ve ever had. Normally these guys are flighty, staying close to the ground in small brush or tall grasses, but this one was putting on a proper show for the mating season. Even when you get a glimpse of one, it is usually just that, as they have jumped away before you can pull out the camera, taunting you with their iconic call. I was very pleased to capture a few choice shots of the bird. Hopefully there are more to come. While we were out, I also got a nice picture of a hermit thrush and a king snake.\nThese images have been compressed quite a bit for a lighter internet footprint. These have all been resized to 25% of their original size. If you would like the full sized images, let me know and I will send you a link!\n","permalink":"https://www.zacharybillman.com/posts/the-uncommon-yellowthroat/","summary":"\u003cp\u003eMy partner and I took a trip to the \u003ca href=\"https://ncbg.unc.edu/visit/mason-farm-biological-reserve/\"\u003eMason Farm Biological Reserve\u003c/a\u003e the other day, and what a glorious day it was. This year, I\u0026rsquo;ve been quite busy in the lab, and missed a lot of the early spring warbler season, so I was very excited by the opportunity to check out the old stomping grounds.\u003c/p\u003e\n\u003cp\u003eI brought the camera with me despite the fact we were going to be there around midday when the birds are much less active. I\u0026rsquo;m glad I did, because I got the best look at a common yellowthroat I\u0026rsquo;ve ever had.\n\u003cspan class=\"sidenote-number\"\u003e\u003csmall class=\"sidenote\"\u003e\nNormally these guys are flighty, staying close to the ground in small brush or tall grasses, but this one was putting on a proper show for the mating season. Even when you get a glimpse of one, it is usually just that, as they have jumped away before you can pull out the camera, taunting you with their \u003ca href=\"https://ebird.org/species/comyel#Modal-playlist\"\u003eiconic call\u003c/a\u003e.\n\u003c/small\u003e\u003c/span\u003e\nI was very pleased to capture a few choice shots of the bird. Hopefully there are more to come. While we were out, I also got a nice picture of a hermit thrush and a king snake.\u003c/p\u003e","title":"The (un)common yellowthroat."},{"content":"Welcome to my site! My name is Zachary Billman. I\u0026rsquo;m a UNC MD-PhD student in my 4th year of med school applying to pathology residency programs. I completed my PhD in Ed Miao\u0026rsquo;s lab. The curious reader may be thinking: \u0026ldquo;But Zach, Dr. Miao\u0026rsquo;s lab is at Duke, how did that come about?\u0026rdquo; What an astute question! Ed\u0026rsquo;s lab moved from UNC to Duke in early 2020, and I followed him down the street. My PhD was awarded by the UNC department of Microbiology and Immunology, but it just so happens that (nearly) all of my research took place at Duke. This move was quite a trial, especially when compounded with the onset of the pandemic. I suspect my research timeline suffered, though this is an extremely minor inconvenience compared to the tragedy the pandemic caused. This makes for very interesting basketball viewing parties with my Duke friends!\nMaybe having a diagram will make my training timeline make a bit more sense.\nMy research and scientific interests. I am broadly interested in innate immunology. I spent most of my time in graduate school studying the host-pathogen interaction between the intracellular fungus Histoplasma capsulatum and macrophages. There are many unstudied curiosities regarding the innate immune response to Histoplasma spp. and other intracellular fungi that I think are quite interesting. I also spent a considerable time thinking about the evolution of proteins involved in the programmed cell death pathway called pyroptosis.\nHobbies I may write about. Besides my science, I am interested in birding, baking sourdough bread (I swear I began years before the pandemic, though hearing of people baking bread brings me joy no matter when they first began!), board games, roasting coffee, and self-hosting free and open source software. Over the course of the pandemic, I have learned how to maintain a basic suite of services spread between a server I rent and a computer at home that have replaced my need for Google Photos and Google Drive. I\u0026rsquo;m hoping to be able to move away from these platforms entirely soon. I think they provide a great service, but at a substantial cost to privacy. Hopefully more to be said about my thoughts on FOSS soon! I also transitioned my old, (and quite frankly, embarrassingly slow) managed WordPress site with this lean, static site made in Hugo that I host myself. Now that I have mangled together some CSS to get my precious sidenotes up and running again, I\u0026rsquo;m ready to begin putting some ideas to paper. I love marginalia (the word to describe these notes on the side of this webpage). I\u0026rsquo;m not sure if this is unique to me, but I seem to get caught up in parenthetical / tangential thoughts very often, and I think using an Edward Tufte-esque sidenote is a great way for me to communicate in this way without distracting the reader too much. It seems marginalia such as this have been used throughout history, so perhaps it is normal, but most people can keep their thoughts focused better than me. The implementation I use is inspired by the Tufte CSS project and largely taken from this incredibly helpful post found at scripter.co. I\u0026rsquo;m quite proud of my progress in administering my server and self-hosting useful services.\nThe future of this site. On this site I plan to post updates about my journey through med school, grad school, and self-hosting I would like to share with the world. I have been helped immensely by many others\u0026rsquo; advice and I hope to impart similar tips to others someday. I suspect most posts will be about much lighter fare, like whatever hobbies tickle my fancy at the time.\n","permalink":"https://www.zacharybillman.com/posts/about-me/","summary":"\u003ch2 id=\"welcome-to-my-site\"\u003eWelcome to my site!\u003c/h2\u003e\n\u003cp\u003eMy name is Zachary Billman. I\u0026rsquo;m a UNC MD-PhD student in my 4th year of med school applying to pathology residency programs. I completed my PhD in Ed Miao\u0026rsquo;s lab. The curious reader may be thinking: \u0026ldquo;But Zach, Dr. Miao\u0026rsquo;s lab is at Duke, how did that come about?\u0026rdquo; What an astute question! Ed\u0026rsquo;s lab moved from UNC to Duke in early 2020, and I followed him down the street. My PhD was awarded by the UNC department of Microbiology and Immunology, but it just so happens that (nearly) all of my research took place at Duke.\n\u003cspan class=\"sidenote-number\"\u003e\u003csmall class=\"sidenote\"\u003e\nThis move was quite a trial, especially when compounded with the onset of the pandemic. I suspect my research timeline suffered, though this is an extremely minor inconvenience compared to the tragedy the pandemic caused.\n\u003c/small\u003e\u003c/span\u003e\nThis makes for very interesting basketball viewing parties with my Duke friends!\u003c/p\u003e","title":"About me. 👋"},{"content":"It\u0026rsquo;s over. My third year of medical school is officially behind me. I managed to get in a grand total of zero blog posts during grad school, so here\u0026rsquo;s to a new year with hopefully some more thoughts being shared. I have a lot to reflect on from the past year. It was wonderful. I wish everyone could experience what I did this past year. I think it goes without saying:\nI loved the third year of med school, but I do not want to do it again.\nA year of change. In the days leading up to my return to med school, I thought \u0026ldquo;Oh no, I really enjoy doing science, do I really have to go to med school?\u0026rdquo;. I also remember at the end of Step 1 and the first two years of med school thinking, \u0026ldquo;Oh no, I really enjoy med school, do I really have to do science again?\u0026rdquo;. I think I have a welcome problem of enjoying what I\u0026rsquo;m doing. The third year of med school is a shift. After years of memorizing and examinations, the doors to the promised land are finally opened. I have experienced nothing like it before It feels intentionally unsettling. You are thrown into the clinic with a modicum of guidance so you aren\u0026rsquo;t totally caught off guard, but you are thrown out to the wolves. I don\u0026rsquo;t mean this as a criticism of the system, it feels necessary. Third year medical students—commonly shorted to MS3s—have just one year to experience a broad swath of medicine and pick a specialty. So you had better be ready to dive in.\nTotal immersion I came to terms with my new reality quickly. Gone were the days of hitting the snooze button and going home when I pleased. I am now beholden to other people\u0026rsquo;s schedules. This came back relatively naturally. Maybe not hitting snooze. A regrettable personal failing of mine. I was, however, immediately faced with a new reality in the patient room. Patients come to the doctor for a number of reasons, but often seek relief. To get to the core of what ails them, they will tell you everything. I was not prepared for how vulnerable patients would be with me. I am not sure if this ever will feel natural. I hope it never does. I was told many stories of experiences living with scary diagnoses, and not knowing what to do with it. Family histories of all sorts. Personal details that were sometimes (oftentimes?) off the wall. I see all of these specifics as flailing, grasping at sand hoping that something could explain their pain. Sometimes it could. Usually it did not. But since I was in a white coat, I was privileged to hear it.\nI think my years spent in the lab have prepared me to face some of the challenges set before me. At the very least, having a few more years under my belt helped me approach the year with a bit of maturity. This seems to have paid off. I guess my recommendation is to simply get old before going to med school. Returning to studying The hospital is how I spent the majority of my time, but a new reality for me was also going back to daily studying. There is a strange dichotomy in medicine of \u0026ldquo;Oh, it doesn\u0026rsquo;t really matter\u0026rdquo; and \u0026ldquo;If you don\u0026rsquo;t get this class/score/grade then you won\u0026rsquo;t be able to be the kind of doctor you want to be, so you had better get your act together.\u0026rdquo; Simultaneously there are no expectations and immense responsibility for the looming specter of Step 2. I\u0026rsquo;m glad that studying regularly came back easily enough. I was concerned I would experience a studying whiplash. I\u0026rsquo;m glad it never came. I did UWorld and Anki nearly every day for a full year and felt alright.\nBecoming invisible I quickly learned I needed to change my understanding of my contribution to the team. Exiting grad school, people understood that they could come to me for help. I was a resource, a seasoned veteran of the lab. If someone needed an experiment done, I could do it, and be trusted to do it. In med school as a third year, I was nothing. A fly on the wall; a worm beneath the feet of the real doctors. In science, I felt like I was treated as a peer with even my committee members with multiple R01s. Even if I didn\u0026rsquo;t understand the science perfectly, I could contribute some different perspective. In medicine, sometimes not being recognized at all by my attendings was the best outcome. Which happened regularly. My role, was not as a contributor—as it was in science—it was simply to get in the reps. Once I understood that the expectations of me were below the ground, I understood that everything I did in third year was for myself. This is taken at face value by the team at times. I would spend 30 minutes working on a presentation, pre-rounding, the works, and at the end of my part, the intern would nod, then turn to the senior resident and say \u0026ldquo;I was thinking that we\u0026hellip;\u0026rdquo; without thinking of my work. This is perhaps a bit of cognitive restructuring, but recognizing this is what gave me the freedom to embed myself in the hospital flow, without a single worry about the outcome. Simply doing my best was the best thing I could do. Obviously. But this was not apparent to me at first. I needed more quality repetitions to develop good habits in the future. And also experience as much of medicine as possible to find what I want to do with my life. This permission allowed me to approach specialties I do not care about with the awe and respect they deserve.\nA year of wonder. Med school prepares you for the standardized tests. I think this is generally useful. The tests on aggregate are reasonable and evaluate your ability to think through common clinical scenarios. There will always be oddball questions that come out of left field, but I let these flow over me. No need to perseverate on the small stuff. The time for that can come later.\nWhat I didn\u0026rsquo;t realize is how much of the \u0026ldquo;classic\u0026rdquo; material we are fed in the first couple years of med school would come to the forefront. The \u0026ldquo;sandpaper rash\u0026rdquo; of scarlet fever really does feel like sandpaper. Nikolsky\u0026rsquo;s sign actually works. Tripoding for epiglottitis gets the physicians worked up. Don\u0026rsquo;t forget about von Willebrand\u0026rsquo;s disease when someone seems to be bleeding a bit too much. TB is out there, watch for hemoptosis. Night sweats, unintended weight loss, is cancer until proven otherwise. And yes, it really can be lupus.\nIn general, facing the unknown with a sense of earnestness was the way I felt best able to respect those who gathered and passed down the medical knowledge I am privileged to learn today. Sometimes, my excitement to see aspects of medicine would rouse a curious response from the residents. I project here, but I felt a sense of surprise, like that of a doting parent seeing their child experience something new, after forgetting the astonishment they once felt.\nEarnestness is next to med studentlyness.\nPerhaps what I\u0026rsquo;m getting at here is that I found it important to bask in the privilege of seeing the pathology I encountered in med school, and to remind the residents of this sensation. I felt childish at times—and perhaps overanimated—but I found this excitement was to my and my resident\u0026rsquo;s benefit.\nMy surgery rotation overflowed with examples of wonder of medicine. Partially because of the team I worked with, and the rest because of the undeniable coolness of surgery. The OR is a cool place. The orderliness and chaos ebb. The spans of steady, industrious work are interrupted with staccato notes of bedlam. The anatomy I learned in class was ever present, but the surgeons bemoaned \u0026ldquo;normal anatomic variation\u0026rdquo;.\nI was struck with wonder at the sight of human anatomy as it unfolded before me. What I was able to experience in the OR felt like the culmination of centuries of human curiosity. There is an ancientness to medicine that I catch flashes of—I could perform the physical exam on humans hundred of millions of years ago and interrogate the same pathologies as I do in the hospital today—and viewing the exposed anatomy is a pressure-bagged infusion of this collective wonder. To gaze upon the peristalsing of the small intestine, or steady beating of the heart is a sight to behold, indeed.\nA year of shame. It weighs upon me the circumstances that resulted in these transcendent experiences. Not one patient was in the hospital without reason. What to make of these patients with horrible pathology? I still feel unsettled about how the cause of their pain sparked wonder. How dare I gain, merely by the circumstance of having their care managed at UNC, Which, as a tertiary care center, layers on more complexity. Many patients end up at UNC because they have no where else they can go for help. And this signs them up for med students? For shame. from the very essence of their malady? I do not know what to do with my discomfort, but I think it is best that I dwell in it. With this, I respect the people before me in the hospital and recognize their humanity.\nBut I often complained of what I say here I was lucky to do. I find myself resentful of my future schedule; when was I supposed to learn that I will be working 13 hour days, 6 days a week for the rest of my life? And what of having a family? Medicine by necessity requires sacrifice. I happened to sign up for sacrifices years before I recognized how profound they were. How might I balance this dread and with the joy of practicing medicine? And why do I seem more concerned about this than others? Am I not grateful enough? Am I not capable of the sacrifices that others seem to offer so effortlessly? I don\u0026rsquo;t necessarily think this to be true, but these questions erode at my will to pursue medicine.\nPerhaps most shameful of all is how my understanding of the patient-provider interaction evolved over the year. It began as an exploration of an open book, a tabula rasa that held within it a diagnosis and how to best intervene. On my first day in the outpatient clinic, it was clear that this is not the case. My preceptor had only 20 minutes for me to ① interview the patient and perform the physical exam, ② present with a plan, ③ return to the room and do everything again, ④ write orders, educate, and get the patient out of the door. It simply is not amenable to the free form, personable, curious interview I hoped to perform. By the end of the year, I had optimized how I asked questions to keep patients from going off the rails. When prerounding in medicine, I was there to extract information and not much else. Small talk had to go, there was no time. I like to chat, so this came at a loss of who I think I am. I am not sure how to do this well, while still feeling like Zachary. And from what I gather from the interns, that may just come later in my career. I found myself questioning, \u0026ldquo;Is this the \u0026lsquo;patient interaction\u0026rsquo; that has been mythologized throughout my training?\u0026rdquo; The carrot at the end of the stick dangled before me with a \u0026ldquo;You are so lucky to be able to do this, so you had better not complain of any abuse that comes your way.\u0026rdquo; It wasn\u0026rsquo;t a genuine interaction as much as me leading the patient along to tell me what I wanted to know. Of course, I used open ended questions, but only open enough. Leave the door a bit too open and next thing you know, you are talking about their dog\u0026rsquo;s breeder while you constantly stare at your watch, imagining what your attending will say when you return. I feel like I am alone in missing the core human element that funnels sprightly youths into medicine. Or worse, finding it a façade.\nThe shame extends beyond the hospital. One aspect of my life that has changed most dramatically is the sheer amount of time I felt I needed to dedicate to medicine, whether at the hospital or at home. I spent all day basking in the wonder of medicine, then I would come home and study for hours. I relied on my partner for keeping our household together more than ever, because I spent all day—all year, rather—in a state of discovery. Her life was largely the same, with the normal challenges of being a scientist, with the added bonus of getting less help from me. The shame built over the year. Again, how dare I?\nA year of glad. This has been an undeniable year of growth and joy, with these quibbles. It is clear that I was happier than I was during grad school. I know this from within myself, and reinforced by my wife\u0026rsquo;s comments on my mood. The pace of the day, and immediacy of problem solving were a welcome change.\nI recall, during the very first days preparing for med school during xTAP, having to do a simulated patient encounter complete with patient presentation to an attending physician. We were told about this encounter days in advance. And yet, I dreaded it. And near the last day of my final rotation, I did 8 of these in a row without breaking a sweat. Progress!\nI think, in a word, what I\u0026rsquo;ve experienced in the third year of med school is gratitude. Gratitude to be privileged to learn what I am learning. Gratitude for the experiences in my life that brought me here. Gratitude for the support from my wife. Gratitude to be involved in people\u0026rsquo;s lives when they are fragile. Ever since reading Braiding Sweetgrass I think one could call me \u0026ldquo;gratitude-pilled\u0026rdquo;. I also selfishly enjoyed the gratitude from patients as I put on my best doctor performance. In reflection on the year, I have spent time thinking of a phrase that I heard a number of times throughout med school from residents, \u0026ldquo;The worst day of residency is better than the best day of med school.\u0026rdquo; I find this hard to believe. This year has been magical. It is hard to imagine a year filled with more wonder and joy of caring for those in need. I will have to rely on the experience of those who have walked this path and trust that the rest of my training has plenty of magic to spare.\n","permalink":"https://www.zacharybillman.com/posts/ms3-year-is-magical/","summary":"\u003ch2 id=\"it-s-over-dot\"\u003eIt\u0026rsquo;s over.\u003c/h2\u003e\n\u003cp\u003eMy third year of medical school is officially behind me. I managed to get in a grand total of \u003cem\u003ezero\u003c/em\u003e blog posts during grad school, so here\u0026rsquo;s to a new year with hopefully some more thoughts being shared. I have a lot to reflect on from the past year. It was wonderful. I wish everyone could experience what I did this past year. I think it goes without saying:\u003c/p\u003e","title":"The third year of medical school is magical."},{"content":"I, like many others, picked up a new hobby during the pandemic. Other people\u0026rsquo;s hobbies may bring them joy. This could be for many reasons. There is the joy of creating something from scratch. You can revel in your thriftiness. You can embrace the pride when you recognize that your creation is on par (or better!) than what you can buy. I feel like these are embodied in the sourdough craze that caught fire early on in COVID. Dare I say that I did this before it was cool? \u0026#x1f60e; I baked two loaves of bread almost every weekend through med school. Maybe I should bring that back, it\u0026rsquo;s been a while since I brought out the ole\u0026rsquo; starter. My pandemic hobby is similar, but different in that it often feels like a chore, costs more money, and often turns out worse than what I can buy. Of course, I am talking about how I\u0026rsquo;ve started roasting my own coffee at home.\nI\u0026rsquo;m not sure where this idea was planted into my brain. I don\u0026rsquo;t think I know anyone who roasts their own beans, and I certainly didn\u0026rsquo;t know how. I didn\u0026rsquo;t even drink coffee regularly until after college! I guess that extra time on the computer sent me down a rabbithole I have yet to emerge from.\nFirst, I want to preface the following with a disclaimer: This is not a detailed guide about how to roast your own coffee. If you are interested, I recommend checking out the How To Roast Your Own Coffee guide at Sweet Maria\u0026rsquo;s as a starting point. There is also the /r/roasting subreddit if that is your cup of tea. My only warning is there will be a lot of smoke. Roast your coffee outside, for Pete\u0026rsquo;s sake!\nIt all started with a trusty popcorn popper. There are a few things you want when you roast coffee:\nAir hot enough to roast coffee Remove the chaff from the beans Turns out that a classic popcorn popper fits the bill, as long as it has an upwards airflow and doesn\u0026rsquo;t let the chaff fall into the heating element. There is a bit of a cult following for the West Bend Poppery 2 model, but that one seemed a bit pricey, so I settled for a very capable popper from Nostalgia.\nFigure 1: I got a good bit of mileage out of my popcorn popper. If you are interested in roasting your own coffee I would give it a whirl.\nThings were simple back then. I still bought most of the coffee I drank, but I roasted enough to enjoy some freshly roasted coffee as an occasional treat. I ordered 10 pounds of green beans from Sweet Maria\u0026rsquo;s and life was good.\nThen I became a bit of a coffee snob.\nI could only roast 100 grams of coffee at a time in the popcorn popper, which is only enough for one pot of coffee in the morning for me. So it was time to upgrade.\nI bought the SR800 fluid bed roaster, which upped my roasting capacity and gave me finer control on temperature and airflow. Suffice to say my roasts improved a lot! At this point, I would consider my coffee good enough to sell at a farmer\u0026rsquo;s market to break even.\nIf you ever find yourself on a coffee roasting forum and bring up the SR800, someone is bound to bring up the famous RazzoRoasting extension tube. If you look for advice for how to use the SR800, I swear it\u0026rsquo;s assumed that you have this very specific accessory. \u0026hellip;And so I bought one.\nDon\u0026rsquo;t worry, that is the extent of all of my coffee spending (for now). I am a very satisfied coffee roaster now. Check out this quick series of images going from the green beans to a nearly finished product! I can spend about 45 minutes and go from nothing to nearly 2 pounds of roasted beans, enough for about a week and a half of coffee. Not bad! The only downside is that now I feel like I need to buy coffee from local roasters to get my fix. There are certainly crueler fates.\nAs a sign off, I will share something that surprised me about coffee roasting. When I roast coffee, the most important cue to determine if the coffee is roasted is the sound. That\u0026rsquo;s right, not the color, not the smell, but the sound. When heating up a coffee bean, the water trapped inside eventually bursts out of the bean in a rapid expansion. This is called \u0026ldquo;first crack\u0026rdquo;, and indicates that the coffee is roasted enough to be drinkable. The expansion also releases the chaff from the bean. If you continue heating up the bean, you will eventually reach \u0026ldquo;second crack\u0026rdquo;. I think a solid medium roast is taken out just before second crack, so I try to take my coffee out to this point and it hasn\u0026rsquo;t proved me wrong yet.\nHappy coffee-ing! \u0026#x2615;\n","permalink":"https://www.zacharybillman.com/posts/roasting-coffee-at-home/","summary":"\u003cp\u003eI, like many others, picked up a new hobby during the pandemic. Other people\u0026rsquo;s hobbies may bring them joy. This could be for many reasons. There is the joy of creating something from scratch. You can revel in your thriftiness. You can embrace the pride when you recognize that your creation is on par (or better!) than what you can buy. I feel like these are embodied in the sourdough craze that caught fire early on in COVID.\n\u003cspan class=\"sidenote-number\"\u003e\u003csmall class=\"sidenote\"\u003e\nDare I say that I did this before it was cool? \u0026#x1f60e; I baked two loaves of bread almost every weekend through med school. Maybe I should bring that back, it\u0026rsquo;s been a while since I brought out the ole\u0026rsquo; starter.\n\u003c/small\u003e\u003c/span\u003e\nMy pandemic hobby is similar, but different in that it often feels like a chore, costs more money, and often turns out worse than what I can buy. Of course, I am talking about how I\u0026rsquo;ve started roasting my own coffee at home.\u003c/p\u003e","title":"Roasting coffee at home. ☕"},{"content":"It is an age-old question: how can one keep up with the continuous output of science? I remember at the beginning of my PhD struggling to figure out how anyone found out when a new paper came out. \u0026#x1f635; Did they sit on nature.com and spam the refresh button? Did they know when each journal released their latest issue?\nBehold the power of RSS! Most websites have a page that contains information about each subpage in a computer-readable format called RSS (Really Simple Syndication). Mine has one right here! These pages can be parsed by a number of RSS feed aggregators. The way these pages are set up make it such that they add any new information hosted at that domain. This is useful in the science world because you can find the RSS feed of a given journal, subscribe to it, then have every new article published online be delivered right to you.\nThere are a plethora of RSS feed aggregators you can pick from manage your feeds. I have previously used Feedly and Inoreader, which are great free solutions, but have moved on to selfhosting my own instance of FreshRSS.\nAfter making an account at your friendly local RSS feed aggregator, you can add whatever feeds your heart desires. To find a journal\u0026rsquo;s rss feed, I often just search \u0026ldquo;$JOURNAL_NAME rss feed\u0026rdquo; and poke around until I find something that looks right. Most of the aggregators will test the feed out first to make sure that you are trying to add a legitimate one. Here are a few of the heavy hitters to get you started:\nhttp://feeds.nature.com/nature/rss/current https://www.science.org/rss/express.xml https://www.cell.com/cell/inpress.rss Nothing like a constant stream of Cell, Science, and Nature to make your project feel like a real winner, eh?\nHere is what my own site looks like.\nFigure 1: My current FreshRSS setup. On the left I have my feeds separated into folders. In the middle you can see the titles of papers that appear in my feed.\nAnd after I hit J to move to the first item in the feed.\nFigure 2: With a title selected, you can see the abstract and authors.\nAfter collecting all of your desired RSS feeds, you cannot forego your responsibility of actually reading them! Most RSS feed aggregators have shortcuts to move through titles quickly (Typically J to move on to the next one and K to move up.) They always seem to use vi keybindings. A bunch of computer nerds have really cornered the keybinding market. I have let them take over my computing life. Each morning when I get into the lab, I quickly set up something, then head to my desk to hit J until the counter reaches zero.\nBut what about my very specific field? You can subscribe to all of the journals you want, but that doesn\u0026rsquo;t make the papers with your specific interests pop out. Fortunately, the NIH has this exact circumstance in mind.\nWhen you make a new search on PubMed you might notice the \u0026ldquo;Create RSS\u0026rdquo; button. Give it a click, then you will have a personal link you can add to your favorite RSS feed aggregator.\nFigure 3: Somehow I never noticed this button until I needed it.\nThis changed the game for me for keeping up with papers. Unfortunately, it doesn\u0026rsquo;t solve the problem of library management, or actually getting around to reading the papers you care about. I will leave library management as an exercise for the interested reader. Here\u0026rsquo;s a tip, the best solution uses the Zotero citation manager. Bonus points for using Zotfile for renaming your PDFs and Better BibTex for Zotero. \u0026#x1f609; I hope this helps you get your eyeballs on that science you crave. If you have solved the problem of accruing papers to read faster than you read them, let me know.\n","permalink":"https://www.zacharybillman.com/posts/rss-feeds-to-find-science-papers/","summary":"\u003cp\u003eIt is an age-old question: how can one keep up with the continuous output of science? I remember at the beginning of my PhD struggling to figure out how anyone found out when a new paper came out. \u0026#x1f635; Did they sit on nature.com and spam the refresh button? Did they know when each journal released their latest issue?\u003c/p\u003e\n\u003ch2 id=\"behold-the-power-of-rss\"\u003eBehold the power of RSS!\u003c/h2\u003e\n\u003cp\u003eMost websites have a page that contains information about each subpage in a computer-readable format called RSS (Really Simple Syndication). \u003ca href=\"https://zacharybillman.com/index.xml\"\u003eMine has one right here!\u003c/a\u003e These pages can be parsed by a number of RSS feed aggregators. The way these pages are set up make it such that they add any new information hosted at that domain. This is useful in the science world because you can find the RSS feed of a given journal, subscribe to it, then have every new article published online be delivered right to you.\u003c/p\u003e","title":"Using RSS feeds to keep on top of science."},{"content":"My interest in self-hosting began in my with my interests in internet privacy. Plastered all over the internet are stories about how much Google, Facebook and Amazon know about you. I deleted my Facebook account years ago, and I\u0026rsquo;m too paranoid to go back to the site because there\u0026rsquo;s a real possibility that Facebook has cached my account, ready to spin it back up in case I try to login again. The ads served to me were too accurate for my liking. This is despite almost never clicking on them! I have become convinced of the idea that, if you are not paying for the product, you are the product. From this assumption, it follows that anywhere I trust with my data that I am not paying for (like Google Drive, Google Photos, Dropbox, Facebook, Twitter) is using my data to earn money. We know that Google uses the labels you add to Photos to train it\u0026rsquo;s AI, and Facebook uses (at least) Instagram photos to train it\u0026rsquo;s AI. For some, the value proposition of allowing a company to use your data for a useful service in return is an acceptable one. I find this to be a reasonable stance, but I took my growing interest in internet privacy as a chance to learn about how I can take control of my data.\nInitially, I lurked on forums like /r/privacy to learn what I could do to avoid big-tech\u0026rsquo;s watchful eye. There were numerous comments along the lines of: \u0026ldquo;The only way to be in control of your data is to self-host your services.\u0026rdquo; I had no idea what this meant! Hard to believe that less than a year later, I learned to use (and love) Linux as my primary OS, and have happily replaced Google Photos, Google Drive and other services with my own self-hosted alternatives. Self-hosting, I have since learned, is when you run useful programs from your own computer. By doing so, you have complete knowledge of where and how your data is stored and how it is being used. It has the additional effect of being a bottomless time sink.\nTo begin, I needed an always-on computer to run these useful programs. I began with a humble Raspberry Pi.\nFigure 1: My humble Raspberry Pi and its hard drive. This dude currently tirelessly runs the excellent Adguard Home and downloads a backup of my data every night.\nThese are tiny, but capable computers that are great for fiddling with. The projects people develop for these are amazing and diverse. With RPi in hand, I began with the ambitious project of replacing Google Drive with Nextcloud. After much frustration with a bare metal installation, I found the NextcloudPi project. Surprisingly, it went pretty okay! At first, I was intimidated by Linux defaults, but over time I grew to appreciate, and indeed, prefer Linux as an operating system. My decision to use Linux over Windows/MacOS is because it is free and open source software (FOSS). This is a topic for a different post, but I think using FOSS when possible is a moral imperative of sorts. I used Nextcloud strictly from my home for a few months, without the ability to connect to it from the internet, to test the self-hosting waters. My first true cloud replacement spun up once I decided to access this lil\u0026rsquo; guy from the internet. To do so, I purchased a domain (not the one this site is hosted on) and pointed it to the IP of my house. I forwarded the appropriate ports of my router to the RPi.\nThis is when the real exploration began. I was able to access my files and images using Nextcloud, but the photo viewing service left something to be desired. No problem, why not spin up an instance of Photoprism? I use RSS feeds to keep on top of the latest science in the journals relevant to my field using Feedly. Why not host my own RSS feed aggregator so I can subscribe to as many feeds as I desire?\nThis cycle continued, and I accrued many cool applications, but in the back of my mind I worried about opening up my home network to the internet. I also struggled to run some programs because the RPi uses the arm64 architecture, and most services are written with amd64 in mind. These two forces eventually convinced me to purchase a server where I could manage all of my services remotely. Some would say that not owning the hardware that is running your own services is not \u0026ldquo;true\u0026rdquo; self-hosting. I think this is needlessly exclusive. Let everyone self host, dangit! Someday, when I have more stable internet and a more permanent home, I hope to host everything from my own home, but until then, I\u0026rsquo;m extremely pleased with my current stack. And that is where I am now. I happily host numerous services on my virtual private server that entirely replace Google Photos, Google Drive and GitHub for me. Even better, there are specialized services that fill a need I never realized I had. What\u0026rsquo;s more, if I ever want to spin up a new service, all I have to do is add it to my to docker-compose file and it will be up within minutes. What a world!\nI thought about making this into a \u0026ldquo;guide\u0026rdquo; style post. I nixed that idea because, quite frankly, I feel like I don\u0026rsquo;t know what I\u0026rsquo;m doing. I am really happy with my setup, but I don\u0026rsquo;t feel like I have the authority to tell people how to administer their own services. If you are interested, allow me to point you toward the guide that really got me rolling: Ultimate Traefik Docker Compose Guide.\nFor those of you wondering what I am currently hosting, check out my current list at the link and let me know what you think!\n","permalink":"https://www.zacharybillman.com/posts/my-selfhosting-journey/","summary":"\u003cp\u003eMy interest in self-hosting began in my with my interests in internet privacy. Plastered all over the internet are stories about how much Google, Facebook and Amazon know about you. I deleted my Facebook account years ago, and I\u0026rsquo;m too paranoid to go back to the site because there\u0026rsquo;s \u003ca href=\"https://www.reddit.com/r/privacy/comments/6nmjfh/facebook_account_fully_recovered_3_years_after/\"\u003ea real possibility that Facebook has cached my account, ready to spin it back up\u003c/a\u003e in case I try to login again. The ads served to me were too accurate for my liking.\n\u003cspan class=\"sidenote-number\"\u003e\u003csmall class=\"sidenote\"\u003e\nThis is despite almost never clicking on them!\n\u003c/small\u003e\u003c/span\u003e\nI have become convinced of the idea that, if you are not paying for the product, you are the product. From this assumption, it follows that anywhere I trust with my data that I am not paying for (like Google Drive, Google Photos, Dropbox, Facebook, Twitter) is using my data to earn money. We know that \u003ca href=\"https://www.theverge.com/2020/11/11/21559930/google-train-ai-photos-image-labelling-app-android-update\"\u003eGoogle uses the labels you add to Photos to train it\u0026rsquo;s AI\u003c/a\u003e, and \u003ca href=\"https://ai.facebook.com/blog/seer-the-start-of-a-more-powerful-flexible-and-accessible-era-for-computer-vision/\"\u003eFacebook uses (at least) Instagram photos to train it\u0026rsquo;s AI\u003c/a\u003e. For some, the value proposition of allowing a company to use your data for a useful service in return is an acceptable one. I find this to be a reasonable stance, but I took my growing interest in internet privacy as a chance to learn about how I can take control of my data.\u003c/p\u003e","title":"My selfhosting journey."},{"content":"N.B.: I hope to add screenshots for each of these eventually. For now, I hope links to each services\u0026rsquo; website will suffice.\nSeafile\nThis is a great tool for managing files. I moved to this from Nextcloud because I am of the philosophy that I would prefer services that do one thing excellently instead of many things well. Nextcloud is an incredible Office365 replacement, but I found myself using a fraction of what it was capable of providing. Enter Seafile. It is cloud file syncing with a robust encryption implementation, just what the doctor ordered.\nPhotoprism\nNextcloud\u0026rsquo;s implementation of photo management was a bit clumsy for my tastes, so I began on a hunt for a more feature complete option. I was very lucky to stumble upon Photoprism early on in my self hosting journey. I am a proud supporter of this project. It brings a ton to the table, and doesn\u0026rsquo;t leave me missing Google Photos one bit. It is also actively developed. For instance, as of 2022-07-02, there was a recent update that improved scrolling a ton, which was one of my remaining quibbles with it\u0026rsquo;s functionality. Some people complain that it doesn\u0026rsquo;t scale up for libraries of 10,000+ photos, but my 2000 photo library works swimmingly. On my phone, I use the Folder Sync app to automatically send any pictures I take on my phone to the Photoprism imports folder. Within 15 minutes of snapping a photo, it is there on my Photoprism instance. I highly recommend giving it a go.\nMealie\nI have to admit that the name leaves something to be desired. Fortunately, the service itself doesn\u0026rsquo;t fall short. Mealie is a recipe management application. It is able to parse your favorite recipe websites to create immortalized versions of the recipe. This helps fight detestable link rot that plagues the internet. It allows you to edit ingredient amounts, make comments about what you would change next time, and plan out your weekly meals. It helps that it is beautiful and intuitive to use. If only I could get my partner to use it\u0026hellip; I want to go on the record here and say that I think it is sensible that she doesn\u0026rsquo;t trust my self hosted services that much. In the early days of my self hosting journey, let\u0026rsquo;s just say that the up-time of my services were extremely finicky. I like to think they are more permanent now, especially because I am hosting everything on a VPS, but I certainly cannot compete with the stability of Google and Amazon. (Or pretty much any other paid service for that matter.) \u0026#x1f609;\nGitea\nGitea is a community managed, lightweight code hosting solution written in Go. I use it to manage my data analysis (using Private repos) and even host the source code for this very website! Using Gitea has given me the surface level introduction to the behemoth that is git. Fortunately, that is all I need. Once I have removed any sensitive data (like passwords, etc.) I will make my docker-compose file public. The docker-compose file is where I determine which services I pick to host, and how to configure them to my liking. Hopefully someone will find this useful.\nSyncthing\nIf I could only tell someone to self host a single service, I would have to pick Syncthing. It is a continuous file synchronization program, which means it keeps a specific file or folder the same between any device running Syncthing. I use it to keep my password database and my org-mode notes Now org-mode might be the biggest rabbithole of them all, and definitely the topic for another blog post. I use it to manage my TODO list, my lab notebook, my shopping lists, write this blog, and maintain my Zettelkasten note database. It is an immensely powerful tool. up to date between all of my devices. With Syncthing, all of my data is stored on my own devices and encrypted in transit.\nFreshRSS\nI keep up to date on the science in my field by subscribing to relevant RSS feeds. Yet another topic to write a post about. This really changed the game for my ability to keep on top of the latest research. 2022-07-14 Update: post complete! Check it out here. FreshRSS replaced Feedly for me, as I ran up against the number of feeds I could subscribe to on a free account. Also, when self hosting, I can save as many articles as my heart desires (even if I will never look at them again \u0026#x1f635; ).\nWallabag\nRemember Pocket for Firefox? (Yes, I know it still exists, okay?) Give Wallabag a spin, it is great for storing articles you want to read later. I set up FreshRSS to save articles to my Wallabag instance to keep for later.\nChangeDetection\nNow this is a fun one! ChangeDetection.io is a service that loads a webpage and checks to see if something has changed since the last time. This might not sound useful at first, but I recently used this to check for when a hot item for my new coffee roasting hobby was back in stock. I got an email the other day to let me know it was in stock. Pretty cool!\nHugo\nHugo is the static site generator I use to make this here blog! I was amazed at how much more response my site was using Hugo compare to when I paid a company to host a WordPress site. I\u0026rsquo;m sure WordPress could be fast, but I just wanted a barebones, pure html experience, and Hugo made it easy.\nCommento++\nYou may have noticed that I have some pretty snazzy comments sections on my site. I initially used Disqus, which you may recognize from a ton of sites around the internet, but didn\u0026rsquo;t like how it would serve ads through my comments section, and provided sign-ins using Google/Facebook/Twitter. I wanted to serve the simplest comments section I could, that still gave me the ability to migrate the comments to wherever I decide to keep my server. Go ahead and use the anonymous comment button, fill in your name, and you are off to the races.\nAuthelia\nThere are a few services I host that I really want to lock down. For these services, Authelia is great. It puts up a \u0026ldquo;Enter the 6 digit code on your phone\u0026rdquo; style 2 factor authentication in front of the services I choose. Or, if you follow the guide here, you can have it send you a DUO push, just like you are one of the big hitters out there. I feel much more secure with Authelia in front of Adminer, Traefik, and Portainer.\nBoring stuff that allows everything else to work!\nPostgreSQL database MariaDB database Traefik reverse proxy Umami privacy respecting site analytics Portainer for docker container management Redis in-memory data store Adminer database management traefik-socket-proxy to prevent pesky backdoors to my server! ","permalink":"https://www.zacharybillman.com/posts/zpb-current-selfhosted/","summary":"\u003cp\u003e\u003cem\u003eN.B.: I hope to add screenshots for each of these eventually. For now, I hope links to each services\u0026rsquo; website will suffice.\u003c/em\u003e\u003c/p\u003e\n\u003col\u003e\n\u003cli\u003e\n\u003cp\u003e\u003ca href=\"https://www.seafile.com/en/home/\"\u003eSeafile\u003c/a\u003e\u003c/p\u003e\n\u003cp\u003eThis is a great tool for managing files. I moved to this from Nextcloud because I am of the philosophy that I would prefer services that do one thing excellently instead of many things well. Nextcloud is an incredible Office365 replacement, but I found myself using a fraction of what it was capable of providing. Enter Seafile. It is cloud file syncing with a robust encryption implementation, just what the doctor ordered.\u003c/p\u003e","title":"What I'm currently selfhosting."},{"content":"My partner and I took a trip to the Mason Farm Biological Reserve the other day, and what a glorious day it was. This year, I\u0026rsquo;ve been quite busy in the lab, and missed a lot of the early spring warbler season, so I was very excited by the opportunity to check out the old stomping grounds.\nI brought the camera with me despite the fact we were going to be there around midday when the birds are much less active. I\u0026rsquo;m glad I did, because I got the best look at a common yellowthroat I\u0026rsquo;ve ever had. Normally these guys are flighty, staying close to the ground in small brush or tall grasses, but this one was putting on a proper show for the mating season. Even when you get a glimpse of one, it is usually just that, as they have jumped away before you can pull out the camera, taunting you with their iconic call. I was very pleased to capture a few choice shots of the bird. Hopefully there are more to come. While we were out, I also got a nice picture of a hermit thrush and a king snake.\nThese images have been compressed quite a bit for a lighter internet footprint. These have all been resized to 25% of their original size. If you would like the full sized images, let me know and I will send you a link!\n","permalink":"https://www.zacharybillman.com/posts/the-uncommon-yellowthroat/","summary":"\u003cp\u003eMy partner and I took a trip to the \u003ca href=\"https://ncbg.unc.edu/visit/mason-farm-biological-reserve/\"\u003eMason Farm Biological Reserve\u003c/a\u003e the other day, and what a glorious day it was. This year, I\u0026rsquo;ve been quite busy in the lab, and missed a lot of the early spring warbler season, so I was very excited by the opportunity to check out the old stomping grounds.\u003c/p\u003e\n\u003cp\u003eI brought the camera with me despite the fact we were going to be there around midday when the birds are much less active. I\u0026rsquo;m glad I did, because I got the best look at a common yellowthroat I\u0026rsquo;ve ever had.\n\u003cspan class=\"sidenote-number\"\u003e\u003csmall class=\"sidenote\"\u003e\nNormally these guys are flighty, staying close to the ground in small brush or tall grasses, but this one was putting on a proper show for the mating season. Even when you get a glimpse of one, it is usually just that, as they have jumped away before you can pull out the camera, taunting you with their \u003ca href=\"https://ebird.org/species/comyel#Modal-playlist\"\u003eiconic call\u003c/a\u003e.\n\u003c/small\u003e\u003c/span\u003e\nI was very pleased to capture a few choice shots of the bird. Hopefully there are more to come. While we were out, I also got a nice picture of a hermit thrush and a king snake.\u003c/p\u003e","title":"The (un)common yellowthroat."},{"content":"Welcome to my site! My name is Zachary Billman. I\u0026rsquo;m a UNC MD-PhD student in my 4th year of med school applying to pathology residency programs. I completed my PhD in Ed Miao\u0026rsquo;s lab. The curious reader may be thinking: \u0026ldquo;But Zach, Dr. Miao\u0026rsquo;s lab is at Duke, how did that come about?\u0026rdquo; What an astute question! Ed\u0026rsquo;s lab moved from UNC to Duke in early 2020, and I followed him down the street. My PhD was awarded by the UNC department of Microbiology and Immunology, but it just so happens that (nearly) all of my research took place at Duke. This move was quite a trial, especially when compounded with the onset of the pandemic. I suspect my research timeline suffered, though this is an extremely minor inconvenience compared to the tragedy the pandemic caused. This makes for very interesting basketball viewing parties with my Duke friends!\nMaybe having a diagram will make my training timeline make a bit more sense.\nHopefully that can clear up the winding road I\u0026rsquo;ve taken!\nMy research and scientific interests. I am broadly interested in innate immunology. I spent most of my time in graduate school studying the host-pathogen interaction between the intracellular fungus Histoplasma capsulatum and macrophages. There are many unstudied curiosities regarding the innate immune response to Histoplasma spp. and other intracellular fungi that I think are quite interesting. I also spent a considerable time thinking about the evolution of proteins involved in the programmed cell death pathway called pyroptosis.\nHobbies I may write about. Besides my science, I am interested in birding, baking sourdough bread (I swear I began years before the pandemic, though hearing of people baking bread brings me joy no matter when they first began!), board games, roasting coffee, and self-hosting free and open source software. Over the course of the pandemic, I have learned how to maintain a basic suite of services spread between a server I rent and a computer at home that have replaced my need for Google Photos and Google Drive. I\u0026rsquo;m hoping to be able to move away from these platforms entirely soon. I think they provide a great service, but at a substantial cost to privacy. Hopefully more to be said about my thoughts on FOSS soon! I also transitioned my old, (and quite frankly, embarrassingly slow) managed WordPress site with this lean, static site made in Hugo that I host myself. Now that I have mangled together some CSS to get my precious sidenotes up and running again, I\u0026rsquo;m ready to begin putting some ideas to paper. I love marginalia (the word to describe these notes on the side of this webpage). I\u0026rsquo;m not sure if this is unique to me, but I seem to get caught up in parenthetical / tangential thoughts very often, and I think using an Edward Tufte-esque sidenote is a great way for me to communicate in this way without distracting the reader too much. It seems marginalia such as this have been used throughout history, so perhaps it is normal, but most people can keep their thoughts focused better than me. The implementation I use is inspired by the Tufte CSS project and largely taken from this incredibly helpful post found at scripter.co. I\u0026rsquo;m quite proud of my progress in administering my server and self-hosting useful services.\nThe future of this site. On this site I plan to post updates about my journey through med school, grad school, and self-hosting I would like to share with the world. I have been helped immensely by many others\u0026rsquo; advice and I hope to impart similar tips to others someday. I suspect most posts will be about much lighter fare, like whatever hobbies tickle my fancy at the time.\n","permalink":"https://www.zacharybillman.com/posts/about-me/","summary":"\u003ch2 id=\"welcome-to-my-site\"\u003eWelcome to my site!\u003c/h2\u003e\n\u003cp\u003eMy name is Zachary Billman. I\u0026rsquo;m a UNC MD-PhD student in my 4th year of med school applying to pathology residency programs. I completed my PhD in Ed Miao\u0026rsquo;s lab. The curious reader may be thinking: \u0026ldquo;But Zach, Dr. Miao\u0026rsquo;s lab is at Duke, how did that come about?\u0026rdquo; What an astute question! Ed\u0026rsquo;s lab moved from UNC to Duke in early 2020, and I followed him down the street. My PhD was awarded by the UNC department of Microbiology and Immunology, but it just so happens that (nearly) all of my research took place at Duke.\n\u003cspan class=\"sidenote-number\"\u003e\u003csmall class=\"sidenote\"\u003e\nThis move was quite a trial, especially when compounded with the onset of the pandemic. I suspect my research timeline suffered, though this is an extremely minor inconvenience compared to the tragedy the pandemic caused.\n\u003c/small\u003e\u003c/span\u003e\nThis makes for very interesting basketball viewing parties with my Duke friends!\u003c/p\u003e","title":"About me. 👋"},{"content":"It\u0026rsquo;s over. My third year of medical school is officially behind me. I managed to get in a grand total of zero blog posts during grad school, so here\u0026rsquo;s to a new year with hopefully some more thoughts being shared. I have a lot to reflect on from the past year. It was wonderful. I wish everyone could experience what I did this past year. I think it goes without saying:\nI loved the third year of med school, but I do not want to do it again.\nA year of change. In the days leading up to my return to med school, I thought \u0026ldquo;Oh no, I really enjoy doing science, do I really have to go to med school?\u0026rdquo;. I also remember at the end of Step 1 and the first two years of med school thinking, \u0026ldquo;Oh no, I really enjoy med school, do I really have to do science again?\u0026rdquo;. I think I have a welcome problem of enjoying what I\u0026rsquo;m doing. The third year of med school is a shift. After years of memorizing and examinations, the doors to the promised land are finally opened. I have experienced nothing like it before It feels intentionally unsettling. You are thrown into the clinic with a modicum of guidance so you aren\u0026rsquo;t totally caught off guard, but you are thrown out to the wolves. I don\u0026rsquo;t mean this as a criticism of the system, it feels necessary. Third year medical students—commonly shorted to MS3s—have just one year to experience a broad swath of medicine and pick a specialty. So you had better be ready to dive in.\nTotal immersion I came to terms with my new reality quickly. Gone were the days of hitting the snooze button and going home when I pleased. I am now beholden to other people\u0026rsquo;s schedules. This came back relatively naturally. Maybe not hitting snooze. A regrettable personal failing of mine. I was, however, immediately faced with a new reality in the patient room. Patients come to the doctor for a number of reasons, but often seek relief. To get to the core of what ails them, they will tell you everything. I was not prepared for how vulnerable patients would be with me. I am not sure if this ever will feel natural. I hope it never does. I was told many stories of experiences living with scary diagnoses, and not knowing what to do with it. Family histories of all sorts. Personal details that were sometimes (oftentimes?) off the wall. I see all of these specifics as flailing, grasping at sand hoping that something could explain their pain. Sometimes it could. Usually it did not. But since I was in a white coat, I was privileged to hear it.\nI think my years spent in the lab have prepared me to face some of the challenges set before me. At the very least, having a few more years under my belt helped me approach the year with a bit of maturity. This seems to have paid off. I guess my recommendation is to simply get old before going to med school. Returning to studying The hospital is how I spent the majority of my time, but a new reality for me was also going back to daily studying. There is a strange dichotomy in medicine of \u0026ldquo;Oh, it doesn\u0026rsquo;t really matter\u0026rdquo; and \u0026ldquo;If you don\u0026rsquo;t get this class/score/grade then you won\u0026rsquo;t be able to be the kind of doctor you want to be, so you had better get your act together.\u0026rdquo; Simultaneously there are no expectations and immense responsibility for the looming specter of Step 2. I\u0026rsquo;m glad that studying regularly came back easily enough. I was concerned I would experience a studying whiplash. I\u0026rsquo;m glad it never came. I did UWorld and Anki nearly every day for a full year and felt alright.\nBecoming invisible I quickly learned I needed to change my understanding of my contribution to the team. Exiting grad school, people understood that they could come to me for help. I was a resource, a seasoned veteran of the lab. If someone needed an experiment done, I could do it, and be trusted to do it. In med school as a third year, I was nothing. A fly on the wall; a worm beneath the feet of the real doctors. In science, I felt like I was treated as a peer with even my committee members with multiple R01s. Even if I didn\u0026rsquo;t understand the science perfectly, I could contribute some different perspective. In medicine, sometimes not being recognized at all by my attendings was the best outcome. Which happened regularly. My role, was not as a contributor—as it was in science—it was simply to get in the reps. Once I understood that the expectations of me were below the ground, I understood that everything I did in third year was for myself. This is taken at face value by the team at times. I would spend 30 minutes working on a presentation, pre-rounding, the works, and at the end of my part, the intern would nod, then turn to the senior resident and say \u0026ldquo;I was thinking that we\u0026hellip;\u0026rdquo; without thinking of my work. This is perhaps a bit of cognitive restructuring, but recognizing this is what gave me the freedom to embed myself in the hospital flow, without a single worry about the outcome. Simply doing my best was the best thing I could do. Obviously. But this was not apparent to me at first. I needed more quality repetitions to develop good habits in the future. And also experience as much of medicine as possible to find what I want to do with my life. This permission allowed me to approach specialties I do not care about with the awe and respect they deserve.\nA year of wonder. Med school prepares you for the standardized tests. I think this is generally useful. The tests on aggregate are reasonable and evaluate your ability to think through common clinical scenarios. There will always be oddball questions that come out of left field, but I let these flow over me. No need to perseverate on the small stuff. The time for that can come later.\nWhat I didn\u0026rsquo;t realize is how much of the \u0026ldquo;classic\u0026rdquo; material we are fed in the first couple years of med school would come to the forefront. The \u0026ldquo;sandpaper rash\u0026rdquo; of scarlet fever really does feel like sandpaper. Nikolsky\u0026rsquo;s sign actually works. Tripoding for epiglottitis gets the physicians worked up. Don\u0026rsquo;t forget about von Willebrand\u0026rsquo;s disease when someone seems to be bleeding a bit too much. TB is out there, watch for hemoptosis. Night sweats, unintended weight loss, is cancer until proven otherwise. And yes, it really can be lupus.\nIn general, facing the unknown with a sense of earnestness was the way I felt best able to respect those who gathered and passed down the medical knowledge I am privileged to learn today. Sometimes, my excitement to see aspects of medicine would rouse a curious response from the residents. I project here, but I felt a sense of surprise, like that of a doting parent seeing their child experience something new, after forgetting the astonishment they once felt.\nEarnestness is next to med studentlyness.\nPerhaps what I\u0026rsquo;m getting at here is that I found it important to bask in the privilege of seeing the pathology I encountered in med school, and to remind the residents of this sensation. I felt childish at times—and perhaps overanimated—but I found this excitement was to my and my resident\u0026rsquo;s benefit.\nMy surgery rotation overflowed with examples of wonder of medicine. Partially because of the team I worked with, and the rest because of the undeniable coolness of surgery. The OR is a cool place. The orderliness and chaos ebb. The spans of steady, industrious work are interrupted with staccato notes of bedlam. The anatomy I learned in class was ever present, but the surgeons bemoaned \u0026ldquo;normal anatomic variation\u0026rdquo;.\nI was struck with wonder at the sight of human anatomy as it unfolded before me. What I was able to experience in the OR felt like the culmination of centuries of human curiosity. There is an ancientness to medicine that I catch flashes of—I could perform the physical exam on humans hundred of millions of years ago and interrogate the same pathologies as I do in the hospital today—and viewing the exposed anatomy is a pressure-bagged infusion of this collective wonder. To gaze upon the peristalsing of the small intestine, or steady beating of the heart is a sight to behold, indeed.\nA year of shame. It weighs upon me the circumstances that resulted in these transcendent experiences. Not one patient was in the hospital without reason. What to make of these patients with horrible pathology? I still feel unsettled about how the cause of their pain sparked wonder. How dare I gain, merely by the circumstance of having their care managed at UNC, Which, as a tertiary care center, layers on more complexity. Many patients end up at UNC because they have no where else they can go for help. And this signs them up for med students? For shame. from the very essence of their malady? I do not know what to do with my discomfort, but I think it is best that I dwell in it. With this, I respect the people before me in the hospital and recognize their humanity.\nBut I often complained of what I say here I was lucky to do. I find myself resentful of my future schedule; when was I supposed to learn that I will be working 13 hour days, 6 days a week for the rest of my life? And what of having a family? Medicine by necessity requires sacrifice. I happened to sign up for sacrifices years before I recognized how profound they were. How might I balance this dread and with the joy of practicing medicine? And why do I seem more concerned about this than others? Am I not grateful enough? Am I not capable of the sacrifices that others seem to offer so effortlessly? I don\u0026rsquo;t necessarily think this to be true, but these questions erode at my will to pursue medicine.\nPerhaps most shameful of all is how my understanding of the patient-provider interaction evolved over the year. It began as an exploration of an open book, a tabula rasa that held within it a diagnosis and how to best intervene. On my first day in the outpatient clinic, it was clear that this is not the case. My preceptor had only 20 minutes for me to ① interview the patient and perform the physical exam, ② present with a plan, ③ return to the room and do everything again, ④ write orders, educate, and get the patient out of the door. It simply is not amenable to the free form, personable, curious interview I hoped to perform. By the end of the year, I had optimized how I asked questions to keep patients from going off the rails. When prerounding in medicine, I was there to extract information and not much else. Small talk had to go, there was no time. I like to chat, so this came at a loss of who I think I am. I am not sure how to do this well, while still feeling like Zachary. And from what I gather from the interns, that may just come later in my career. I found myself questioning, \u0026ldquo;Is this the \u0026lsquo;patient interaction\u0026rsquo; that has been mythologized throughout my training?\u0026rdquo; The carrot at the end of the stick dangled before me with a \u0026ldquo;You are so lucky to be able to do this, so you had better not complain of any abuse that comes your way.\u0026rdquo; It wasn\u0026rsquo;t a genuine interaction as much as me leading the patient along to tell me what I wanted to know. Of course, I used open ended questions, but only open enough. Leave the door a bit too open and next thing you know, you are talking about their dog\u0026rsquo;s breeder while you constantly stare at your watch, imagining what your attending will say when you return. I feel like I am alone in missing the core human element that funnels sprightly youths into medicine. Or worse, finding it a façade.\nThe shame extends beyond the hospital. One aspect of my life that has changed most dramatically is the sheer amount of time I felt I needed to dedicate to medicine, whether at the hospital or at home. I spent all day basking in the wonder of medicine, then I would come home and study for hours. I relied on my partner for keeping our household together more than ever, because I spent all day—all year, rather—in a state of discovery. Her life was largely the same, with the normal challenges of being a scientist, with the added bonus of getting less help from me. The shame built over the year. Again, how dare I?\nA year of glad. This has been an undeniable year of growth and joy, with these quibbles. It is clear that I was happier than I was during grad school. I know this from within myself, and reinforced by my wife\u0026rsquo;s comments on my mood. The pace of the day, and immediacy of problem solving were a welcome change.\nI recall, during the very first days preparing for med school during xTAP, having to do a simulated patient encounter complete with patient presentation to an attending physician. We were told about this encounter days in advance. And yet, I dreaded it. And near the last day of my final rotation, I did 8 of these in a row without breaking a sweat. Progress!\nI think, in a word, what I\u0026rsquo;ve experienced in the third year of med school is gratitude. Gratitude to be privileged to learn what I am learning. Gratitude for the experiences in my life that brought me here. Gratitude for the support from my wife. Gratitude to be involved in people\u0026rsquo;s lives when they are fragile. Ever since reading Braiding Sweetgrass I think one could call me \u0026ldquo;gratitude-pilled\u0026rdquo;. I also selfishly enjoyed the gratitude from patients as I put on my best doctor performance. In reflection on the year, I have spent time thinking of a phrase that I heard a number of times throughout med school from residents, \u0026ldquo;The worst day of residency is better than the best day of med school.\u0026rdquo; I find this hard to believe. This year has been magical. It is hard to imagine a year filled with more wonder and joy of caring for those in need. I will have to rely on the experience of those who have walked this path and trust that the rest of my training has plenty of magic to spare.\n","permalink":"https://www.zacharybillman.com/posts/ms3-year-is-magical/","summary":"\u003ch2 id=\"it-s-over-dot\"\u003eIt\u0026rsquo;s over.\u003c/h2\u003e\n\u003cp\u003eMy third year of medical school is officially behind me. I managed to get in a grand total of \u003cem\u003ezero\u003c/em\u003e blog posts during grad school, so here\u0026rsquo;s to a new year with hopefully some more thoughts being shared. I have a lot to reflect on from the past year. It was wonderful. I wish everyone could experience what I did this past year. I think it goes without saying:\u003c/p\u003e","title":"The third year of medical school is magical."},{"content":"I, like many others, picked up a new hobby during the pandemic. Other people\u0026rsquo;s hobbies may bring them joy. This could be for many reasons. There is the joy of creating something from scratch. You can revel in your thriftiness. You can embrace the pride when you recognize that your creation is on par (or better!) than what you can buy. I feel like these are embodied in the sourdough craze that caught fire early on in COVID. Dare I say that I did this before it was cool? \u0026#x1f60e; I baked two loaves of bread almost every weekend through med school. Maybe I should bring that back, it\u0026rsquo;s been a while since I brought out the ole\u0026rsquo; starter. My pandemic hobby is similar, but different in that it often feels like a chore, costs more money, and often turns out worse than what I can buy. Of course, I am talking about how I\u0026rsquo;ve started roasting my own coffee at home.\nI\u0026rsquo;m not sure where this idea was planted into my brain. I don\u0026rsquo;t think I know anyone who roasts their own beans, and I certainly didn\u0026rsquo;t know how. I didn\u0026rsquo;t even drink coffee regularly until after college! I guess that extra time on the computer sent me down a rabbithole I have yet to emerge from.\nFirst, I want to preface the following with a disclaimer: This is not a detailed guide about how to roast your own coffee. If you are interested, I recommend checking out the How To Roast Your Own Coffee guide at Sweet Maria\u0026rsquo;s as a starting point. There is also the /r/roasting subreddit if that is your cup of tea. My only warning is there will be a lot of smoke. Roast your coffee outside, for Pete\u0026rsquo;s sake!\nIt all started with a trusty popcorn popper. There are a few things you want when you roast coffee:\nAir hot enough to roast coffee Remove the chaff from the beans Turns out that a classic popcorn popper fits the bill, as long as it has an upwards airflow and doesn\u0026rsquo;t let the chaff fall into the heating element. There is a bit of a cult following for the West Bend Poppery 2 model, but that one seemed a bit pricey, so I settled for a very capable popper from Nostalgia.\nFigure 1: I got a good bit of mileage out of my popcorn popper. If you are interested in roasting your own coffee I would give it a whirl.\nThings were simple back then. I still bought most of the coffee I drank, but I roasted enough to enjoy some freshly roasted coffee as an occasional treat. I ordered 10 pounds of green beans from Sweet Maria\u0026rsquo;s and life was good.\nThen I became a bit of a coffee snob.\nI could only roast 100 grams of coffee at a time in the popcorn popper, which is only enough for one pot of coffee in the morning for me. So it was time to upgrade.\nI bought the SR800 fluid bed roaster, which upped my roasting capacity and gave me finer control on temperature and airflow. Suffice to say my roasts improved a lot! At this point, I would consider my coffee good enough to sell at a farmer\u0026rsquo;s market to break even.\nIf you ever find yourself on a coffee roasting forum and bring up the SR800, someone is bound to bring up the famous RazzoRoasting extension tube. If you look for advice for how to use the SR800, I swear it\u0026rsquo;s assumed that you have this very specific accessory. \u0026hellip;And so I bought one.\nDon\u0026rsquo;t worry, that is the extent of all of my coffee spending (for now). I am a very satisfied coffee roaster now. Check out this quick series of images going from the green beans to a nearly finished product! I can spend about 45 minutes and go from nothing to nearly 2 pounds of roasted beans, enough for about a week and a half of coffee. Not bad! The only downside is that now I feel like I need to buy coffee from local roasters to get my fix. There are certainly crueler fates.\nAs a sign off, I will share something that surprised me about coffee roasting. When I roast coffee, the most important cue to determine if the coffee is roasted is the sound. That\u0026rsquo;s right, not the color, not the smell, but the sound. When heating up a coffee bean, the water trapped inside eventually bursts out of the bean in a rapid expansion. This is called \u0026ldquo;first crack\u0026rdquo;, and indicates that the coffee is roasted enough to be drinkable. The expansion also releases the chaff from the bean. If you continue heating up the bean, you will eventually reach \u0026ldquo;second crack\u0026rdquo;. I think a solid medium roast is taken out just before second crack, so I try to take my coffee out to this point and it hasn\u0026rsquo;t proved me wrong yet.\nHappy coffee-ing! \u0026#x2615;\n","permalink":"https://www.zacharybillman.com/posts/roasting-coffee-at-home/","summary":"\u003cp\u003eI, like many others, picked up a new hobby during the pandemic. Other people\u0026rsquo;s hobbies may bring them joy. This could be for many reasons. There is the joy of creating something from scratch. You can revel in your thriftiness. You can embrace the pride when you recognize that your creation is on par (or better!) than what you can buy. I feel like these are embodied in the sourdough craze that caught fire early on in COVID.\n\u003cspan class=\"sidenote-number\"\u003e\u003csmall class=\"sidenote\"\u003e\nDare I say that I did this before it was cool? \u0026#x1f60e; I baked two loaves of bread almost every weekend through med school. Maybe I should bring that back, it\u0026rsquo;s been a while since I brought out the ole\u0026rsquo; starter.\n\u003c/small\u003e\u003c/span\u003e\nMy pandemic hobby is similar, but different in that it often feels like a chore, costs more money, and often turns out worse than what I can buy. Of course, I am talking about how I\u0026rsquo;ve started roasting my own coffee at home.\u003c/p\u003e","title":"Roasting coffee at home. ☕"},{"content":"It is an age-old question: how can one keep up with the continuous output of science? I remember at the beginning of my PhD struggling to figure out how anyone found out when a new paper came out. \u0026#x1f635; Did they sit on nature.com and spam the refresh button? Did they know when each journal released their latest issue?\nBehold the power of RSS! Most websites have a page that contains information about each subpage in a computer-readable format called RSS (Really Simple Syndication). Mine has one right here! These pages can be parsed by a number of RSS feed aggregators. The way these pages are set up make it such that they add any new information hosted at that domain. This is useful in the science world because you can find the RSS feed of a given journal, subscribe to it, then have every new article published online be delivered right to you.\nThere are a plethora of RSS feed aggregators you can pick from manage your feeds. I have previously used Feedly and Inoreader, which are great free solutions, but have moved on to selfhosting my own instance of FreshRSS.\nAfter making an account at your friendly local RSS feed aggregator, you can add whatever feeds your heart desires. To find a journal\u0026rsquo;s rss feed, I often just search \u0026ldquo;$JOURNAL_NAME rss feed\u0026rdquo; and poke around until I find something that looks right. Most of the aggregators will test the feed out first to make sure that you are trying to add a legitimate one. Here are a few of the heavy hitters to get you started:\nhttp://feeds.nature.com/nature/rss/current https://www.science.org/rss/express.xml https://www.cell.com/cell/inpress.rss Nothing like a constant stream of Cell, Science, and Nature to make your project feel like a real winner, eh?\nHere is what my own site looks like.\nFigure 1: My current FreshRSS setup. On the left I have my feeds separated into folders. In the middle you can see the titles of papers that appear in my feed.\nAnd after I hit J to move to the first item in the feed.\nFigure 2: With a title selected, you can see the abstract and authors.\nAfter collecting all of your desired RSS feeds, you cannot forego your responsibility of actually reading them! Most RSS feed aggregators have shortcuts to move through titles quickly (Typically J to move on to the next one and K to move up.) They always seem to use vi keybindings. A bunch of computer nerds have really cornered the keybinding market. I have let them take over my computing life. Each morning when I get into the lab, I quickly set up something, then head to my desk to hit J until the counter reaches zero.\nBut what about my very specific field? You can subscribe to all of the journals you want, but that doesn\u0026rsquo;t make the papers with your specific interests pop out. Fortunately, the NIH has this exact circumstance in mind.\nWhen you make a new search on PubMed you might notice the \u0026ldquo;Create RSS\u0026rdquo; button. Give it a click, then you will have a personal link you can add to your favorite RSS feed aggregator.\nFigure 3: Somehow I never noticed this button until I needed it.\nThis changed the game for me for keeping up with papers. Unfortunately, it doesn\u0026rsquo;t solve the problem of library management, or actually getting around to reading the papers you care about. I will leave library management as an exercise for the interested reader. Here\u0026rsquo;s a tip, the best solution uses the Zotero citation manager. Bonus points for using Zotfile for renaming your PDFs and Better BibTex for Zotero. \u0026#x1f609; I hope this helps you get your eyeballs on that science you crave. If you have solved the problem of accruing papers to read faster than you read them, let me know.\n","permalink":"https://www.zacharybillman.com/posts/rss-feeds-to-find-science-papers/","summary":"\u003cp\u003eIt is an age-old question: how can one keep up with the continuous output of science? I remember at the beginning of my PhD struggling to figure out how anyone found out when a new paper came out. \u0026#x1f635; Did they sit on nature.com and spam the refresh button? Did they know when each journal released their latest issue?\u003c/p\u003e\n\u003ch2 id=\"behold-the-power-of-rss\"\u003eBehold the power of RSS!\u003c/h2\u003e\n\u003cp\u003eMost websites have a page that contains information about each subpage in a computer-readable format called RSS (Really Simple Syndication). \u003ca href=\"https://zacharybillman.com/index.xml\"\u003eMine has one right here!\u003c/a\u003e These pages can be parsed by a number of RSS feed aggregators. The way these pages are set up make it such that they add any new information hosted at that domain. This is useful in the science world because you can find the RSS feed of a given journal, subscribe to it, then have every new article published online be delivered right to you.\u003c/p\u003e","title":"Using RSS feeds to keep on top of science."},{"content":"My interest in self-hosting began in my with my interests in internet privacy. Plastered all over the internet are stories about how much Google, Facebook and Amazon know about you. I deleted my Facebook account years ago, and I\u0026rsquo;m too paranoid to go back to the site because there\u0026rsquo;s a real possibility that Facebook has cached my account, ready to spin it back up in case I try to login again. The ads served to me were too accurate for my liking. This is despite almost never clicking on them! I have become convinced of the idea that, if you are not paying for the product, you are the product. From this assumption, it follows that anywhere I trust with my data that I am not paying for (like Google Drive, Google Photos, Dropbox, Facebook, Twitter) is using my data to earn money. We know that Google uses the labels you add to Photos to train it\u0026rsquo;s AI, and Facebook uses (at least) Instagram photos to train it\u0026rsquo;s AI. For some, the value proposition of allowing a company to use your data for a useful service in return is an acceptable one. I find this to be a reasonable stance, but I took my growing interest in internet privacy as a chance to learn about how I can take control of my data.\nInitially, I lurked on forums like /r/privacy to learn what I could do to avoid big-tech\u0026rsquo;s watchful eye. There were numerous comments along the lines of: \u0026ldquo;The only way to be in control of your data is to self-host your services.\u0026rdquo; I had no idea what this meant! Hard to believe that less than a year later, I learned to use (and love) Linux as my primary OS, and have happily replaced Google Photos, Google Drive and other services with my own self-hosted alternatives. Self-hosting, I have since learned, is when you run useful programs from your own computer. By doing so, you have complete knowledge of where and how your data is stored and how it is being used. It has the additional effect of being a bottomless time sink.\nTo begin, I needed an always-on computer to run these useful programs. I began with a humble Raspberry Pi.\nFigure 1: My humble Raspberry Pi and its hard drive. This dude currently tirelessly runs the excellent Adguard Home and downloads a backup of my data every night.\nThese are tiny, but capable computers that are great for fiddling with. The projects people develop for these are amazing and diverse. With RPi in hand, I began with the ambitious project of replacing Google Drive with Nextcloud. After much frustration with a bare metal installation, I found the NextcloudPi project. Surprisingly, it went pretty okay! At first, I was intimidated by Linux defaults, but over time I grew to appreciate, and indeed, prefer Linux as an operating system. My decision to use Linux over Windows/MacOS is because it is free and open source software (FOSS). This is a topic for a different post, but I think using FOSS when possible is a moral imperative of sorts. I used Nextcloud strictly from my home for a few months, without the ability to connect to it from the internet, to test the self-hosting waters. My first true cloud replacement spun up once I decided to access this lil\u0026rsquo; guy from the internet. To do so, I purchased a domain (not the one this site is hosted on) and pointed it to the IP of my house. I forwarded the appropriate ports of my router to the RPi.\nThis is when the real exploration began. I was able to access my files and images using Nextcloud, but the photo viewing service left something to be desired. No problem, why not spin up an instance of Photoprism? I use RSS feeds to keep on top of the latest science in the journals relevant to my field using Feedly. Why not host my own RSS feed aggregator so I can subscribe to as many feeds as I desire?\nThis cycle continued, and I accrued many cool applications, but in the back of my mind I worried about opening up my home network to the internet. I also struggled to run some programs because the RPi uses the arm64 architecture, and most services are written with amd64 in mind. These two forces eventually convinced me to purchase a server where I could manage all of my services remotely. Some would say that not owning the hardware that is running your own services is not \u0026ldquo;true\u0026rdquo; self-hosting. I think this is needlessly exclusive. Let everyone self host, dangit! Someday, when I have more stable internet and a more permanent home, I hope to host everything from my own home, but until then, I\u0026rsquo;m extremely pleased with my current stack. And that is where I am now. I happily host numerous services on my virtual private server that entirely replace Google Photos, Google Drive and GitHub for me. Even better, there are specialized services that fill a need I never realized I had. What\u0026rsquo;s more, if I ever want to spin up a new service, all I have to do is add it to my to docker-compose file and it will be up within minutes. What a world!\nI thought about making this into a \u0026ldquo;guide\u0026rdquo; style post. I nixed that idea because, quite frankly, I feel like I don\u0026rsquo;t know what I\u0026rsquo;m doing. I am really happy with my setup, but I don\u0026rsquo;t feel like I have the authority to tell people how to administer their own services. If you are interested, allow me to point you toward the guide that really got me rolling: Ultimate Traefik Docker Compose Guide.\nFor those of you wondering what I am currently hosting, check out my current list at the link and let me know what you think!\n","permalink":"https://www.zacharybillman.com/posts/my-selfhosting-journey/","summary":"\u003cp\u003eMy interest in self-hosting began in my with my interests in internet privacy. Plastered all over the internet are stories about how much Google, Facebook and Amazon know about you. I deleted my Facebook account years ago, and I\u0026rsquo;m too paranoid to go back to the site because there\u0026rsquo;s \u003ca href=\"https://www.reddit.com/r/privacy/comments/6nmjfh/facebook_account_fully_recovered_3_years_after/\"\u003ea real possibility that Facebook has cached my account, ready to spin it back up\u003c/a\u003e in case I try to login again. The ads served to me were too accurate for my liking.\n\u003cspan class=\"sidenote-number\"\u003e\u003csmall class=\"sidenote\"\u003e\nThis is despite almost never clicking on them!\n\u003c/small\u003e\u003c/span\u003e\nI have become convinced of the idea that, if you are not paying for the product, you are the product. From this assumption, it follows that anywhere I trust with my data that I am not paying for (like Google Drive, Google Photos, Dropbox, Facebook, Twitter) is using my data to earn money. We know that \u003ca href=\"https://www.theverge.com/2020/11/11/21559930/google-train-ai-photos-image-labelling-app-android-update\"\u003eGoogle uses the labels you add to Photos to train it\u0026rsquo;s AI\u003c/a\u003e, and \u003ca href=\"https://ai.facebook.com/blog/seer-the-start-of-a-more-powerful-flexible-and-accessible-era-for-computer-vision/\"\u003eFacebook uses (at least) Instagram photos to train it\u0026rsquo;s AI\u003c/a\u003e. For some, the value proposition of allowing a company to use your data for a useful service in return is an acceptable one. I find this to be a reasonable stance, but I took my growing interest in internet privacy as a chance to learn about how I can take control of my data.\u003c/p\u003e","title":"My selfhosting journey."},{"content":"N.B.: I hope to add screenshots for each of these eventually. For now, I hope links to each services\u0026rsquo; website will suffice.\nSeafile\nThis is a great tool for managing files. I moved to this from Nextcloud because I am of the philosophy that I would prefer services that do one thing excellently instead of many things well. Nextcloud is an incredible Office365 replacement, but I found myself using a fraction of what it was capable of providing. Enter Seafile. It is cloud file syncing with a robust encryption implementation, just what the doctor ordered.\nPhotoprism\nNextcloud\u0026rsquo;s implementation of photo management was a bit clumsy for my tastes, so I began on a hunt for a more feature complete option. I was very lucky to stumble upon Photoprism early on in my self hosting journey. I am a proud supporter of this project. It brings a ton to the table, and doesn\u0026rsquo;t leave me missing Google Photos one bit. It is also actively developed. For instance, as of 2022-07-02, there was a recent update that improved scrolling a ton, which was one of my remaining quibbles with it\u0026rsquo;s functionality. Some people complain that it doesn\u0026rsquo;t scale up for libraries of 10,000+ photos, but my 2000 photo library works swimmingly. On my phone, I use the Folder Sync app to automatically send any pictures I take on my phone to the Photoprism imports folder. Within 15 minutes of snapping a photo, it is there on my Photoprism instance. I highly recommend giving it a go.\nMealie\nI have to admit that the name leaves something to be desired. Fortunately, the service itself doesn\u0026rsquo;t fall short. Mealie is a recipe management application. It is able to parse your favorite recipe websites to create immortalized versions of the recipe. This helps fight detestable link rot that plagues the internet. It allows you to edit ingredient amounts, make comments about what you would change next time, and plan out your weekly meals. It helps that it is beautiful and intuitive to use. If only I could get my partner to use it\u0026hellip; I want to go on the record here and say that I think it is sensible that she doesn\u0026rsquo;t trust my self hosted services that much. In the early days of my self hosting journey, let\u0026rsquo;s just say that the up-time of my services were extremely finicky. I like to think they are more permanent now, especially because I am hosting everything on a VPS, but I certainly cannot compete with the stability of Google and Amazon. (Or pretty much any other paid service for that matter.) \u0026#x1f609;\nGitea\nGitea is a community managed, lightweight code hosting solution written in Go. I use it to manage my data analysis (using Private repos) and even host the source code for this very website! Using Gitea has given me the surface level introduction to the behemoth that is git. Fortunately, that is all I need. Once I have removed any sensitive data (like passwords, etc.) I will make my docker-compose file public. The docker-compose file is where I determine which services I pick to host, and how to configure them to my liking. Hopefully someone will find this useful.\nSyncthing\nIf I could only tell someone to self host a single service, I would have to pick Syncthing. It is a continuous file synchronization program, which means it keeps a specific file or folder the same between any device running Syncthing. I use it to keep my password database and my org-mode notes Now org-mode might be the biggest rabbithole of them all, and definitely the topic for another blog post. I use it to manage my TODO list, my lab notebook, my shopping lists, write this blog, and maintain my Zettelkasten note database. It is an immensely powerful tool. up to date between all of my devices. With Syncthing, all of my data is stored on my own devices and encrypted in transit.\nFreshRSS\nI keep up to date on the science in my field by subscribing to relevant RSS feeds. Yet another topic to write a post about. This really changed the game for my ability to keep on top of the latest research. 2022-07-14 Update: post complete! Check it out here. FreshRSS replaced Feedly for me, as I ran up against the number of feeds I could subscribe to on a free account. Also, when self hosting, I can save as many articles as my heart desires (even if I will never look at them again \u0026#x1f635; ).\nWallabag\nRemember Pocket for Firefox? (Yes, I know it still exists, okay?) Give Wallabag a spin, it is great for storing articles you want to read later. I set up FreshRSS to save articles to my Wallabag instance to keep for later.\nChangeDetection\nNow this is a fun one! ChangeDetection.io is a service that loads a webpage and checks to see if something has changed since the last time. This might not sound useful at first, but I recently used this to check for when a hot item for my new coffee roasting hobby was back in stock. I got an email the other day to let me know it was in stock. Pretty cool!\nHugo\nHugo is the static site generator I use to make this here blog! I was amazed at how much more response my site was using Hugo compare to when I paid a company to host a WordPress site. I\u0026rsquo;m sure WordPress could be fast, but I just wanted a barebones, pure html experience, and Hugo made it easy.\nCommento++\nYou may have noticed that I have some pretty snazzy comments sections on my site. I initially used Disqus, which you may recognize from a ton of sites around the internet, but didn\u0026rsquo;t like how it would serve ads through my comments section, and provided sign-ins using Google/Facebook/Twitter. I wanted to serve the simplest comments section I could, that still gave me the ability to migrate the comments to wherever I decide to keep my server. Go ahead and use the anonymous comment button, fill in your name, and you are off to the races.\nAuthelia\nThere are a few services I host that I really want to lock down. For these services, Authelia is great. It puts up a \u0026ldquo;Enter the 6 digit code on your phone\u0026rdquo; style 2 factor authentication in front of the services I choose. Or, if you follow the guide here, you can have it send you a DUO push, just like you are one of the big hitters out there. I feel much more secure with Authelia in front of Adminer, Traefik, and Portainer.\nBoring stuff that allows everything else to work!\nPostgreSQL database MariaDB database Traefik reverse proxy Umami privacy respecting site analytics Portainer for docker container management Redis in-memory data store Adminer database management traefik-socket-proxy to prevent pesky backdoors to my server! ","permalink":"https://www.zacharybillman.com/posts/zpb-current-selfhosted/","summary":"\u003cp\u003e\u003cem\u003eN.B.: I hope to add screenshots for each of these eventually. For now, I hope links to each services\u0026rsquo; website will suffice.\u003c/em\u003e\u003c/p\u003e\n\u003col\u003e\n\u003cli\u003e\n\u003cp\u003e\u003ca href=\"https://www.seafile.com/en/home/\"\u003eSeafile\u003c/a\u003e\u003c/p\u003e\n\u003cp\u003eThis is a great tool for managing files. I moved to this from Nextcloud because I am of the philosophy that I would prefer services that do one thing excellently instead of many things well. Nextcloud is an incredible Office365 replacement, but I found myself using a fraction of what it was capable of providing. Enter Seafile. It is cloud file syncing with a robust encryption implementation, just what the doctor ordered.\u003c/p\u003e","title":"What I'm currently selfhosting."},{"content":"My partner and I took a trip to the Mason Farm Biological Reserve the other day, and what a glorious day it was. This year, I\u0026rsquo;ve been quite busy in the lab, and missed a lot of the early spring warbler season, so I was very excited by the opportunity to check out the old stomping grounds.\nI brought the camera with me despite the fact we were going to be there around midday when the birds are much less active. I\u0026rsquo;m glad I did, because I got the best look at a common yellowthroat I\u0026rsquo;ve ever had. Normally these guys are flighty, staying close to the ground in small brush or tall grasses, but this one was putting on a proper show for the mating season. Even when you get a glimpse of one, it is usually just that, as they have jumped away before you can pull out the camera, taunting you with their iconic call. I was very pleased to capture a few choice shots of the bird. Hopefully there are more to come. While we were out, I also got a nice picture of a hermit thrush and a king snake.\nThese images have been compressed quite a bit for a lighter internet footprint. These have all been resized to 25% of their original size. If you would like the full sized images, let me know and I will send you a link!\n","permalink":"https://www.zacharybillman.com/posts/the-uncommon-yellowthroat/","summary":"\u003cp\u003eMy partner and I took a trip to the \u003ca href=\"https://ncbg.unc.edu/visit/mason-farm-biological-reserve/\"\u003eMason Farm Biological Reserve\u003c/a\u003e the other day, and what a glorious day it was. This year, I\u0026rsquo;ve been quite busy in the lab, and missed a lot of the early spring warbler season, so I was very excited by the opportunity to check out the old stomping grounds.\u003c/p\u003e\n\u003cp\u003eI brought the camera with me despite the fact we were going to be there around midday when the birds are much less active. I\u0026rsquo;m glad I did, because I got the best look at a common yellowthroat I\u0026rsquo;ve ever had.\n\u003cspan class=\"sidenote-number\"\u003e\u003csmall class=\"sidenote\"\u003e\nNormally these guys are flighty, staying close to the ground in small brush or tall grasses, but this one was putting on a proper show for the mating season. Even when you get a glimpse of one, it is usually just that, as they have jumped away before you can pull out the camera, taunting you with their \u003ca href=\"https://ebird.org/species/comyel#Modal-playlist\"\u003eiconic call\u003c/a\u003e.\n\u003c/small\u003e\u003c/span\u003e\nI was very pleased to capture a few choice shots of the bird. Hopefully there are more to come. While we were out, I also got a nice picture of a hermit thrush and a king snake.\u003c/p\u003e","title":"The (un)common yellowthroat."},{"content":"Welcome to my site! My name is Zachary Billman. I\u0026rsquo;m a UNC MD-PhD student in my 4th year of med school applying to pathology residency programs. I completed my PhD in Ed Miao\u0026rsquo;s lab. The curious reader may be thinking: \u0026ldquo;But Zach, Dr. Miao\u0026rsquo;s lab is at Duke, how did that come about?\u0026rdquo; What an astute question! Ed\u0026rsquo;s lab moved from UNC to Duke in early 2020, and I followed him down the street. My PhD was awarded by the UNC department of Microbiology and Immunology, but it just so happens that (nearly) all of my research took place at Duke. This move was quite a trial, especially when compounded with the onset of the pandemic. I suspect my research timeline suffered, though this is an extremely minor inconvenience compared to the tragedy the pandemic caused. This makes for very interesting basketball viewing parties with my Duke friends!\nMaybe having a diagram will make my training timeline make a bit more sense.\nFigure 1: An overview of my research training. I first began working for Dr. Sean Murphy in undergrad, then worked as a research scientist/lab manager for 3 years before heading to UNC for my MSTP training. During grad school, my lab moved from UNC to Duke, though my degree was awarded by UNC. The \u0026ldquo;Present\u0026rdquo; diamond was used on an older version of my CV and represents September 1st, 2025. Created using PlantUML.\nHopefully that can clear up the winding road I\u0026rsquo;ve taken a bit!\nMy research and scientific interests. I am broadly interested in innate immunology. I spent most of my time in graduate school studying the host-pathogen interaction between the intracellular fungus Histoplasma capsulatum and macrophages. There are many unstudied curiosities regarding the innate immune response to Histoplasma spp. and other intracellular fungi that I think are quite interesting. I also spent a considerable time thinking about the evolution of proteins involved in the programmed cell death pathway called pyroptosis.\nHobbies I may write about. Besides my science, I am interested in birding, baking sourdough bread (I swear I began years before the pandemic, though hearing of people baking bread brings me joy no matter when they first began!), board games, roasting coffee, and self-hosting free and open source software. Over the course of the pandemic, I have learned how to maintain a basic suite of services spread between a server I rent and a computer at home that have replaced my need for Google Photos and Google Drive. I\u0026rsquo;m hoping to be able to move away from these platforms entirely soon. I think they provide a great service, but at a substantial cost to privacy. Hopefully more to be said about my thoughts on FOSS soon! I also transitioned my old, (and quite frankly, embarrassingly slow) managed WordPress site with this lean, static site made in Hugo that I host myself. Now that I have mangled together some CSS to get my precious sidenotes up and running again, I\u0026rsquo;m ready to begin putting some ideas to paper. I love marginalia (the word to describe these notes on the side of this webpage). I\u0026rsquo;m not sure if this is unique to me, but I seem to get caught up in parenthetical / tangential thoughts very often, and I think using an Edward Tufte-esque sidenote is a great way for me to communicate in this way without distracting the reader too much. It seems marginalia such as this have been used throughout history, so perhaps it is normal, but most people can keep their thoughts focused better than me. The implementation I use is inspired by the Tufte CSS project and largely taken from this incredibly helpful post found at scripter.co. I\u0026rsquo;m quite proud of my progress in administering my server and self-hosting useful services.\nThe future of this site. On this site I plan to post updates about my journey through med school, grad school, and self-hosting I would like to share with the world. I have been helped immensely by many others\u0026rsquo; advice and I hope to impart similar tips to others someday. I suspect most posts will be about much lighter fare, like whatever hobbies tickle my fancy at the time.\n","permalink":"https://www.zacharybillman.com/posts/about-me/","summary":"\u003ch2 id=\"welcome-to-my-site\"\u003eWelcome to my site!\u003c/h2\u003e\n\u003cp\u003eMy name is Zachary Billman. I\u0026rsquo;m a UNC MD-PhD student in my 4th year of med school applying to pathology residency programs. I completed my PhD in Ed Miao\u0026rsquo;s lab. The curious reader may be thinking: \u0026ldquo;But Zach, Dr. Miao\u0026rsquo;s lab is at Duke, how did that come about?\u0026rdquo; What an astute question! Ed\u0026rsquo;s lab moved from UNC to Duke in early 2020, and I followed him down the street. My PhD was awarded by the UNC department of Microbiology and Immunology, but it just so happens that (nearly) all of my research took place at Duke.\n\u003cspan class=\"sidenote-number\"\u003e\u003csmall class=\"sidenote\"\u003e\nThis move was quite a trial, especially when compounded with the onset of the pandemic. I suspect my research timeline suffered, though this is an extremely minor inconvenience compared to the tragedy the pandemic caused.\n\u003c/small\u003e\u003c/span\u003e\nThis makes for very interesting basketball viewing parties with my Duke friends!\u003c/p\u003e","title":"About me. 👋"},{"content":"It\u0026rsquo;s over. My third year of medical school is officially behind me. I managed to get in a grand total of zero blog posts during grad school, so here\u0026rsquo;s to a new year with hopefully some more thoughts being shared. I have a lot to reflect on from the past year. It was wonderful. I wish everyone could experience what I did this past year. I think it goes without saying:\nI loved the third year of med school, but I do not want to do it again.\nA year of change. In the days leading up to my return to med school, I thought \u0026ldquo;Oh no, I really enjoy doing science, do I really have to go to med school?\u0026rdquo;. I also remember at the end of Step 1 and the first two years of med school thinking, \u0026ldquo;Oh no, I really enjoy med school, do I really have to do science again?\u0026rdquo;. I think I have a welcome problem of enjoying what I\u0026rsquo;m doing. The third year of med school is a shift. After years of memorizing and examinations, the doors to the promised land are finally opened. I have experienced nothing like it before It feels intentionally unsettling. You are thrown into the clinic with a modicum of guidance so you aren\u0026rsquo;t totally caught off guard, but you are thrown out to the wolves. I don\u0026rsquo;t mean this as a criticism of the system, it feels necessary. Third year medical students—commonly shorted to MS3s—have just one year to experience a broad swath of medicine and pick a specialty. So you had better be ready to dive in.\nTotal immersion I came to terms with my new reality quickly. Gone were the days of hitting the snooze button and going home when I pleased. I am now beholden to other people\u0026rsquo;s schedules. This came back relatively naturally. Maybe not hitting snooze. A regrettable personal failing of mine. I was, however, immediately faced with a new reality in the patient room. Patients come to the doctor for a number of reasons, but often seek relief. To get to the core of what ails them, they will tell you everything. I was not prepared for how vulnerable patients would be with me. I am not sure if this ever will feel natural. I hope it never does. I was told many stories of experiences living with scary diagnoses, and not knowing what to do with it. Family histories of all sorts. Personal details that were sometimes (oftentimes?) off the wall. I see all of these specifics as flailing, grasping at sand hoping that something could explain their pain. Sometimes it could. Usually it did not. But since I was in a white coat, I was privileged to hear it.\nI think my years spent in the lab have prepared me to face some of the challenges set before me. At the very least, having a few more years under my belt helped me approach the year with a bit of maturity. This seems to have paid off. I guess my recommendation is to simply get old before going to med school. Returning to studying The hospital is how I spent the majority of my time, but a new reality for me was also going back to daily studying. There is a strange dichotomy in medicine of \u0026ldquo;Oh, it doesn\u0026rsquo;t really matter\u0026rdquo; and \u0026ldquo;If you don\u0026rsquo;t get this class/score/grade then you won\u0026rsquo;t be able to be the kind of doctor you want to be, so you had better get your act together.\u0026rdquo; Simultaneously there are no expectations and immense responsibility for the looming specter of Step 2. I\u0026rsquo;m glad that studying regularly came back easily enough. I was concerned I would experience a studying whiplash. I\u0026rsquo;m glad it never came. I did UWorld and Anki nearly every day for a full year and felt alright.\nBecoming invisible I quickly learned I needed to change my understanding of my contribution to the team. Exiting grad school, people understood that they could come to me for help. I was a resource, a seasoned veteran of the lab. If someone needed an experiment done, I could do it, and be trusted to do it. In med school as a third year, I was nothing. A fly on the wall; a worm beneath the feet of the real doctors. In science, I felt like I was treated as a peer with even my committee members with multiple R01s. Even if I didn\u0026rsquo;t understand the science perfectly, I could contribute some different perspective. In medicine, sometimes not being recognized at all by my attendings was the best outcome. Which happened regularly. My role, was not as a contributor—as it was in science—it was simply to get in the reps. Once I understood that the expectations of me were below the ground, I understood that everything I did in third year was for myself. This is taken at face value by the team at times. I would spend 30 minutes working on a presentation, pre-rounding, the works, and at the end of my part, the intern would nod, then turn to the senior resident and say \u0026ldquo;I was thinking that we\u0026hellip;\u0026rdquo; without thinking of my work. This is perhaps a bit of cognitive restructuring, but recognizing this is what gave me the freedom to embed myself in the hospital flow, without a single worry about the outcome. Simply doing my best was the best thing I could do. Obviously. But this was not apparent to me at first. I needed more quality repetitions to develop good habits in the future. And also experience as much of medicine as possible to find what I want to do with my life. This permission allowed me to approach specialties I do not care about with the awe and respect they deserve.\nA year of wonder. Med school prepares you for the standardized tests. I think this is generally useful. The tests on aggregate are reasonable and evaluate your ability to think through common clinical scenarios. There will always be oddball questions that come out of left field, but I let these flow over me. No need to perseverate on the small stuff. The time for that can come later.\nWhat I didn\u0026rsquo;t realize is how much of the \u0026ldquo;classic\u0026rdquo; material we are fed in the first couple years of med school would come to the forefront. The \u0026ldquo;sandpaper rash\u0026rdquo; of scarlet fever really does feel like sandpaper. Nikolsky\u0026rsquo;s sign actually works. Tripoding for epiglottitis gets the physicians worked up. Don\u0026rsquo;t forget about von Willebrand\u0026rsquo;s disease when someone seems to be bleeding a bit too much. TB is out there, watch for hemoptosis. Night sweats, unintended weight loss, is cancer until proven otherwise. And yes, it really can be lupus.\nIn general, facing the unknown with a sense of earnestness was the way I felt best able to respect those who gathered and passed down the medical knowledge I am privileged to learn today. Sometimes, my excitement to see aspects of medicine would rouse a curious response from the residents. I project here, but I felt a sense of surprise, like that of a doting parent seeing their child experience something new, after forgetting the astonishment they once felt.\nEarnestness is next to med studentlyness.\nPerhaps what I\u0026rsquo;m getting at here is that I found it important to bask in the privilege of seeing the pathology I encountered in med school, and to remind the residents of this sensation. I felt childish at times—and perhaps overanimated—but I found this excitement was to my and my resident\u0026rsquo;s benefit.\nMy surgery rotation overflowed with examples of wonder of medicine. Partially because of the team I worked with, and the rest because of the undeniable coolness of surgery. The OR is a cool place. The orderliness and chaos ebb. The spans of steady, industrious work are interrupted with staccato notes of bedlam. The anatomy I learned in class was ever present, but the surgeons bemoaned \u0026ldquo;normal anatomic variation\u0026rdquo;.\nI was struck with wonder at the sight of human anatomy as it unfolded before me. What I was able to experience in the OR felt like the culmination of centuries of human curiosity. There is an ancientness to medicine that I catch flashes of—I could perform the physical exam on humans hundred of millions of years ago and interrogate the same pathologies as I do in the hospital today—and viewing the exposed anatomy is a pressure-bagged infusion of this collective wonder. To gaze upon the peristalsing of the small intestine, or steady beating of the heart is a sight to behold, indeed.\nA year of shame. It weighs upon me the circumstances that resulted in these transcendent experiences. Not one patient was in the hospital without reason. What to make of these patients with horrible pathology? I still feel unsettled about how the cause of their pain sparked wonder. How dare I gain, merely by the circumstance of having their care managed at UNC, Which, as a tertiary care center, layers on more complexity. Many patients end up at UNC because they have no where else they can go for help. And this signs them up for med students? For shame. from the very essence of their malady? I do not know what to do with my discomfort, but I think it is best that I dwell in it. With this, I respect the people before me in the hospital and recognize their humanity.\nBut I often complained of what I say here I was lucky to do. I find myself resentful of my future schedule; when was I supposed to learn that I will be working 13 hour days, 6 days a week for the rest of my life? And what of having a family? Medicine by necessity requires sacrifice. I happened to sign up for sacrifices years before I recognized how profound they were. How might I balance this dread and with the joy of practicing medicine? And why do I seem more concerned about this than others? Am I not grateful enough? Am I not capable of the sacrifices that others seem to offer so effortlessly? I don\u0026rsquo;t necessarily think this to be true, but these questions erode at my will to pursue medicine.\nPerhaps most shameful of all is how my understanding of the patient-provider interaction evolved over the year. It began as an exploration of an open book, a tabula rasa that held within it a diagnosis and how to best intervene. On my first day in the outpatient clinic, it was clear that this is not the case. My preceptor had only 20 minutes for me to ① interview the patient and perform the physical exam, ② present with a plan, ③ return to the room and do everything again, ④ write orders, educate, and get the patient out of the door. It simply is not amenable to the free form, personable, curious interview I hoped to perform. By the end of the year, I had optimized how I asked questions to keep patients from going off the rails. When prerounding in medicine, I was there to extract information and not much else. Small talk had to go, there was no time. I like to chat, so this came at a loss of who I think I am. I am not sure how to do this well, while still feeling like Zachary. And from what I gather from the interns, that may just come later in my career. I found myself questioning, \u0026ldquo;Is this the \u0026lsquo;patient interaction\u0026rsquo; that has been mythologized throughout my training?\u0026rdquo; The carrot at the end of the stick dangled before me with a \u0026ldquo;You are so lucky to be able to do this, so you had better not complain of any abuse that comes your way.\u0026rdquo; It wasn\u0026rsquo;t a genuine interaction as much as me leading the patient along to tell me what I wanted to know. Of course, I used open ended questions, but only open enough. Leave the door a bit too open and next thing you know, you are talking about their dog\u0026rsquo;s breeder while you constantly stare at your watch, imagining what your attending will say when you return. I feel like I am alone in missing the core human element that funnels sprightly youths into medicine. Or worse, finding it a façade.\nThe shame extends beyond the hospital. One aspect of my life that has changed most dramatically is the sheer amount of time I felt I needed to dedicate to medicine, whether at the hospital or at home. I spent all day basking in the wonder of medicine, then I would come home and study for hours. I relied on my partner for keeping our household together more than ever, because I spent all day—all year, rather—in a state of discovery. Her life was largely the same, with the normal challenges of being a scientist, with the added bonus of getting less help from me. The shame built over the year. Again, how dare I?\nA year of glad. This has been an undeniable year of growth and joy, with these quibbles. It is clear that I was happier than I was during grad school. I know this from within myself, and reinforced by my wife\u0026rsquo;s comments on my mood. The pace of the day, and immediacy of problem solving were a welcome change.\nI recall, during the very first days preparing for med school during xTAP, having to do a simulated patient encounter complete with patient presentation to an attending physician. We were told about this encounter days in advance. And yet, I dreaded it. And near the last day of my final rotation, I did 8 of these in a row without breaking a sweat. Progress!\nI think, in a word, what I\u0026rsquo;ve experienced in the third year of med school is gratitude. Gratitude to be privileged to learn what I am learning. Gratitude for the experiences in my life that brought me here. Gratitude for the support from my wife. Gratitude to be involved in people\u0026rsquo;s lives when they are fragile. Ever since reading Braiding Sweetgrass I think one could call me \u0026ldquo;gratitude-pilled\u0026rdquo;. I also selfishly enjoyed the gratitude from patients as I put on my best doctor performance. In reflection on the year, I have spent time thinking of a phrase that I heard a number of times throughout med school from residents, \u0026ldquo;The worst day of residency is better than the best day of med school.\u0026rdquo; I find this hard to believe. This year has been magical. It is hard to imagine a year filled with more wonder and joy of caring for those in need. I will have to rely on the experience of those who have walked this path and trust that the rest of my training has plenty of magic to spare.\n","permalink":"https://www.zacharybillman.com/posts/ms3-year-is-magical/","summary":"\u003ch2 id=\"it-s-over-dot\"\u003eIt\u0026rsquo;s over.\u003c/h2\u003e\n\u003cp\u003eMy third year of medical school is officially behind me. I managed to get in a grand total of \u003cem\u003ezero\u003c/em\u003e blog posts during grad school, so here\u0026rsquo;s to a new year with hopefully some more thoughts being shared. I have a lot to reflect on from the past year. It was wonderful. I wish everyone could experience what I did this past year. I think it goes without saying:\u003c/p\u003e","title":"The third year of medical school is magical."},{"content":"I, like many others, picked up a new hobby during the pandemic. Other people\u0026rsquo;s hobbies may bring them joy. This could be for many reasons. There is the joy of creating something from scratch. You can revel in your thriftiness. You can embrace the pride when you recognize that your creation is on par (or better!) than what you can buy. I feel like these are embodied in the sourdough craze that caught fire early on in COVID. Dare I say that I did this before it was cool? \u0026#x1f60e; I baked two loaves of bread almost every weekend through med school. Maybe I should bring that back, it\u0026rsquo;s been a while since I brought out the ole\u0026rsquo; starter. My pandemic hobby is similar, but different in that it often feels like a chore, costs more money, and often turns out worse than what I can buy. Of course, I am talking about how I\u0026rsquo;ve started roasting my own coffee at home.\nI\u0026rsquo;m not sure where this idea was planted into my brain. I don\u0026rsquo;t think I know anyone who roasts their own beans, and I certainly didn\u0026rsquo;t know how. I didn\u0026rsquo;t even drink coffee regularly until after college! I guess that extra time on the computer sent me down a rabbithole I have yet to emerge from.\nFirst, I want to preface the following with a disclaimer: This is not a detailed guide about how to roast your own coffee. If you are interested, I recommend checking out the How To Roast Your Own Coffee guide at Sweet Maria\u0026rsquo;s as a starting point. There is also the /r/roasting subreddit if that is your cup of tea. My only warning is there will be a lot of smoke. Roast your coffee outside, for Pete\u0026rsquo;s sake!\nIt all started with a trusty popcorn popper. There are a few things you want when you roast coffee:\nAir hot enough to roast coffee Remove the chaff from the beans Turns out that a classic popcorn popper fits the bill, as long as it has an upwards airflow and doesn\u0026rsquo;t let the chaff fall into the heating element. There is a bit of a cult following for the West Bend Poppery 2 model, but that one seemed a bit pricey, so I settled for a very capable popper from Nostalgia.\nFigure 1: I got a good bit of mileage out of my popcorn popper. If you are interested in roasting your own coffee I would give it a whirl.\nThings were simple back then. I still bought most of the coffee I drank, but I roasted enough to enjoy some freshly roasted coffee as an occasional treat. I ordered 10 pounds of green beans from Sweet Maria\u0026rsquo;s and life was good.\nThen I became a bit of a coffee snob.\nI could only roast 100 grams of coffee at a time in the popcorn popper, which is only enough for one pot of coffee in the morning for me. So it was time to upgrade.\nI bought the SR800 fluid bed roaster, which upped my roasting capacity and gave me finer control on temperature and airflow. Suffice to say my roasts improved a lot! At this point, I would consider my coffee good enough to sell at a farmer\u0026rsquo;s market to break even.\nIf you ever find yourself on a coffee roasting forum and bring up the SR800, someone is bound to bring up the famous RazzoRoasting extension tube. If you look for advice for how to use the SR800, I swear it\u0026rsquo;s assumed that you have this very specific accessory. \u0026hellip;And so I bought one.\nDon\u0026rsquo;t worry, that is the extent of all of my coffee spending (for now). I am a very satisfied coffee roaster now. Check out this quick series of images going from the green beans to a nearly finished product! I can spend about 45 minutes and go from nothing to nearly 2 pounds of roasted beans, enough for about a week and a half of coffee. Not bad! The only downside is that now I feel like I need to buy coffee from local roasters to get my fix. There are certainly crueler fates.\nAs a sign off, I will share something that surprised me about coffee roasting. When I roast coffee, the most important cue to determine if the coffee is roasted is the sound. That\u0026rsquo;s right, not the color, not the smell, but the sound. When heating up a coffee bean, the water trapped inside eventually bursts out of the bean in a rapid expansion. This is called \u0026ldquo;first crack\u0026rdquo;, and indicates that the coffee is roasted enough to be drinkable. The expansion also releases the chaff from the bean. If you continue heating up the bean, you will eventually reach \u0026ldquo;second crack\u0026rdquo;. I think a solid medium roast is taken out just before second crack, so I try to take my coffee out to this point and it hasn\u0026rsquo;t proved me wrong yet.\nHappy coffee-ing! \u0026#x2615;\n","permalink":"https://www.zacharybillman.com/posts/roasting-coffee-at-home/","summary":"\u003cp\u003eI, like many others, picked up a new hobby during the pandemic. Other people\u0026rsquo;s hobbies may bring them joy. This could be for many reasons. There is the joy of creating something from scratch. You can revel in your thriftiness. You can embrace the pride when you recognize that your creation is on par (or better!) than what you can buy. I feel like these are embodied in the sourdough craze that caught fire early on in COVID.\n\u003cspan class=\"sidenote-number\"\u003e\u003csmall class=\"sidenote\"\u003e\nDare I say that I did this before it was cool? \u0026#x1f60e; I baked two loaves of bread almost every weekend through med school. Maybe I should bring that back, it\u0026rsquo;s been a while since I brought out the ole\u0026rsquo; starter.\n\u003c/small\u003e\u003c/span\u003e\nMy pandemic hobby is similar, but different in that it often feels like a chore, costs more money, and often turns out worse than what I can buy. Of course, I am talking about how I\u0026rsquo;ve started roasting my own coffee at home.\u003c/p\u003e","title":"Roasting coffee at home. ☕"},{"content":"It is an age-old question: how can one keep up with the continuous output of science? I remember at the beginning of my PhD struggling to figure out how anyone found out when a new paper came out. \u0026#x1f635; Did they sit on nature.com and spam the refresh button? Did they know when each journal released their latest issue?\nBehold the power of RSS! Most websites have a page that contains information about each subpage in a computer-readable format called RSS (Really Simple Syndication). Mine has one right here! These pages can be parsed by a number of RSS feed aggregators. The way these pages are set up make it such that they add any new information hosted at that domain. This is useful in the science world because you can find the RSS feed of a given journal, subscribe to it, then have every new article published online be delivered right to you.\nThere are a plethora of RSS feed aggregators you can pick from manage your feeds. I have previously used Feedly and Inoreader, which are great free solutions, but have moved on to selfhosting my own instance of FreshRSS.\nAfter making an account at your friendly local RSS feed aggregator, you can add whatever feeds your heart desires. To find a journal\u0026rsquo;s rss feed, I often just search \u0026ldquo;$JOURNAL_NAME rss feed\u0026rdquo; and poke around until I find something that looks right. Most of the aggregators will test the feed out first to make sure that you are trying to add a legitimate one. Here are a few of the heavy hitters to get you started:\nhttp://feeds.nature.com/nature/rss/current https://www.science.org/rss/express.xml https://www.cell.com/cell/inpress.rss Nothing like a constant stream of Cell, Science, and Nature to make your project feel like a real winner, eh?\nHere is what my own site looks like.\nFigure 1: My current FreshRSS setup. On the left I have my feeds separated into folders. In the middle you can see the titles of papers that appear in my feed.\nAnd after I hit J to move to the first item in the feed.\nFigure 2: With a title selected, you can see the abstract and authors.\nAfter collecting all of your desired RSS feeds, you cannot forego your responsibility of actually reading them! Most RSS feed aggregators have shortcuts to move through titles quickly (Typically J to move on to the next one and K to move up.) They always seem to use vi keybindings. A bunch of computer nerds have really cornered the keybinding market. I have let them take over my computing life. Each morning when I get into the lab, I quickly set up something, then head to my desk to hit J until the counter reaches zero.\nBut what about my very specific field? You can subscribe to all of the journals you want, but that doesn\u0026rsquo;t make the papers with your specific interests pop out. Fortunately, the NIH has this exact circumstance in mind.\nWhen you make a new search on PubMed you might notice the \u0026ldquo;Create RSS\u0026rdquo; button. Give it a click, then you will have a personal link you can add to your favorite RSS feed aggregator.\nFigure 3: Somehow I never noticed this button until I needed it.\nThis changed the game for me for keeping up with papers. Unfortunately, it doesn\u0026rsquo;t solve the problem of library management, or actually getting around to reading the papers you care about. I will leave library management as an exercise for the interested reader. Here\u0026rsquo;s a tip, the best solution uses the Zotero citation manager. Bonus points for using Zotfile for renaming your PDFs and Better BibTex for Zotero. \u0026#x1f609; I hope this helps you get your eyeballs on that science you crave. If you have solved the problem of accruing papers to read faster than you read them, let me know.\n","permalink":"https://www.zacharybillman.com/posts/rss-feeds-to-find-science-papers/","summary":"\u003cp\u003eIt is an age-old question: how can one keep up with the continuous output of science? I remember at the beginning of my PhD struggling to figure out how anyone found out when a new paper came out. \u0026#x1f635; Did they sit on nature.com and spam the refresh button? Did they know when each journal released their latest issue?\u003c/p\u003e\n\u003ch2 id=\"behold-the-power-of-rss\"\u003eBehold the power of RSS!\u003c/h2\u003e\n\u003cp\u003eMost websites have a page that contains information about each subpage in a computer-readable format called RSS (Really Simple Syndication). \u003ca href=\"https://zacharybillman.com/index.xml\"\u003eMine has one right here!\u003c/a\u003e These pages can be parsed by a number of RSS feed aggregators. The way these pages are set up make it such that they add any new information hosted at that domain. This is useful in the science world because you can find the RSS feed of a given journal, subscribe to it, then have every new article published online be delivered right to you.\u003c/p\u003e","title":"Using RSS feeds to keep on top of science."},{"content":"My interest in self-hosting began in my with my interests in internet privacy. Plastered all over the internet are stories about how much Google, Facebook and Amazon know about you. I deleted my Facebook account years ago, and I\u0026rsquo;m too paranoid to go back to the site because there\u0026rsquo;s a real possibility that Facebook has cached my account, ready to spin it back up in case I try to login again. The ads served to me were too accurate for my liking. This is despite almost never clicking on them! I have become convinced of the idea that, if you are not paying for the product, you are the product. From this assumption, it follows that anywhere I trust with my data that I am not paying for (like Google Drive, Google Photos, Dropbox, Facebook, Twitter) is using my data to earn money. We know that Google uses the labels you add to Photos to train it\u0026rsquo;s AI, and Facebook uses (at least) Instagram photos to train it\u0026rsquo;s AI. For some, the value proposition of allowing a company to use your data for a useful service in return is an acceptable one. I find this to be a reasonable stance, but I took my growing interest in internet privacy as a chance to learn about how I can take control of my data.\nInitially, I lurked on forums like /r/privacy to learn what I could do to avoid big-tech\u0026rsquo;s watchful eye. There were numerous comments along the lines of: \u0026ldquo;The only way to be in control of your data is to self-host your services.\u0026rdquo; I had no idea what this meant! Hard to believe that less than a year later, I learned to use (and love) Linux as my primary OS, and have happily replaced Google Photos, Google Drive and other services with my own self-hosted alternatives. Self-hosting, I have since learned, is when you run useful programs from your own computer. By doing so, you have complete knowledge of where and how your data is stored and how it is being used. It has the additional effect of being a bottomless time sink.\nTo begin, I needed an always-on computer to run these useful programs. I began with a humble Raspberry Pi.\nFigure 1: My humble Raspberry Pi and its hard drive. This dude currently tirelessly runs the excellent Adguard Home and downloads a backup of my data every night.\nThese are tiny, but capable computers that are great for fiddling with. The projects people develop for these are amazing and diverse. With RPi in hand, I began with the ambitious project of replacing Google Drive with Nextcloud. After much frustration with a bare metal installation, I found the NextcloudPi project. Surprisingly, it went pretty okay! At first, I was intimidated by Linux defaults, but over time I grew to appreciate, and indeed, prefer Linux as an operating system. My decision to use Linux over Windows/MacOS is because it is free and open source software (FOSS). This is a topic for a different post, but I think using FOSS when possible is a moral imperative of sorts. I used Nextcloud strictly from my home for a few months, without the ability to connect to it from the internet, to test the self-hosting waters. My first true cloud replacement spun up once I decided to access this lil\u0026rsquo; guy from the internet. To do so, I purchased a domain (not the one this site is hosted on) and pointed it to the IP of my house. I forwarded the appropriate ports of my router to the RPi.\nThis is when the real exploration began. I was able to access my files and images using Nextcloud, but the photo viewing service left something to be desired. No problem, why not spin up an instance of Photoprism? I use RSS feeds to keep on top of the latest science in the journals relevant to my field using Feedly. Why not host my own RSS feed aggregator so I can subscribe to as many feeds as I desire?\nThis cycle continued, and I accrued many cool applications, but in the back of my mind I worried about opening up my home network to the internet. I also struggled to run some programs because the RPi uses the arm64 architecture, and most services are written with amd64 in mind. These two forces eventually convinced me to purchase a server where I could manage all of my services remotely. Some would say that not owning the hardware that is running your own services is not \u0026ldquo;true\u0026rdquo; self-hosting. I think this is needlessly exclusive. Let everyone self host, dangit! Someday, when I have more stable internet and a more permanent home, I hope to host everything from my own home, but until then, I\u0026rsquo;m extremely pleased with my current stack. And that is where I am now. I happily host numerous services on my virtual private server that entirely replace Google Photos, Google Drive and GitHub for me. Even better, there are specialized services that fill a need I never realized I had. What\u0026rsquo;s more, if I ever want to spin up a new service, all I have to do is add it to my to docker-compose file and it will be up within minutes. What a world!\nI thought about making this into a \u0026ldquo;guide\u0026rdquo; style post. I nixed that idea because, quite frankly, I feel like I don\u0026rsquo;t know what I\u0026rsquo;m doing. I am really happy with my setup, but I don\u0026rsquo;t feel like I have the authority to tell people how to administer their own services. If you are interested, allow me to point you toward the guide that really got me rolling: Ultimate Traefik Docker Compose Guide.\nFor those of you wondering what I am currently hosting, check out my current list at the link and let me know what you think!\n","permalink":"https://www.zacharybillman.com/posts/my-selfhosting-journey/","summary":"\u003cp\u003eMy interest in self-hosting began in my with my interests in internet privacy. Plastered all over the internet are stories about how much Google, Facebook and Amazon know about you. I deleted my Facebook account years ago, and I\u0026rsquo;m too paranoid to go back to the site because there\u0026rsquo;s \u003ca href=\"https://www.reddit.com/r/privacy/comments/6nmjfh/facebook_account_fully_recovered_3_years_after/\"\u003ea real possibility that Facebook has cached my account, ready to spin it back up\u003c/a\u003e in case I try to login again. The ads served to me were too accurate for my liking.\n\u003cspan class=\"sidenote-number\"\u003e\u003csmall class=\"sidenote\"\u003e\nThis is despite almost never clicking on them!\n\u003c/small\u003e\u003c/span\u003e\nI have become convinced of the idea that, if you are not paying for the product, you are the product. From this assumption, it follows that anywhere I trust with my data that I am not paying for (like Google Drive, Google Photos, Dropbox, Facebook, Twitter) is using my data to earn money. We know that \u003ca href=\"https://www.theverge.com/2020/11/11/21559930/google-train-ai-photos-image-labelling-app-android-update\"\u003eGoogle uses the labels you add to Photos to train it\u0026rsquo;s AI\u003c/a\u003e, and \u003ca href=\"https://ai.facebook.com/blog/seer-the-start-of-a-more-powerful-flexible-and-accessible-era-for-computer-vision/\"\u003eFacebook uses (at least) Instagram photos to train it\u0026rsquo;s AI\u003c/a\u003e. For some, the value proposition of allowing a company to use your data for a useful service in return is an acceptable one. I find this to be a reasonable stance, but I took my growing interest in internet privacy as a chance to learn about how I can take control of my data.\u003c/p\u003e","title":"My selfhosting journey."},{"content":"N.B.: I hope to add screenshots for each of these eventually. For now, I hope links to each services\u0026rsquo; website will suffice.\nSeafile\nThis is a great tool for managing files. I moved to this from Nextcloud because I am of the philosophy that I would prefer services that do one thing excellently instead of many things well. Nextcloud is an incredible Office365 replacement, but I found myself using a fraction of what it was capable of providing. Enter Seafile. It is cloud file syncing with a robust encryption implementation, just what the doctor ordered.\nPhotoprism\nNextcloud\u0026rsquo;s implementation of photo management was a bit clumsy for my tastes, so I began on a hunt for a more feature complete option. I was very lucky to stumble upon Photoprism early on in my self hosting journey. I am a proud supporter of this project. It brings a ton to the table, and doesn\u0026rsquo;t leave me missing Google Photos one bit. It is also actively developed. For instance, as of 2022-07-02, there was a recent update that improved scrolling a ton, which was one of my remaining quibbles with it\u0026rsquo;s functionality. Some people complain that it doesn\u0026rsquo;t scale up for libraries of 10,000+ photos, but my 2000 photo library works swimmingly. On my phone, I use the Folder Sync app to automatically send any pictures I take on my phone to the Photoprism imports folder. Within 15 minutes of snapping a photo, it is there on my Photoprism instance. I highly recommend giving it a go.\nMealie\nI have to admit that the name leaves something to be desired. Fortunately, the service itself doesn\u0026rsquo;t fall short. Mealie is a recipe management application. It is able to parse your favorite recipe websites to create immortalized versions of the recipe. This helps fight detestable link rot that plagues the internet. It allows you to edit ingredient amounts, make comments about what you would change next time, and plan out your weekly meals. It helps that it is beautiful and intuitive to use. If only I could get my partner to use it\u0026hellip; I want to go on the record here and say that I think it is sensible that she doesn\u0026rsquo;t trust my self hosted services that much. In the early days of my self hosting journey, let\u0026rsquo;s just say that the up-time of my services were extremely finicky. I like to think they are more permanent now, especially because I am hosting everything on a VPS, but I certainly cannot compete with the stability of Google and Amazon. (Or pretty much any other paid service for that matter.) \u0026#x1f609;\nGitea\nGitea is a community managed, lightweight code hosting solution written in Go. I use it to manage my data analysis (using Private repos) and even host the source code for this very website! Using Gitea has given me the surface level introduction to the behemoth that is git. Fortunately, that is all I need. Once I have removed any sensitive data (like passwords, etc.) I will make my docker-compose file public. The docker-compose file is where I determine which services I pick to host, and how to configure them to my liking. Hopefully someone will find this useful.\nSyncthing\nIf I could only tell someone to self host a single service, I would have to pick Syncthing. It is a continuous file synchronization program, which means it keeps a specific file or folder the same between any device running Syncthing. I use it to keep my password database and my org-mode notes Now org-mode might be the biggest rabbithole of them all, and definitely the topic for another blog post. I use it to manage my TODO list, my lab notebook, my shopping lists, write this blog, and maintain my Zettelkasten note database. It is an immensely powerful tool. up to date between all of my devices. With Syncthing, all of my data is stored on my own devices and encrypted in transit.\nFreshRSS\nI keep up to date on the science in my field by subscribing to relevant RSS feeds. Yet another topic to write a post about. This really changed the game for my ability to keep on top of the latest research. 2022-07-14 Update: post complete! Check it out here. FreshRSS replaced Feedly for me, as I ran up against the number of feeds I could subscribe to on a free account. Also, when self hosting, I can save as many articles as my heart desires (even if I will never look at them again \u0026#x1f635; ).\nWallabag\nRemember Pocket for Firefox? (Yes, I know it still exists, okay?) Give Wallabag a spin, it is great for storing articles you want to read later. I set up FreshRSS to save articles to my Wallabag instance to keep for later.\nChangeDetection\nNow this is a fun one! ChangeDetection.io is a service that loads a webpage and checks to see if something has changed since the last time. This might not sound useful at first, but I recently used this to check for when a hot item for my new coffee roasting hobby was back in stock. I got an email the other day to let me know it was in stock. Pretty cool!\nHugo\nHugo is the static site generator I use to make this here blog! I was amazed at how much more response my site was using Hugo compare to when I paid a company to host a WordPress site. I\u0026rsquo;m sure WordPress could be fast, but I just wanted a barebones, pure html experience, and Hugo made it easy.\nCommento++\nYou may have noticed that I have some pretty snazzy comments sections on my site. I initially used Disqus, which you may recognize from a ton of sites around the internet, but didn\u0026rsquo;t like how it would serve ads through my comments section, and provided sign-ins using Google/Facebook/Twitter. I wanted to serve the simplest comments section I could, that still gave me the ability to migrate the comments to wherever I decide to keep my server. Go ahead and use the anonymous comment button, fill in your name, and you are off to the races.\nAuthelia\nThere are a few services I host that I really want to lock down. For these services, Authelia is great. It puts up a \u0026ldquo;Enter the 6 digit code on your phone\u0026rdquo; style 2 factor authentication in front of the services I choose. Or, if you follow the guide here, you can have it send you a DUO push, just like you are one of the big hitters out there. I feel much more secure with Authelia in front of Adminer, Traefik, and Portainer.\nBoring stuff that allows everything else to work!\nPostgreSQL database MariaDB database Traefik reverse proxy Umami privacy respecting site analytics Portainer for docker container management Redis in-memory data store Adminer database management traefik-socket-proxy to prevent pesky backdoors to my server! ","permalink":"https://www.zacharybillman.com/posts/zpb-current-selfhosted/","summary":"\u003cp\u003e\u003cem\u003eN.B.: I hope to add screenshots for each of these eventually. For now, I hope links to each services\u0026rsquo; website will suffice.\u003c/em\u003e\u003c/p\u003e\n\u003col\u003e\n\u003cli\u003e\n\u003cp\u003e\u003ca href=\"https://www.seafile.com/en/home/\"\u003eSeafile\u003c/a\u003e\u003c/p\u003e\n\u003cp\u003eThis is a great tool for managing files. I moved to this from Nextcloud because I am of the philosophy that I would prefer services that do one thing excellently instead of many things well. Nextcloud is an incredible Office365 replacement, but I found myself using a fraction of what it was capable of providing. Enter Seafile. It is cloud file syncing with a robust encryption implementation, just what the doctor ordered.\u003c/p\u003e","title":"What I'm currently selfhosting."},{"content":"My partner and I took a trip to the Mason Farm Biological Reserve the other day, and what a glorious day it was. This year, I\u0026rsquo;ve been quite busy in the lab, and missed a lot of the early spring warbler season, so I was very excited by the opportunity to check out the old stomping grounds.\nI brought the camera with me despite the fact we were going to be there around midday when the birds are much less active. I\u0026rsquo;m glad I did, because I got the best look at a common yellowthroat I\u0026rsquo;ve ever had. Normally these guys are flighty, staying close to the ground in small brush or tall grasses, but this one was putting on a proper show for the mating season. Even when you get a glimpse of one, it is usually just that, as they have jumped away before you can pull out the camera, taunting you with their iconic call. I was very pleased to capture a few choice shots of the bird. Hopefully there are more to come. While we were out, I also got a nice picture of a hermit thrush and a king snake.\nThese images have been compressed quite a bit for a lighter internet footprint. These have all been resized to 25% of their original size. If you would like the full sized images, let me know and I will send you a link!\n","permalink":"https://www.zacharybillman.com/posts/the-uncommon-yellowthroat/","summary":"\u003cp\u003eMy partner and I took a trip to the \u003ca href=\"https://ncbg.unc.edu/visit/mason-farm-biological-reserve/\"\u003eMason Farm Biological Reserve\u003c/a\u003e the other day, and what a glorious day it was. This year, I\u0026rsquo;ve been quite busy in the lab, and missed a lot of the early spring warbler season, so I was very excited by the opportunity to check out the old stomping grounds.\u003c/p\u003e\n\u003cp\u003eI brought the camera with me despite the fact we were going to be there around midday when the birds are much less active. I\u0026rsquo;m glad I did, because I got the best look at a common yellowthroat I\u0026rsquo;ve ever had.\n\u003cspan class=\"sidenote-number\"\u003e\u003csmall class=\"sidenote\"\u003e\nNormally these guys are flighty, staying close to the ground in small brush or tall grasses, but this one was putting on a proper show for the mating season. Even when you get a glimpse of one, it is usually just that, as they have jumped away before you can pull out the camera, taunting you with their \u003ca href=\"https://ebird.org/species/comyel#Modal-playlist\"\u003eiconic call\u003c/a\u003e.\n\u003c/small\u003e\u003c/span\u003e\nI was very pleased to capture a few choice shots of the bird. Hopefully there are more to come. While we were out, I also got a nice picture of a hermit thrush and a king snake.\u003c/p\u003e","title":"The (un)common yellowthroat."},{"content":"Welcome to my site! My name is Zachary Billman. I\u0026rsquo;m a UNC MD-PhD student in my 4th year of med school applying to pathology residency programs. I completed my PhD in Ed Miao\u0026rsquo;s lab. The curious reader may be thinking: \u0026ldquo;But Zach, Dr. Miao\u0026rsquo;s lab is at Duke, how did that come about?\u0026rdquo; What an astute question! Ed\u0026rsquo;s lab moved from UNC to Duke in early 2020, and I followed him down the street. My PhD was awarded by the UNC department of Microbiology and Immunology, but it just so happens that (nearly) all of my research took place at Duke. This move was quite a trial, especially when compounded with the onset of the pandemic. I suspect my research timeline suffered, though this is an extremely minor inconvenience compared to the tragedy the pandemic caused. This makes for very interesting basketball viewing parties with my Duke friends!\nMaybe having a diagram will make my training timeline make a bit more sense.\nFigure 1: An overview of my research training. I first began working for Dr. Sean Murphy in undergrad, then worked as a research scientist/lab manager for 3 years before heading to UNC for my MSTP training. During grad school, my lab moved from UNC to Duke, though my degree was awarded by UNC. The \u0026ldquo;Present\u0026rdquo; diamond was used on an older version of my CV and represents September 1st, 2025. Created using PlantUML.\nHopefully that can clear up the winding road I\u0026rsquo;ve taken a bit!\nMy research and scientific interests. I am broadly interested in innate immunology. I spent most of my time in graduate school studying the host-pathogen interaction between the intracellular fungus Histoplasma capsulatum and macrophages. There are many unstudied curiosities regarding the innate immune response to Histoplasma spp. and other intracellular fungi that I think are quite interesting. I also spent a considerable time thinking about the evolution of proteins involved in the programmed cell death pathway called pyroptosis.\nHobbies I may write about. Besides my science, I am interested in birding, baking sourdough bread (I swear I began years before the pandemic, though hearing of people baking bread brings me joy no matter when they first began!), board games, roasting coffee, and self-hosting free and open source software. Over the course of the pandemic, I have learned how to maintain a basic suite of services spread between a server I rent and a computer at home that have replaced my need for Google Photos and Google Drive. I\u0026rsquo;m hoping to be able to move away from these platforms entirely soon. I think they provide a great service, but at a substantial cost to privacy. Hopefully more to be said about my thoughts on FOSS soon! I also transitioned my old, (and quite frankly, embarrassingly slow) managed WordPress site with this lean, static site made in Hugo that I host myself. Now that I have mangled together some CSS to get my precious sidenotes up and running again, I\u0026rsquo;m ready to begin putting some ideas to paper. I love marginalia (the word to describe these notes on the side of this webpage). I\u0026rsquo;m not sure if this is unique to me, but I seem to get caught up in parenthetical / tangential thoughts very often, and I think using an Edward Tufte-esque sidenote is a great way for me to communicate in this way without distracting the reader too much. It seems marginalia such as this have been used throughout history, so perhaps it is normal, but most people can keep their thoughts focused better than me. The implementation I use is inspired by the Tufte CSS project and largely taken from this incredibly helpful post found at scripter.co. I\u0026rsquo;m quite proud of my progress in administering my server and self-hosting useful services.\nThe future of this site. On this site I plan to post updates about my journey through med school, grad school, and self-hosting I would like to share with the world. I have been helped immensely by many others\u0026rsquo; advice and I hope to impart similar tips to others someday. I suspect most posts will be about much lighter fare, like whatever hobbies tickle my fancy at the time.\n","permalink":"https://www.zacharybillman.com/posts/about-me/","summary":"\u003ch2 id=\"welcome-to-my-site\"\u003eWelcome to my site!\u003c/h2\u003e\n\u003cp\u003eMy name is Zachary Billman. I\u0026rsquo;m a UNC MD-PhD student in my 4th year of med school applying to pathology residency programs. I completed my PhD in Ed Miao\u0026rsquo;s lab. The curious reader may be thinking: \u0026ldquo;But Zach, Dr. Miao\u0026rsquo;s lab is at Duke, how did that come about?\u0026rdquo; What an astute question! Ed\u0026rsquo;s lab moved from UNC to Duke in early 2020, and I followed him down the street. My PhD was awarded by the UNC department of Microbiology and Immunology, but it just so happens that (nearly) all of my research took place at Duke.\n\u003cspan class=\"sidenote-number\"\u003e\u003csmall class=\"sidenote\"\u003e\nThis move was quite a trial, especially when compounded with the onset of the pandemic. I suspect my research timeline suffered, though this is an extremely minor inconvenience compared to the tragedy the pandemic caused.\n\u003c/small\u003e\u003c/span\u003e\nThis makes for very interesting basketball viewing parties with my Duke friends!\u003c/p\u003e","title":"About me. 👋"},{"content":"It\u0026rsquo;s over. My third year of medical school is officially behind me. I managed to get in a grand total of zero blog posts during grad school, so here\u0026rsquo;s to a new year with hopefully some more thoughts being shared. I have a lot to reflect on from the past year. It was wonderful. I wish everyone could experience what I did this past year. I think it goes without saying:\nI loved the third year of med school, but I do not want to do it again.\nA year of change. In the days leading up to my return to med school, I thought \u0026ldquo;Oh no, I really enjoy doing science, do I really have to go to med school?\u0026rdquo;. I also remember at the end of Step 1 and the first two years of med school thinking, \u0026ldquo;Oh no, I really enjoy med school, do I really have to do science again?\u0026rdquo;. I think I have a welcome problem of enjoying what I\u0026rsquo;m doing. The third year of med school is a shift. After years of memorizing and examinations, the doors to the promised land are finally opened. I have experienced nothing like it before It feels intentionally unsettling. You are thrown into the clinic with a modicum of guidance so you aren\u0026rsquo;t totally caught off guard, but you are thrown out to the wolves. I don\u0026rsquo;t mean this as a criticism of the system, it feels necessary. Third year medical students—commonly shorted to MS3s—have just one year to experience a broad swath of medicine and pick a specialty. So you had better be ready to dive in.\nTotal immersion I came to terms with my new reality quickly. Gone were the days of hitting the snooze button and going home when I pleased. I am now beholden to other people\u0026rsquo;s schedules. This came back relatively naturally. Maybe not hitting snooze. A regrettable personal failing of mine. I was, however, immediately faced with a new reality in the patient room. Patients come to the doctor for a number of reasons, but often seek relief. To get to the core of what ails them, they will tell you everything. I was not prepared for how vulnerable patients would be with me. I am not sure if this ever will feel natural. I hope it never does. I was told many stories of experiences living with scary diagnoses, and not knowing what to do with it. Family histories of all sorts. Personal details that were sometimes (oftentimes?) off the wall. I see all of these specifics as flailing, grasping at sand hoping that something could explain their pain. Sometimes it could. Usually it did not. But since I was in a white coat, I was privileged to hear it.\nI think my years spent in the lab have prepared me to face some of the challenges set before me. At the very least, having a few more years under my belt helped me approach the year with a bit of maturity. This seems to have paid off. I guess my recommendation is to simply get old before going to med school. Returning to studying The hospital is how I spent the majority of my time, but a new reality for me was also going back to daily studying. There is a strange dichotomy in medicine of \u0026ldquo;Oh, it doesn\u0026rsquo;t really matter\u0026rdquo; and \u0026ldquo;If you don\u0026rsquo;t get this class/score/grade then you won\u0026rsquo;t be able to be the kind of doctor you want to be, so you had better get your act together.\u0026rdquo; Simultaneously there are no expectations and immense responsibility for the looming specter of Step 2. I\u0026rsquo;m glad that studying regularly came back easily enough. I was concerned I would experience a studying whiplash. I\u0026rsquo;m glad it never came. I did UWorld and Anki nearly every day for a full year and felt alright.\nBecoming invisible I quickly learned I needed to change my understanding of my contribution to the team. Exiting grad school, people understood that they could come to me for help. I was a resource, a seasoned veteran of the lab. If someone needed an experiment done, I could do it, and be trusted to do it. In med school as a third year, I was nothing. A fly on the wall; a worm beneath the feet of the real doctors. In science, I felt like I was treated as a peer with even my committee members with multiple R01s. Even if I didn\u0026rsquo;t understand the science perfectly, I could contribute some different perspective. In medicine, sometimes not being recognized at all by my attendings was the best outcome. Which happened regularly. My role, was not as a contributor—as it was in science—it was simply to get in the reps. Once I understood that the expectations of me were below the ground, I understood that everything I did in third year was for myself. This is taken at face value by the team at times. I would spend 30 minutes working on a presentation, pre-rounding, the works, and at the end of my part, the intern would nod, then turn to the senior resident and say \u0026ldquo;I was thinking that we\u0026hellip;\u0026rdquo; without thinking of my work. This is perhaps a bit of cognitive restructuring, but recognizing this is what gave me the freedom to embed myself in the hospital flow, without a single worry about the outcome. Simply doing my best was the best thing I could do. Obviously. But this was not apparent to me at first. I needed more quality repetitions to develop good habits in the future. And also experience as much of medicine as possible to find what I want to do with my life. This permission allowed me to approach specialties I do not care about with the awe and respect they deserve.\nA year of wonder. Med school prepares you for the standardized tests. I think this is generally useful. The tests on aggregate are reasonable and evaluate your ability to think through common clinical scenarios. There will always be oddball questions that come out of left field, but I let these flow over me. No need to perseverate on the small stuff. The time for that can come later.\nWhat I didn\u0026rsquo;t realize is how much of the \u0026ldquo;classic\u0026rdquo; material we are fed in the first couple years of med school would come to the forefront. The \u0026ldquo;sandpaper rash\u0026rdquo; of scarlet fever really does feel like sandpaper. Nikolsky\u0026rsquo;s sign actually works. Tripoding for epiglottitis gets the physicians worked up. Don\u0026rsquo;t forget about von Willebrand\u0026rsquo;s disease when someone seems to be bleeding a bit too much. TB is out there, watch for hemoptosis. Night sweats, unintended weight loss, is cancer until proven otherwise. And yes, it really can be lupus.\nIn general, facing the unknown with a sense of earnestness was the way I felt best able to respect those who gathered and passed down the medical knowledge I am privileged to learn today. Sometimes, my excitement to see aspects of medicine would rouse a curious response from the residents. I project here, but I felt a sense of surprise, like that of a doting parent seeing their child experience something new, after forgetting the astonishment they once felt.\nEarnestness is next to med studentlyness.\nPerhaps what I\u0026rsquo;m getting at here is that I found it important to bask in the privilege of seeing the pathology I encountered in med school, and to remind the residents of this sensation. I felt childish at times—and perhaps overanimated—but I found this excitement was to my and my resident\u0026rsquo;s benefit.\nMy surgery rotation overflowed with examples of wonder of medicine. Partially because of the team I worked with, and the rest because of the undeniable coolness of surgery. The OR is a cool place. The orderliness and chaos ebb. The spans of steady, industrious work are interrupted with staccato notes of bedlam. The anatomy I learned in class was ever present, but the surgeons bemoaned \u0026ldquo;normal anatomic variation\u0026rdquo;.\nI was struck with wonder at the sight of human anatomy as it unfolded before me. What I was able to experience in the OR felt like the culmination of centuries of human curiosity. There is an ancientness to medicine that I catch flashes of—I could perform the physical exam on humans hundred of millions of years ago and interrogate the same pathologies as I do in the hospital today—and viewing the exposed anatomy is a pressure-bagged infusion of this collective wonder. To gaze upon the peristalsing of the small intestine, or steady beating of the heart is a sight to behold, indeed.\nA year of shame. It weighs upon me the circumstances that resulted in these transcendent experiences. Not one patient was in the hospital without reason. What to make of these patients with horrible pathology? I still feel unsettled about how the cause of their pain sparked wonder. How dare I gain, merely by the circumstance of having their care managed at UNC, Which, as a tertiary care center, layers on more complexity. Many patients end up at UNC because they have no where else they can go for help. And this signs them up for med students? For shame. from the very essence of their malady? I do not know what to do with my discomfort, but I think it is best that I dwell in it. With this, I respect the people before me in the hospital and recognize their humanity.\nBut I often complained of what I say here I was lucky to do. I find myself resentful of my future schedule; when was I supposed to learn that I will be working 13 hour days, 6 days a week for the rest of my life? And what of having a family? Medicine by necessity requires sacrifice. I happened to sign up for sacrifices years before I recognized how profound they were. How might I balance this dread and with the joy of practicing medicine? And why do I seem more concerned about this than others? Am I not grateful enough? Am I not capable of the sacrifices that others seem to offer so effortlessly? I don\u0026rsquo;t necessarily think this to be true, but these questions erode at my will to pursue medicine.\nPerhaps most shameful of all is how my understanding of the patient-provider interaction evolved over the year. It began as an exploration of an open book, a tabula rasa that held within it a diagnosis and how to best intervene. On my first day in the outpatient clinic, it was clear that this is not the case. My preceptor had only 20 minutes for me to ① interview the patient and perform the physical exam, ② present with a plan, ③ return to the room and do everything again, ④ write orders, educate, and get the patient out of the door. It simply is not amenable to the free form, personable, curious interview I hoped to perform. By the end of the year, I had optimized how I asked questions to keep patients from going off the rails. When prerounding in medicine, I was there to extract information and not much else. Small talk had to go, there was no time. I like to chat, so this came at a loss of who I think I am. I am not sure how to do this well, while still feeling like Zachary. And from what I gather from the interns, that may just come later in my career. I found myself questioning, \u0026ldquo;Is this the \u0026lsquo;patient interaction\u0026rsquo; that has been mythologized throughout my training?\u0026rdquo; The carrot at the end of the stick dangled before me with a \u0026ldquo;You are so lucky to be able to do this, so you had better not complain of any abuse that comes your way.\u0026rdquo; It wasn\u0026rsquo;t a genuine interaction as much as me leading the patient along to tell me what I wanted to know. Of course, I used open ended questions, but only open enough. Leave the door a bit too open and next thing you know, you are talking about their dog\u0026rsquo;s breeder while you constantly stare at your watch, imagining what your attending will say when you return. I feel like I am alone in missing the core human element that funnels sprightly youths into medicine. Or worse, finding it a façade.\nThe shame extends beyond the hospital. One aspect of my life that has changed most dramatically is the sheer amount of time I felt I needed to dedicate to medicine, whether at the hospital or at home. I spent all day basking in the wonder of medicine, then I would come home and study for hours. I relied on my partner for keeping our household together more than ever, because I spent all day—all year, rather—in a state of discovery. Her life was largely the same, with the normal challenges of being a scientist, with the added bonus of getting less help from me. The shame built over the year. Again, how dare I?\nA year of glad. This has been an undeniable year of growth and joy, with these quibbles. It is clear that I was happier than I was during grad school. I know this from within myself, and reinforced by my wife\u0026rsquo;s comments on my mood. The pace of the day, and immediacy of problem solving were a welcome change.\nI recall, during the very first days preparing for med school during xTAP, having to do a simulated patient encounter complete with patient presentation to an attending physician. We were told about this encounter days in advance. And yet, I dreaded it. And near the last day of my final rotation, I did 8 of these in a row without breaking a sweat. Progress!\nI think, in a word, what I\u0026rsquo;ve experienced in the third year of med school is gratitude. Gratitude to be privileged to learn what I am learning. Gratitude for the experiences in my life that brought me here. Gratitude for the support from my wife. Gratitude to be involved in people\u0026rsquo;s lives when they are fragile. Ever since reading Braiding Sweetgrass I think one could call me \u0026ldquo;gratitude-pilled\u0026rdquo;. I also selfishly enjoyed the gratitude from patients as I put on my best doctor performance. In reflection on the year, I have spent time thinking of a phrase that I heard a number of times throughout med school from residents, \u0026ldquo;The worst day of residency is better than the best day of med school.\u0026rdquo; I find this hard to believe. This year has been magical. It is hard to imagine a year filled with more wonder and joy of caring for those in need. I will have to rely on the experience of those who have walked this path and trust that the rest of my training has plenty of magic to spare.\n","permalink":"https://www.zacharybillman.com/posts/ms3-year-is-magical/","summary":"\u003ch2 id=\"it-s-over-dot\"\u003eIt\u0026rsquo;s over.\u003c/h2\u003e\n\u003cp\u003eMy third year of medical school is officially behind me. I managed to get in a grand total of \u003cem\u003ezero\u003c/em\u003e blog posts during grad school, so here\u0026rsquo;s to a new year with hopefully some more thoughts being shared. I have a lot to reflect on from the past year. It was wonderful. I wish everyone could experience what I did this past year. I think it goes without saying:\u003c/p\u003e","title":"The third year of medical school is magical."},{"content":"I, like many others, picked up a new hobby during the pandemic. Other people\u0026rsquo;s hobbies may bring them joy. This could be for many reasons. There is the joy of creating something from scratch. You can revel in your thriftiness. You can embrace the pride when you recognize that your creation is on par (or better!) than what you can buy. I feel like these are embodied in the sourdough craze that caught fire early on in COVID. Dare I say that I did this before it was cool? \u0026#x1f60e; I baked two loaves of bread almost every weekend through med school. Maybe I should bring that back, it\u0026rsquo;s been a while since I brought out the ole\u0026rsquo; starter. My pandemic hobby is similar, but different in that it often feels like a chore, costs more money, and often turns out worse than what I can buy. Of course, I am talking about how I\u0026rsquo;ve started roasting my own coffee at home.\nI\u0026rsquo;m not sure where this idea was planted into my brain. I don\u0026rsquo;t think I know anyone who roasts their own beans, and I certainly didn\u0026rsquo;t know how. I didn\u0026rsquo;t even drink coffee regularly until after college! I guess that extra time on the computer sent me down a rabbithole I have yet to emerge from.\nFirst, I want to preface the following with a disclaimer: This is not a detailed guide about how to roast your own coffee. If you are interested, I recommend checking out the How To Roast Your Own Coffee guide at Sweet Maria\u0026rsquo;s as a starting point. There is also the /r/roasting subreddit if that is your cup of tea. My only warning is there will be a lot of smoke. Roast your coffee outside, for Pete\u0026rsquo;s sake!\nIt all started with a trusty popcorn popper. There are a few things you want when you roast coffee:\nAir hot enough to roast coffee Remove the chaff from the beans Turns out that a classic popcorn popper fits the bill, as long as it has an upwards airflow and doesn\u0026rsquo;t let the chaff fall into the heating element. There is a bit of a cult following for the West Bend Poppery 2 model, but that one seemed a bit pricey, so I settled for a very capable popper from Nostalgia.\nFigure 1: I got a good bit of mileage out of my popcorn popper. If you are interested in roasting your own coffee I would give it a whirl.\nThings were simple back then. I still bought most of the coffee I drank, but I roasted enough to enjoy some freshly roasted coffee as an occasional treat. I ordered 10 pounds of green beans from Sweet Maria\u0026rsquo;s and life was good.\nThen I became a bit of a coffee snob.\nI could only roast 100 grams of coffee at a time in the popcorn popper, which is only enough for one pot of coffee in the morning for me. So it was time to upgrade.\nI bought the SR800 fluid bed roaster, which upped my roasting capacity and gave me finer control on temperature and airflow. Suffice to say my roasts improved a lot! At this point, I would consider my coffee good enough to sell at a farmer\u0026rsquo;s market to break even.\nIf you ever find yourself on a coffee roasting forum and bring up the SR800, someone is bound to bring up the famous RazzoRoasting extension tube. If you look for advice for how to use the SR800, I swear it\u0026rsquo;s assumed that you have this very specific accessory. \u0026hellip;And so I bought one.\nDon\u0026rsquo;t worry, that is the extent of all of my coffee spending (for now). I am a very satisfied coffee roaster now. Check out this quick series of images going from the green beans to a nearly finished product! I can spend about 45 minutes and go from nothing to nearly 2 pounds of roasted beans, enough for about a week and a half of coffee. Not bad! The only downside is that now I feel like I need to buy coffee from local roasters to get my fix. There are certainly crueler fates.\nAs a sign off, I will share something that surprised me about coffee roasting. When I roast coffee, the most important cue to determine if the coffee is roasted is the sound. That\u0026rsquo;s right, not the color, not the smell, but the sound. When heating up a coffee bean, the water trapped inside eventually bursts out of the bean in a rapid expansion. This is called \u0026ldquo;first crack\u0026rdquo;, and indicates that the coffee is roasted enough to be drinkable. The expansion also releases the chaff from the bean. If you continue heating up the bean, you will eventually reach \u0026ldquo;second crack\u0026rdquo;. I think a solid medium roast is taken out just before second crack, so I try to take my coffee out to this point and it hasn\u0026rsquo;t proved me wrong yet.\nHappy coffee-ing! \u0026#x2615;\n","permalink":"https://www.zacharybillman.com/posts/roasting-coffee-at-home/","summary":"\u003cp\u003eI, like many others, picked up a new hobby during the pandemic. Other people\u0026rsquo;s hobbies may bring them joy. This could be for many reasons. There is the joy of creating something from scratch. You can revel in your thriftiness. You can embrace the pride when you recognize that your creation is on par (or better!) than what you can buy. I feel like these are embodied in the sourdough craze that caught fire early on in COVID.\n\u003cspan class=\"sidenote-number\"\u003e\u003csmall class=\"sidenote\"\u003e\nDare I say that I did this before it was cool? \u0026#x1f60e; I baked two loaves of bread almost every weekend through med school. Maybe I should bring that back, it\u0026rsquo;s been a while since I brought out the ole\u0026rsquo; starter.\n\u003c/small\u003e\u003c/span\u003e\nMy pandemic hobby is similar, but different in that it often feels like a chore, costs more money, and often turns out worse than what I can buy. Of course, I am talking about how I\u0026rsquo;ve started roasting my own coffee at home.\u003c/p\u003e","title":"Roasting coffee at home. ☕"},{"content":"It is an age-old question: how can one keep up with the continuous output of science? I remember at the beginning of my PhD struggling to figure out how anyone found out when a new paper came out. \u0026#x1f635; Did they sit on nature.com and spam the refresh button? Did they know when each journal released their latest issue?\nBehold the power of RSS! Most websites have a page that contains information about each subpage in a computer-readable format called RSS (Really Simple Syndication). Mine has one right here! These pages can be parsed by a number of RSS feed aggregators. The way these pages are set up make it such that they add any new information hosted at that domain. This is useful in the science world because you can find the RSS feed of a given journal, subscribe to it, then have every new article published online be delivered right to you.\nThere are a plethora of RSS feed aggregators you can pick from manage your feeds. I have previously used Feedly and Inoreader, which are great free solutions, but have moved on to selfhosting my own instance of FreshRSS.\nAfter making an account at your friendly local RSS feed aggregator, you can add whatever feeds your heart desires. To find a journal\u0026rsquo;s rss feed, I often just search \u0026ldquo;$JOURNAL_NAME rss feed\u0026rdquo; and poke around until I find something that looks right. Most of the aggregators will test the feed out first to make sure that you are trying to add a legitimate one. Here are a few of the heavy hitters to get you started:\nhttp://feeds.nature.com/nature/rss/current https://www.science.org/rss/express.xml https://www.cell.com/cell/inpress.rss Nothing like a constant stream of Cell, Science, and Nature to make your project feel like a real winner, eh?\nHere is what my own site looks like.\nFigure 1: My current FreshRSS setup. On the left I have my feeds separated into folders. In the middle you can see the titles of papers that appear in my feed.\nAnd after I hit J to move to the first item in the feed.\nFigure 2: With a title selected, you can see the abstract and authors.\nAfter collecting all of your desired RSS feeds, you cannot forego your responsibility of actually reading them! Most RSS feed aggregators have shortcuts to move through titles quickly (Typically J to move on to the next one and K to move up.) They always seem to use vi keybindings. A bunch of computer nerds have really cornered the keybinding market. I have let them take over my computing life. Each morning when I get into the lab, I quickly set up something, then head to my desk to hit J until the counter reaches zero.\nBut what about my very specific field? You can subscribe to all of the journals you want, but that doesn\u0026rsquo;t make the papers with your specific interests pop out. Fortunately, the NIH has this exact circumstance in mind.\nWhen you make a new search on PubMed you might notice the \u0026ldquo;Create RSS\u0026rdquo; button. Give it a click, then you will have a personal link you can add to your favorite RSS feed aggregator.\nFigure 3: Somehow I never noticed this button until I needed it.\nThis changed the game for me for keeping up with papers. Unfortunately, it doesn\u0026rsquo;t solve the problem of library management, or actually getting around to reading the papers you care about. I will leave library management as an exercise for the interested reader. Here\u0026rsquo;s a tip, the best solution uses the Zotero citation manager. Bonus points for using Zotfile for renaming your PDFs and Better BibTex for Zotero. \u0026#x1f609; I hope this helps you get your eyeballs on that science you crave. If you have solved the problem of accruing papers to read faster than you read them, let me know.\n","permalink":"https://www.zacharybillman.com/posts/rss-feeds-to-find-science-papers/","summary":"\u003cp\u003eIt is an age-old question: how can one keep up with the continuous output of science? I remember at the beginning of my PhD struggling to figure out how anyone found out when a new paper came out. \u0026#x1f635; Did they sit on nature.com and spam the refresh button? Did they know when each journal released their latest issue?\u003c/p\u003e\n\u003ch2 id=\"behold-the-power-of-rss\"\u003eBehold the power of RSS!\u003c/h2\u003e\n\u003cp\u003eMost websites have a page that contains information about each subpage in a computer-readable format called RSS (Really Simple Syndication). \u003ca href=\"https://zacharybillman.com/index.xml\"\u003eMine has one right here!\u003c/a\u003e These pages can be parsed by a number of RSS feed aggregators. The way these pages are set up make it such that they add any new information hosted at that domain. This is useful in the science world because you can find the RSS feed of a given journal, subscribe to it, then have every new article published online be delivered right to you.\u003c/p\u003e","title":"Using RSS feeds to keep on top of science."},{"content":"My interest in self-hosting began in my with my interests in internet privacy. Plastered all over the internet are stories about how much Google, Facebook and Amazon know about you. I deleted my Facebook account years ago, and I\u0026rsquo;m too paranoid to go back to the site because there\u0026rsquo;s a real possibility that Facebook has cached my account, ready to spin it back up in case I try to login again. The ads served to me were too accurate for my liking. This is despite almost never clicking on them! I have become convinced of the idea that, if you are not paying for the product, you are the product. From this assumption, it follows that anywhere I trust with my data that I am not paying for (like Google Drive, Google Photos, Dropbox, Facebook, Twitter) is using my data to earn money. We know that Google uses the labels you add to Photos to train it\u0026rsquo;s AI, and Facebook uses (at least) Instagram photos to train it\u0026rsquo;s AI. For some, the value proposition of allowing a company to use your data for a useful service in return is an acceptable one. I find this to be a reasonable stance, but I took my growing interest in internet privacy as a chance to learn about how I can take control of my data.\nInitially, I lurked on forums like /r/privacy to learn what I could do to avoid big-tech\u0026rsquo;s watchful eye. There were numerous comments along the lines of: \u0026ldquo;The only way to be in control of your data is to self-host your services.\u0026rdquo; I had no idea what this meant! Hard to believe that less than a year later, I learned to use (and love) Linux as my primary OS, and have happily replaced Google Photos, Google Drive and other services with my own self-hosted alternatives. Self-hosting, I have since learned, is when you run useful programs from your own computer. By doing so, you have complete knowledge of where and how your data is stored and how it is being used. It has the additional effect of being a bottomless time sink.\nTo begin, I needed an always-on computer to run these useful programs. I began with a humble Raspberry Pi.\nFigure 1: My humble Raspberry Pi and its hard drive. This dude currently tirelessly runs the excellent Adguard Home and downloads a backup of my data every night.\nThese are tiny, but capable computers that are great for fiddling with. The projects people develop for these are amazing and diverse. With RPi in hand, I began with the ambitious project of replacing Google Drive with Nextcloud. After much frustration with a bare metal installation, I found the NextcloudPi project. Surprisingly, it went pretty okay! At first, I was intimidated by Linux defaults, but over time I grew to appreciate, and indeed, prefer Linux as an operating system. My decision to use Linux over Windows/MacOS is because it is free and open source software (FOSS). This is a topic for a different post, but I think using FOSS when possible is a moral imperative of sorts. I used Nextcloud strictly from my home for a few months, without the ability to connect to it from the internet, to test the self-hosting waters. My first true cloud replacement spun up once I decided to access this lil\u0026rsquo; guy from the internet. To do so, I purchased a domain (not the one this site is hosted on) and pointed it to the IP of my house. I forwarded the appropriate ports of my router to the RPi.\nThis is when the real exploration began. I was able to access my files and images using Nextcloud, but the photo viewing service left something to be desired. No problem, why not spin up an instance of Photoprism? I use RSS feeds to keep on top of the latest science in the journals relevant to my field using Feedly. Why not host my own RSS feed aggregator so I can subscribe to as many feeds as I desire?\nThis cycle continued, and I accrued many cool applications, but in the back of my mind I worried about opening up my home network to the internet. I also struggled to run some programs because the RPi uses the arm64 architecture, and most services are written with amd64 in mind. These two forces eventually convinced me to purchase a server where I could manage all of my services remotely. Some would say that not owning the hardware that is running your own services is not \u0026ldquo;true\u0026rdquo; self-hosting. I think this is needlessly exclusive. Let everyone self host, dangit! Someday, when I have more stable internet and a more permanent home, I hope to host everything from my own home, but until then, I\u0026rsquo;m extremely pleased with my current stack. And that is where I am now. I happily host numerous services on my virtual private server that entirely replace Google Photos, Google Drive and GitHub for me. Even better, there are specialized services that fill a need I never realized I had. What\u0026rsquo;s more, if I ever want to spin up a new service, all I have to do is add it to my to docker-compose file and it will be up within minutes. What a world!\nI thought about making this into a \u0026ldquo;guide\u0026rdquo; style post. I nixed that idea because, quite frankly, I feel like I don\u0026rsquo;t know what I\u0026rsquo;m doing. I am really happy with my setup, but I don\u0026rsquo;t feel like I have the authority to tell people how to administer their own services. If you are interested, allow me to point you toward the guide that really got me rolling: Ultimate Traefik Docker Compose Guide.\nFor those of you wondering what I am currently hosting, check out my current list at the link and let me know what you think!\n","permalink":"https://www.zacharybillman.com/posts/my-selfhosting-journey/","summary":"\u003cp\u003eMy interest in self-hosting began in my with my interests in internet privacy. Plastered all over the internet are stories about how much Google, Facebook and Amazon know about you. I deleted my Facebook account years ago, and I\u0026rsquo;m too paranoid to go back to the site because there\u0026rsquo;s \u003ca href=\"https://www.reddit.com/r/privacy/comments/6nmjfh/facebook_account_fully_recovered_3_years_after/\"\u003ea real possibility that Facebook has cached my account, ready to spin it back up\u003c/a\u003e in case I try to login again. The ads served to me were too accurate for my liking.\n\u003cspan class=\"sidenote-number\"\u003e\u003csmall class=\"sidenote\"\u003e\nThis is despite almost never clicking on them!\n\u003c/small\u003e\u003c/span\u003e\nI have become convinced of the idea that, if you are not paying for the product, you are the product. From this assumption, it follows that anywhere I trust with my data that I am not paying for (like Google Drive, Google Photos, Dropbox, Facebook, Twitter) is using my data to earn money. We know that \u003ca href=\"https://www.theverge.com/2020/11/11/21559930/google-train-ai-photos-image-labelling-app-android-update\"\u003eGoogle uses the labels you add to Photos to train it\u0026rsquo;s AI\u003c/a\u003e, and \u003ca href=\"https://ai.facebook.com/blog/seer-the-start-of-a-more-powerful-flexible-and-accessible-era-for-computer-vision/\"\u003eFacebook uses (at least) Instagram photos to train it\u0026rsquo;s AI\u003c/a\u003e. For some, the value proposition of allowing a company to use your data for a useful service in return is an acceptable one. I find this to be a reasonable stance, but I took my growing interest in internet privacy as a chance to learn about how I can take control of my data.\u003c/p\u003e","title":"My selfhosting journey."},{"content":"N.B.: I hope to add screenshots for each of these eventually. For now, I hope links to each services\u0026rsquo; website will suffice.\nSeafile\nThis is a great tool for managing files. I moved to this from Nextcloud because I am of the philosophy that I would prefer services that do one thing excellently instead of many things well. Nextcloud is an incredible Office365 replacement, but I found myself using a fraction of what it was capable of providing. Enter Seafile. It is cloud file syncing with a robust encryption implementation, just what the doctor ordered.\nPhotoprism\nNextcloud\u0026rsquo;s implementation of photo management was a bit clumsy for my tastes, so I began on a hunt for a more feature complete option. I was very lucky to stumble upon Photoprism early on in my self hosting journey. I am a proud supporter of this project. It brings a ton to the table, and doesn\u0026rsquo;t leave me missing Google Photos one bit. It is also actively developed. For instance, as of 2022-07-02, there was a recent update that improved scrolling a ton, which was one of my remaining quibbles with it\u0026rsquo;s functionality. Some people complain that it doesn\u0026rsquo;t scale up for libraries of 10,000+ photos, but my 2000 photo library works swimmingly. On my phone, I use the Folder Sync app to automatically send any pictures I take on my phone to the Photoprism imports folder. Within 15 minutes of snapping a photo, it is there on my Photoprism instance. I highly recommend giving it a go.\nMealie\nI have to admit that the name leaves something to be desired. Fortunately, the service itself doesn\u0026rsquo;t fall short. Mealie is a recipe management application. It is able to parse your favorite recipe websites to create immortalized versions of the recipe. This helps fight detestable link rot that plagues the internet. It allows you to edit ingredient amounts, make comments about what you would change next time, and plan out your weekly meals. It helps that it is beautiful and intuitive to use. If only I could get my partner to use it\u0026hellip; I want to go on the record here and say that I think it is sensible that she doesn\u0026rsquo;t trust my self hosted services that much. In the early days of my self hosting journey, let\u0026rsquo;s just say that the up-time of my services were extremely finicky. I like to think they are more permanent now, especially because I am hosting everything on a VPS, but I certainly cannot compete with the stability of Google and Amazon. (Or pretty much any other paid service for that matter.) \u0026#x1f609;\nGitea\nGitea is a community managed, lightweight code hosting solution written in Go. I use it to manage my data analysis (using Private repos) and even host the source code for this very website! Using Gitea has given me the surface level introduction to the behemoth that is git. Fortunately, that is all I need. Once I have removed any sensitive data (like passwords, etc.) I will make my docker-compose file public. The docker-compose file is where I determine which services I pick to host, and how to configure them to my liking. Hopefully someone will find this useful.\nSyncthing\nIf I could only tell someone to self host a single service, I would have to pick Syncthing. It is a continuous file synchronization program, which means it keeps a specific file or folder the same between any device running Syncthing. I use it to keep my password database and my org-mode notes Now org-mode might be the biggest rabbithole of them all, and definitely the topic for another blog post. I use it to manage my TODO list, my lab notebook, my shopping lists, write this blog, and maintain my Zettelkasten note database. It is an immensely powerful tool. up to date between all of my devices. With Syncthing, all of my data is stored on my own devices and encrypted in transit.\nFreshRSS\nI keep up to date on the science in my field by subscribing to relevant RSS feeds. Yet another topic to write a post about. This really changed the game for my ability to keep on top of the latest research. 2022-07-14 Update: post complete! Check it out here. FreshRSS replaced Feedly for me, as I ran up against the number of feeds I could subscribe to on a free account. Also, when self hosting, I can save as many articles as my heart desires (even if I will never look at them again \u0026#x1f635; ).\nWallabag\nRemember Pocket for Firefox? (Yes, I know it still exists, okay?) Give Wallabag a spin, it is great for storing articles you want to read later. I set up FreshRSS to save articles to my Wallabag instance to keep for later.\nChangeDetection\nNow this is a fun one! ChangeDetection.io is a service that loads a webpage and checks to see if something has changed since the last time. This might not sound useful at first, but I recently used this to check for when a hot item for my new coffee roasting hobby was back in stock. I got an email the other day to let me know it was in stock. Pretty cool!\nHugo\nHugo is the static site generator I use to make this here blog! I was amazed at how much more response my site was using Hugo compare to when I paid a company to host a WordPress site. I\u0026rsquo;m sure WordPress could be fast, but I just wanted a barebones, pure html experience, and Hugo made it easy.\nCommento++\nYou may have noticed that I have some pretty snazzy comments sections on my site. I initially used Disqus, which you may recognize from a ton of sites around the internet, but didn\u0026rsquo;t like how it would serve ads through my comments section, and provided sign-ins using Google/Facebook/Twitter. I wanted to serve the simplest comments section I could, that still gave me the ability to migrate the comments to wherever I decide to keep my server. Go ahead and use the anonymous comment button, fill in your name, and you are off to the races.\nAuthelia\nThere are a few services I host that I really want to lock down. For these services, Authelia is great. It puts up a \u0026ldquo;Enter the 6 digit code on your phone\u0026rdquo; style 2 factor authentication in front of the services I choose. Or, if you follow the guide here, you can have it send you a DUO push, just like you are one of the big hitters out there. I feel much more secure with Authelia in front of Adminer, Traefik, and Portainer.\nBoring stuff that allows everything else to work!\nPostgreSQL database MariaDB database Traefik reverse proxy Umami privacy respecting site analytics Portainer for docker container management Redis in-memory data store Adminer database management traefik-socket-proxy to prevent pesky backdoors to my server! ","permalink":"https://www.zacharybillman.com/posts/zpb-current-selfhosted/","summary":"\u003cp\u003e\u003cem\u003eN.B.: I hope to add screenshots for each of these eventually. For now, I hope links to each services\u0026rsquo; website will suffice.\u003c/em\u003e\u003c/p\u003e\n\u003col\u003e\n\u003cli\u003e\n\u003cp\u003e\u003ca href=\"https://www.seafile.com/en/home/\"\u003eSeafile\u003c/a\u003e\u003c/p\u003e\n\u003cp\u003eThis is a great tool for managing files. I moved to this from Nextcloud because I am of the philosophy that I would prefer services that do one thing excellently instead of many things well. Nextcloud is an incredible Office365 replacement, but I found myself using a fraction of what it was capable of providing. Enter Seafile. It is cloud file syncing with a robust encryption implementation, just what the doctor ordered.\u003c/p\u003e","title":"What I'm currently selfhosting."},{"content":"My partner and I took a trip to the Mason Farm Biological Reserve the other day, and what a glorious day it was. This year, I\u0026rsquo;ve been quite busy in the lab, and missed a lot of the early spring warbler season, so I was very excited by the opportunity to check out the old stomping grounds.\nI brought the camera with me despite the fact we were going to be there around midday when the birds are much less active. I\u0026rsquo;m glad I did, because I got the best look at a common yellowthroat I\u0026rsquo;ve ever had. Normally these guys are flighty, staying close to the ground in small brush or tall grasses, but this one was putting on a proper show for the mating season. Even when you get a glimpse of one, it is usually just that, as they have jumped away before you can pull out the camera, taunting you with their iconic call. I was very pleased to capture a few choice shots of the bird. Hopefully there are more to come. While we were out, I also got a nice picture of a hermit thrush and a king snake.\nThese images have been compressed quite a bit for a lighter internet footprint. These have all been resized to 25% of their original size. If you would like the full sized images, let me know and I will send you a link!\n","permalink":"https://www.zacharybillman.com/posts/the-uncommon-yellowthroat/","summary":"\u003cp\u003eMy partner and I took a trip to the \u003ca href=\"https://ncbg.unc.edu/visit/mason-farm-biological-reserve/\"\u003eMason Farm Biological Reserve\u003c/a\u003e the other day, and what a glorious day it was. This year, I\u0026rsquo;ve been quite busy in the lab, and missed a lot of the early spring warbler season, so I was very excited by the opportunity to check out the old stomping grounds.\u003c/p\u003e\n\u003cp\u003eI brought the camera with me despite the fact we were going to be there around midday when the birds are much less active. I\u0026rsquo;m glad I did, because I got the best look at a common yellowthroat I\u0026rsquo;ve ever had.\n\u003cspan class=\"sidenote-number\"\u003e\u003csmall class=\"sidenote\"\u003e\nNormally these guys are flighty, staying close to the ground in small brush or tall grasses, but this one was putting on a proper show for the mating season. Even when you get a glimpse of one, it is usually just that, as they have jumped away before you can pull out the camera, taunting you with their \u003ca href=\"https://ebird.org/species/comyel#Modal-playlist\"\u003eiconic call\u003c/a\u003e.\n\u003c/small\u003e\u003c/span\u003e\nI was very pleased to capture a few choice shots of the bird. Hopefully there are more to come. While we were out, I also got a nice picture of a hermit thrush and a king snake.\u003c/p\u003e","title":"The (un)common yellowthroat."},{"content":"Welcome to my site! My name is Zachary Billman. I\u0026rsquo;m a UNC MD-PhD student in my 4th year of med school applying to pathology residency programs. I completed my PhD in Ed Miao\u0026rsquo;s lab. The curious reader may be thinking: \u0026ldquo;But Zach, Dr. Miao\u0026rsquo;s lab is at Duke, how did that come about?\u0026rdquo; What an astute question! Ed\u0026rsquo;s lab moved from UNC to Duke in early 2020, and I followed him down the street. My PhD was awarded by the UNC department of Microbiology and Immunology, but it just so happens that (nearly) all of my research took place at Duke. This move was quite a trial, especially when compounded with the onset of the pandemic. I suspect my research timeline suffered, though this is an extremely minor inconvenience compared to the tragedy the pandemic caused. This makes for very interesting basketball viewing parties with my Duke friends!\nMaybe having a diagram will make my training timeline make a bit more sense.\nFigure 1: An overview of my research training. I first began working for Dr. Sean Murphy in undergrad, then worked as a research scientist/lab manager for 3 years before heading to UNC for my MSTP training. During grad school, my lab moved from UNC to Duke, though my degree was awarded by UNC. The \u0026ldquo;Present\u0026rdquo; diamond was used on an older version of my CV and represents September 1st, 2025. Created using PlantUML.\nHopefully that can clear up the winding road I\u0026rsquo;ve taken a bit!\nMy research and scientific interests. I am broadly interested in innate immunology. I spent most of my time in graduate school studying the host-pathogen interaction between the intracellular fungus Histoplasma capsulatum and macrophages. There are many unstudied curiosities regarding the innate immune response to Histoplasma spp. and other intracellular fungi that I think are quite interesting. I also spent a considerable time thinking about the evolution of proteins involved in the programmed cell death pathway called pyroptosis.\nHobbies I may write about. Besides my science, I am interested in birding, baking sourdough bread (I swear I began years before the pandemic, though hearing of people baking bread brings me joy no matter when they first began!), board games, roasting coffee, and self-hosting free and open source software. Over the course of the pandemic, I have learned how to maintain a basic suite of services spread between a server I rent and a computer at home that have replaced my need for Google Photos and Google Drive. I\u0026rsquo;m hoping to be able to move away from these platforms entirely soon. I think they provide a great service, but at a substantial cost to privacy. Hopefully more to be said about my thoughts on FOSS soon! I also transitioned my old, (and quite frankly, embarrassingly slow) managed WordPress site with this lean, static site made in Hugo that I host myself. Now that I have mangled together some CSS to get my precious sidenotes up and running again, I\u0026rsquo;m ready to begin putting some ideas to paper. I love marginalia (the word to describe these notes on the side of this webpage). I\u0026rsquo;m not sure if this is unique to me, but I seem to get caught up in parenthetical / tangential thoughts very often, and I think using an Edward Tufte-esque sidenote is a great way for me to communicate in this way without distracting the reader too much. It seems marginalia such as this have been used throughout history, so perhaps it is normal, but most people can keep their thoughts focused better than me. The implementation I use is inspired by the Tufte CSS project and largely taken from this incredibly helpful post found at scripter.co. I\u0026rsquo;m quite proud of my progress in administering my server and self-hosting useful services.\nThe future of this site. On this site I plan to post updates about my journey through med school, grad school, and self-hosting I would like to share with the world. I have been helped immensely by many others\u0026rsquo; advice and I hope to impart similar tips to others someday. I suspect most posts will be about much lighter fare, like whatever hobbies tickle my fancy at the time.\n","permalink":"https://www.zacharybillman.com/posts/about-me/","summary":"\u003ch2 id=\"welcome-to-my-site\"\u003eWelcome to my site!\u003c/h2\u003e\n\u003cp\u003eMy name is Zachary Billman. I\u0026rsquo;m a UNC MD-PhD student in my 4th year of med school applying to pathology residency programs. I completed my PhD in Ed Miao\u0026rsquo;s lab. The curious reader may be thinking: \u0026ldquo;But Zach, Dr. Miao\u0026rsquo;s lab is at Duke, how did that come about?\u0026rdquo; What an astute question! Ed\u0026rsquo;s lab moved from UNC to Duke in early 2020, and I followed him down the street. My PhD was awarded by the UNC department of Microbiology and Immunology, but it just so happens that (nearly) all of my research took place at Duke.\n\u003cspan class=\"sidenote-number\"\u003e\u003csmall class=\"sidenote\"\u003e\nThis move was quite a trial, especially when compounded with the onset of the pandemic. I suspect my research timeline suffered, though this is an extremely minor inconvenience compared to the tragedy the pandemic caused.\n\u003c/small\u003e\u003c/span\u003e\nThis makes for very interesting basketball viewing parties with my Duke friends!\u003c/p\u003e","title":"About me. 👋"},{"content":"It\u0026rsquo;s over. My third year of medical school is officially behind me. I managed to get in a grand total of zero blog posts during grad school, so here\u0026rsquo;s to a new year with hopefully some more thoughts being shared. I have a lot to reflect on from the past year. It was wonderful. I wish everyone could experience what I did this past year. I think it goes without saying:\nI loved the third year of med school, but I do not want to do it again.\nA year of change. In the days leading up to my return to med school, I thought \u0026ldquo;Oh no, I really enjoy doing science, do I really have to go to med school?\u0026rdquo;. I also remember at the end of Step 1 and the first two years of med school thinking, \u0026ldquo;Oh no, I really enjoy med school, do I really have to do science again?\u0026rdquo;. I think I have a welcome problem of enjoying what I\u0026rsquo;m doing. The third year of med school is a shift. After years of memorizing and examinations, the doors to the promised land are finally opened. I have experienced nothing like it before It feels intentionally unsettling. You are thrown into the clinic with a modicum of guidance so you aren\u0026rsquo;t totally caught off guard, but you are thrown out to the wolves. I don\u0026rsquo;t mean this as a criticism of the system, it feels necessary. Third year medical students—commonly shorted to MS3s—have just one year to experience a broad swath of medicine and pick a specialty. So you had better be ready to dive in.\nTotal immersion I came to terms with my new reality quickly. Gone were the days of hitting the snooze button and going home when I pleased. I am now beholden to other people\u0026rsquo;s schedules. This came back relatively naturally. Maybe not hitting snooze. A regrettable personal failing of mine. I was, however, immediately faced with a new reality in the patient room. Patients come to the doctor for a number of reasons, but often seek relief. To get to the core of what ails them, they will tell you everything. I was not prepared for how vulnerable patients would be with me. I am not sure if this ever will feel natural. I hope it never does. I was told many stories of experiences living with scary diagnoses, and not knowing what to do with it. Family histories of all sorts. Personal details that were sometimes (oftentimes?) off the wall. I see all of these specifics as flailing, grasping at sand hoping that something could explain their pain. Sometimes it could. Usually it did not. But since I was in a white coat, I was privileged to hear it.\nI think my years spent in the lab have prepared me to face some of the challenges set before me. At the very least, having a few more years under my belt helped me approach the year with a bit of maturity. This seems to have paid off. I guess my recommendation is to simply get old before going to med school. Returning to studying The hospital is how I spent the majority of my time, but a new reality for me was also going back to daily studying. There is a strange dichotomy in medicine of \u0026ldquo;Oh, it doesn\u0026rsquo;t really matter\u0026rdquo; and \u0026ldquo;If you don\u0026rsquo;t get this class/score/grade then you won\u0026rsquo;t be able to be the kind of doctor you want to be, so you had better get your act together.\u0026rdquo; Simultaneously there are no expectations and immense responsibility for the looming specter of Step 2. I\u0026rsquo;m glad that studying regularly came back easily enough. I was concerned I would experience a studying whiplash. I\u0026rsquo;m glad it never came. I did UWorld and Anki nearly every day for a full year and felt alright.\nBecoming invisible I quickly learned I needed to change my understanding of my contribution to the team. Exiting grad school, people understood that they could come to me for help. I was a resource, a seasoned veteran of the lab. If someone needed an experiment done, I could do it, and be trusted to do it. In med school as a third year, I was nothing. A fly on the wall; a worm beneath the feet of the real doctors. In science, I felt like I was treated as a peer with even my committee members with multiple R01s. Even if I didn\u0026rsquo;t understand the science perfectly, I could contribute some different perspective. In medicine, sometimes not being recognized at all by my attendings was the best outcome. Which happened regularly. My role, was not as a contributor—as it was in science—it was simply to get in the reps. Once I understood that the expectations of me were below the ground, I understood that everything I did in third year was for myself. This is taken at face value by the team at times. I would spend 30 minutes working on a presentation, pre-rounding, the works, and at the end of my part, the intern would nod, then turn to the senior resident and say \u0026ldquo;I was thinking that we\u0026hellip;\u0026rdquo; without thinking of my work. This is perhaps a bit of cognitive restructuring, but recognizing this is what gave me the freedom to embed myself in the hospital flow, without a single worry about the outcome. Simply doing my best was the best thing I could do. Obviously. But this was not apparent to me at first. I needed more quality repetitions to develop good habits in the future. And also experience as much of medicine as possible to find what I want to do with my life. This permission allowed me to approach specialties I do not care about with the awe and respect they deserve.\nA year of wonder. Med school prepares you for the standardized tests. I think this is generally useful. The tests on aggregate are reasonable and evaluate your ability to think through common clinical scenarios. There will always be oddball questions that come out of left field, but I let these flow over me. No need to perseverate on the small stuff. The time for that can come later.\nWhat I didn\u0026rsquo;t realize is how much of the \u0026ldquo;classic\u0026rdquo; material we are fed in the first couple years of med school would come to the forefront. The \u0026ldquo;sandpaper rash\u0026rdquo; of scarlet fever really does feel like sandpaper. Nikolsky\u0026rsquo;s sign actually works. Tripoding for epiglottitis gets the physicians worked up. Don\u0026rsquo;t forget about von Willebrand\u0026rsquo;s disease when someone seems to be bleeding a bit too much. TB is out there, watch for hemoptosis. Night sweats, unintended weight loss, is cancer until proven otherwise. And yes, it really can be lupus.\nIn general, facing the unknown with a sense of earnestness was the way I felt best able to respect those who gathered and passed down the medical knowledge I am privileged to learn today. Sometimes, my excitement to see aspects of medicine would rouse a curious response from the residents. I project here, but I felt a sense of surprise, like that of a doting parent seeing their child experience something new, after forgetting the astonishment they once felt.\nEarnestness is next to med studentlyness.\nPerhaps what I\u0026rsquo;m getting at here is that I found it important to bask in the privilege of seeing the pathology I encountered in med school, and to remind the residents of this sensation. I felt childish at times—and perhaps overanimated—but I found this excitement was to my and my resident\u0026rsquo;s benefit.\nMy surgery rotation overflowed with examples of wonder of medicine. Partially because of the team I worked with, and the rest because of the undeniable coolness of surgery. The OR is a cool place. The orderliness and chaos ebb. The spans of steady, industrious work are interrupted with staccato notes of bedlam. The anatomy I learned in class was ever present, but the surgeons bemoaned \u0026ldquo;normal anatomic variation\u0026rdquo;.\nI was struck with wonder at the sight of human anatomy as it unfolded before me. What I was able to experience in the OR felt like the culmination of centuries of human curiosity. There is an ancientness to medicine that I catch flashes of—I could perform the physical exam on humans hundred of millions of years ago and interrogate the same pathologies as I do in the hospital today—and viewing the exposed anatomy is a pressure-bagged infusion of this collective wonder. To gaze upon the peristalsing of the small intestine, or steady beating of the heart is a sight to behold, indeed.\nA year of shame. It weighs upon me the circumstances that resulted in these transcendent experiences. Not one patient was in the hospital without reason. What to make of these patients with horrible pathology? I still feel unsettled about how the cause of their pain sparked wonder. How dare I gain, merely by the circumstance of having their care managed at UNC, Which, as a tertiary care center, layers on more complexity. Many patients end up at UNC because they have no where else they can go for help. And this signs them up for med students? For shame. from the very essence of their malady? I do not know what to do with my discomfort, but I think it is best that I dwell in it. With this, I respect the people before me in the hospital and recognize their humanity.\nBut I often complained of what I say here I was lucky to do. I find myself resentful of my future schedule; when was I supposed to learn that I will be working 13 hour days, 6 days a week for the rest of my life? And what of having a family? Medicine by necessity requires sacrifice. I happened to sign up for sacrifices years before I recognized how profound they were. How might I balance this dread and with the joy of practicing medicine? And why do I seem more concerned about this than others? Am I not grateful enough? Am I not capable of the sacrifices that others seem to offer so effortlessly? I don\u0026rsquo;t necessarily think this to be true, but these questions erode at my will to pursue medicine.\nPerhaps most shameful of all is how my understanding of the patient-provider interaction evolved over the year. It began as an exploration of an open book, a tabula rasa that held within it a diagnosis and how to best intervene. On my first day in the outpatient clinic, it was clear that this is not the case. My preceptor had only 20 minutes for me to ① interview the patient and perform the physical exam, ② present with a plan, ③ return to the room and do everything again, ④ write orders, educate, and get the patient out of the door. It simply is not amenable to the free form, personable, curious interview I hoped to perform. By the end of the year, I had optimized how I asked questions to keep patients from going off the rails. When prerounding in medicine, I was there to extract information and not much else. Small talk had to go, there was no time. I like to chat, so this came at a loss of who I think I am. I am not sure how to do this well, while still feeling like Zachary. And from what I gather from the interns, that may just come later in my career. I found myself questioning, \u0026ldquo;Is this the \u0026lsquo;patient interaction\u0026rsquo; that has been mythologized throughout my training?\u0026rdquo; The carrot at the end of the stick dangled before me with a \u0026ldquo;You are so lucky to be able to do this, so you had better not complain of any abuse that comes your way.\u0026rdquo; It wasn\u0026rsquo;t a genuine interaction as much as me leading the patient along to tell me what I wanted to know. Of course, I used open ended questions, but only open enough. Leave the door a bit too open and next thing you know, you are talking about their dog\u0026rsquo;s breeder while you constantly stare at your watch, imagining what your attending will say when you return. I feel like I am alone in missing the core human element that funnels sprightly youths into medicine. Or worse, finding it a façade.\nThe shame extends beyond the hospital. One aspect of my life that has changed most dramatically is the sheer amount of time I felt I needed to dedicate to medicine, whether at the hospital or at home. I spent all day basking in the wonder of medicine, then I would come home and study for hours. I relied on my partner for keeping our household together more than ever, because I spent all day—all year, rather—in a state of discovery. Her life was largely the same, with the normal challenges of being a scientist, with the added bonus of getting less help from me. The shame built over the year. Again, how dare I?\nA year of glad. This has been an undeniable year of growth and joy, with these quibbles. It is clear that I was happier than I was during grad school. I know this from within myself, and reinforced by my wife\u0026rsquo;s comments on my mood. The pace of the day, and immediacy of problem solving were a welcome change.\nI recall, during the very first days preparing for med school during xTAP, having to do a simulated patient encounter complete with patient presentation to an attending physician. We were told about this encounter days in advance. And yet, I dreaded it. And near the last day of my final rotation, I did 8 of these in a row without breaking a sweat. Progress!\nI think, in a word, what I\u0026rsquo;ve experienced in the third year of med school is gratitude. Gratitude to be privileged to learn what I am learning. Gratitude for the experiences in my life that brought me here. Gratitude for the support from my wife. Gratitude to be involved in people\u0026rsquo;s lives when they are fragile. Ever since reading Braiding Sweetgrass I think one could call me \u0026ldquo;gratitude-pilled\u0026rdquo;. I also selfishly enjoyed the gratitude from patients as I put on my best doctor performance. In reflection on the year, I have spent time thinking of a phrase that I heard a number of times throughout med school from residents, \u0026ldquo;The worst day of residency is better than the best day of med school.\u0026rdquo; I find this hard to believe. This year has been magical. It is hard to imagine a year filled with more wonder and joy of caring for those in need. I will have to rely on the experience of those who have walked this path and trust that the rest of my training has plenty of magic to spare.\n","permalink":"https://www.zacharybillman.com/posts/ms3-year-is-magical/","summary":"\u003ch2 id=\"it-s-over-dot\"\u003eIt\u0026rsquo;s over.\u003c/h2\u003e\n\u003cp\u003eMy third year of medical school is officially behind me. I managed to get in a grand total of \u003cem\u003ezero\u003c/em\u003e blog posts during grad school, so here\u0026rsquo;s to a new year with hopefully some more thoughts being shared. I have a lot to reflect on from the past year. It was wonderful. I wish everyone could experience what I did this past year. I think it goes without saying:\u003c/p\u003e","title":"The third year of medical school is magical."},{"content":"I, like many others, picked up a new hobby during the pandemic. Other people\u0026rsquo;s hobbies may bring them joy. This could be for many reasons. There is the joy of creating something from scratch. You can revel in your thriftiness. You can embrace the pride when you recognize that your creation is on par (or better!) than what you can buy. I feel like these are embodied in the sourdough craze that caught fire early on in COVID. Dare I say that I did this before it was cool? \u0026#x1f60e; I baked two loaves of bread almost every weekend through med school. Maybe I should bring that back, it\u0026rsquo;s been a while since I brought out the ole\u0026rsquo; starter. My pandemic hobby is similar, but different in that it often feels like a chore, costs more money, and often turns out worse than what I can buy. Of course, I am talking about how I\u0026rsquo;ve started roasting my own coffee at home.\nI\u0026rsquo;m not sure where this idea was planted into my brain. I don\u0026rsquo;t think I know anyone who roasts their own beans, and I certainly didn\u0026rsquo;t know how. I didn\u0026rsquo;t even drink coffee regularly until after college! I guess that extra time on the computer sent me down a rabbithole I have yet to emerge from.\nFirst, I want to preface the following with a disclaimer: This is not a detailed guide about how to roast your own coffee. If you are interested, I recommend checking out the How To Roast Your Own Coffee guide at Sweet Maria\u0026rsquo;s as a starting point. There is also the /r/roasting subreddit if that is your cup of tea. My only warning is there will be a lot of smoke. Roast your coffee outside, for Pete\u0026rsquo;s sake!\nIt all started with a trusty popcorn popper. There are a few things you want when you roast coffee:\nAir hot enough to roast coffee Remove the chaff from the beans Turns out that a classic popcorn popper fits the bill, as long as it has an upwards airflow and doesn\u0026rsquo;t let the chaff fall into the heating element. There is a bit of a cult following for the West Bend Poppery 2 model, but that one seemed a bit pricey, so I settled for a very capable popper from Nostalgia.\nFigure 1: I got a good bit of mileage out of my popcorn popper. If you are interested in roasting your own coffee I would give it a whirl.\nThings were simple back then. I still bought most of the coffee I drank, but I roasted enough to enjoy some freshly roasted coffee as an occasional treat. I ordered 10 pounds of green beans from Sweet Maria\u0026rsquo;s and life was good.\nThen I became a bit of a coffee snob.\nI could only roast 100 grams of coffee at a time in the popcorn popper, which is only enough for one pot of coffee in the morning for me. So it was time to upgrade.\nI bought the SR800 fluid bed roaster, which upped my roasting capacity and gave me finer control on temperature and airflow. Suffice to say my roasts improved a lot! At this point, I would consider my coffee good enough to sell at a farmer\u0026rsquo;s market to break even.\nIf you ever find yourself on a coffee roasting forum and bring up the SR800, someone is bound to bring up the famous RazzoRoasting extension tube. If you look for advice for how to use the SR800, I swear it\u0026rsquo;s assumed that you have this very specific accessory. \u0026hellip;And so I bought one.\nDon\u0026rsquo;t worry, that is the extent of all of my coffee spending (for now). I am a very satisfied coffee roaster now. Check out this quick series of images going from the green beans to a nearly finished product! I can spend about 45 minutes and go from nothing to nearly 2 pounds of roasted beans, enough for about a week and a half of coffee. Not bad! The only downside is that now I feel like I need to buy coffee from local roasters to get my fix. There are certainly crueler fates.\nAs a sign off, I will share something that surprised me about coffee roasting. When I roast coffee, the most important cue to determine if the coffee is roasted is the sound. That\u0026rsquo;s right, not the color, not the smell, but the sound. When heating up a coffee bean, the water trapped inside eventually bursts out of the bean in a rapid expansion. This is called \u0026ldquo;first crack\u0026rdquo;, and indicates that the coffee is roasted enough to be drinkable. The expansion also releases the chaff from the bean. If you continue heating up the bean, you will eventually reach \u0026ldquo;second crack\u0026rdquo;. I think a solid medium roast is taken out just before second crack, so I try to take my coffee out to this point and it hasn\u0026rsquo;t proved me wrong yet.\nHappy coffee-ing! \u0026#x2615;\n","permalink":"https://www.zacharybillman.com/posts/roasting-coffee-at-home/","summary":"\u003cp\u003eI, like many others, picked up a new hobby during the pandemic. Other people\u0026rsquo;s hobbies may bring them joy. This could be for many reasons. There is the joy of creating something from scratch. You can revel in your thriftiness. You can embrace the pride when you recognize that your creation is on par (or better!) than what you can buy. I feel like these are embodied in the sourdough craze that caught fire early on in COVID.\n\u003cspan class=\"sidenote-number\"\u003e\u003csmall class=\"sidenote\"\u003e\nDare I say that I did this before it was cool? \u0026#x1f60e; I baked two loaves of bread almost every weekend through med school. Maybe I should bring that back, it\u0026rsquo;s been a while since I brought out the ole\u0026rsquo; starter.\n\u003c/small\u003e\u003c/span\u003e\nMy pandemic hobby is similar, but different in that it often feels like a chore, costs more money, and often turns out worse than what I can buy. Of course, I am talking about how I\u0026rsquo;ve started roasting my own coffee at home.\u003c/p\u003e","title":"Roasting coffee at home. ☕"},{"content":"It is an age-old question: how can one keep up with the continuous output of science? I remember at the beginning of my PhD struggling to figure out how anyone found out when a new paper came out. \u0026#x1f635; Did they sit on nature.com and spam the refresh button? Did they know when each journal released their latest issue?\nBehold the power of RSS! Most websites have a page that contains information about each subpage in a computer-readable format called RSS (Really Simple Syndication). Mine has one right here! These pages can be parsed by a number of RSS feed aggregators. The way these pages are set up make it such that they add any new information hosted at that domain. This is useful in the science world because you can find the RSS feed of a given journal, subscribe to it, then have every new article published online be delivered right to you.\nThere are a plethora of RSS feed aggregators you can pick from manage your feeds. I have previously used Feedly and Inoreader, which are great free solutions, but have moved on to selfhosting my own instance of FreshRSS.\nAfter making an account at your friendly local RSS feed aggregator, you can add whatever feeds your heart desires. To find a journal\u0026rsquo;s rss feed, I often just search \u0026ldquo;$JOURNAL_NAME rss feed\u0026rdquo; and poke around until I find something that looks right. Most of the aggregators will test the feed out first to make sure that you are trying to add a legitimate one. Here are a few of the heavy hitters to get you started:\nhttp://feeds.nature.com/nature/rss/current https://www.science.org/rss/express.xml https://www.cell.com/cell/inpress.rss Nothing like a constant stream of Cell, Science, and Nature to make your project feel like a real winner, eh?\nHere is what my own site looks like.\nFigure 1: My current FreshRSS setup. On the left I have my feeds separated into folders. In the middle you can see the titles of papers that appear in my feed.\nAnd after I hit J to move to the first item in the feed.\nFigure 2: With a title selected, you can see the abstract and authors.\nAfter collecting all of your desired RSS feeds, you cannot forego your responsibility of actually reading them! Most RSS feed aggregators have shortcuts to move through titles quickly (Typically J to move on to the next one and K to move up.) They always seem to use vi keybindings. A bunch of computer nerds have really cornered the keybinding market. I have let them take over my computing life. Each morning when I get into the lab, I quickly set up something, then head to my desk to hit J until the counter reaches zero.\nBut what about my very specific field? You can subscribe to all of the journals you want, but that doesn\u0026rsquo;t make the papers with your specific interests pop out. Fortunately, the NIH has this exact circumstance in mind.\nWhen you make a new search on PubMed you might notice the \u0026ldquo;Create RSS\u0026rdquo; button. Give it a click, then you will have a personal link you can add to your favorite RSS feed aggregator.\nFigure 3: Somehow I never noticed this button until I needed it.\nThis changed the game for me for keeping up with papers. Unfortunately, it doesn\u0026rsquo;t solve the problem of library management, or actually getting around to reading the papers you care about. I will leave library management as an exercise for the interested reader. Here\u0026rsquo;s a tip, the best solution uses the Zotero citation manager. Bonus points for using Zotfile for renaming your PDFs and Better BibTex for Zotero. \u0026#x1f609; I hope this helps you get your eyeballs on that science you crave. If you have solved the problem of accruing papers to read faster than you read them, let me know.\n","permalink":"https://www.zacharybillman.com/posts/rss-feeds-to-find-science-papers/","summary":"\u003cp\u003eIt is an age-old question: how can one keep up with the continuous output of science? I remember at the beginning of my PhD struggling to figure out how anyone found out when a new paper came out. \u0026#x1f635; Did they sit on nature.com and spam the refresh button? Did they know when each journal released their latest issue?\u003c/p\u003e\n\u003ch2 id=\"behold-the-power-of-rss\"\u003eBehold the power of RSS!\u003c/h2\u003e\n\u003cp\u003eMost websites have a page that contains information about each subpage in a computer-readable format called RSS (Really Simple Syndication). \u003ca href=\"https://zacharybillman.com/index.xml\"\u003eMine has one right here!\u003c/a\u003e These pages can be parsed by a number of RSS feed aggregators. The way these pages are set up make it such that they add any new information hosted at that domain. This is useful in the science world because you can find the RSS feed of a given journal, subscribe to it, then have every new article published online be delivered right to you.\u003c/p\u003e","title":"Using RSS feeds to keep on top of science."},{"content":"My interest in self-hosting began in my with my interests in internet privacy. Plastered all over the internet are stories about how much Google, Facebook and Amazon know about you. I deleted my Facebook account years ago, and I\u0026rsquo;m too paranoid to go back to the site because there\u0026rsquo;s a real possibility that Facebook has cached my account, ready to spin it back up in case I try to login again. The ads served to me were too accurate for my liking. This is despite almost never clicking on them! I have become convinced of the idea that, if you are not paying for the product, you are the product. From this assumption, it follows that anywhere I trust with my data that I am not paying for (like Google Drive, Google Photos, Dropbox, Facebook, Twitter) is using my data to earn money. We know that Google uses the labels you add to Photos to train it\u0026rsquo;s AI, and Facebook uses (at least) Instagram photos to train it\u0026rsquo;s AI. For some, the value proposition of allowing a company to use your data for a useful service in return is an acceptable one. I find this to be a reasonable stance, but I took my growing interest in internet privacy as a chance to learn about how I can take control of my data.\nInitially, I lurked on forums like /r/privacy to learn what I could do to avoid big-tech\u0026rsquo;s watchful eye. There were numerous comments along the lines of: \u0026ldquo;The only way to be in control of your data is to self-host your services.\u0026rdquo; I had no idea what this meant! Hard to believe that less than a year later, I learned to use (and love) Linux as my primary OS, and have happily replaced Google Photos, Google Drive and other services with my own self-hosted alternatives. Self-hosting, I have since learned, is when you run useful programs from your own computer. By doing so, you have complete knowledge of where and how your data is stored and how it is being used. It has the additional effect of being a bottomless time sink.\nTo begin, I needed an always-on computer to run these useful programs. I began with a humble Raspberry Pi.\nFigure 1: My humble Raspberry Pi and its hard drive. This dude currently tirelessly runs the excellent Adguard Home and downloads a backup of my data every night.\nThese are tiny, but capable computers that are great for fiddling with. The projects people develop for these are amazing and diverse. With RPi in hand, I began with the ambitious project of replacing Google Drive with Nextcloud. After much frustration with a bare metal installation, I found the NextcloudPi project. Surprisingly, it went pretty okay! At first, I was intimidated by Linux defaults, but over time I grew to appreciate, and indeed, prefer Linux as an operating system. My decision to use Linux over Windows/MacOS is because it is free and open source software (FOSS). This is a topic for a different post, but I think using FOSS when possible is a moral imperative of sorts. I used Nextcloud strictly from my home for a few months, without the ability to connect to it from the internet, to test the self-hosting waters. My first true cloud replacement spun up once I decided to access this lil\u0026rsquo; guy from the internet. To do so, I purchased a domain (not the one this site is hosted on) and pointed it to the IP of my house. I forwarded the appropriate ports of my router to the RPi.\nThis is when the real exploration began. I was able to access my files and images using Nextcloud, but the photo viewing service left something to be desired. No problem, why not spin up an instance of Photoprism? I use RSS feeds to keep on top of the latest science in the journals relevant to my field using Feedly. Why not host my own RSS feed aggregator so I can subscribe to as many feeds as I desire?\nThis cycle continued, and I accrued many cool applications, but in the back of my mind I worried about opening up my home network to the internet. I also struggled to run some programs because the RPi uses the arm64 architecture, and most services are written with amd64 in mind. These two forces eventually convinced me to purchase a server where I could manage all of my services remotely. Some would say that not owning the hardware that is running your own services is not \u0026ldquo;true\u0026rdquo; self-hosting. I think this is needlessly exclusive. Let everyone self host, dangit! Someday, when I have more stable internet and a more permanent home, I hope to host everything from my own home, but until then, I\u0026rsquo;m extremely pleased with my current stack. And that is where I am now. I happily host numerous services on my virtual private server that entirely replace Google Photos, Google Drive and GitHub for me. Even better, there are specialized services that fill a need I never realized I had. What\u0026rsquo;s more, if I ever want to spin up a new service, all I have to do is add it to my to docker-compose file and it will be up within minutes. What a world!\nI thought about making this into a \u0026ldquo;guide\u0026rdquo; style post. I nixed that idea because, quite frankly, I feel like I don\u0026rsquo;t know what I\u0026rsquo;m doing. I am really happy with my setup, but I don\u0026rsquo;t feel like I have the authority to tell people how to administer their own services. If you are interested, allow me to point you toward the guide that really got me rolling: Ultimate Traefik Docker Compose Guide.\nFor those of you wondering what I am currently hosting, check out my current list at the link and let me know what you think!\n","permalink":"https://www.zacharybillman.com/posts/my-selfhosting-journey/","summary":"\u003cp\u003eMy interest in self-hosting began in my with my interests in internet privacy. Plastered all over the internet are stories about how much Google, Facebook and Amazon know about you. I deleted my Facebook account years ago, and I\u0026rsquo;m too paranoid to go back to the site because there\u0026rsquo;s \u003ca href=\"https://www.reddit.com/r/privacy/comments/6nmjfh/facebook_account_fully_recovered_3_years_after/\"\u003ea real possibility that Facebook has cached my account, ready to spin it back up\u003c/a\u003e in case I try to login again. The ads served to me were too accurate for my liking.\n\u003cspan class=\"sidenote-number\"\u003e\u003csmall class=\"sidenote\"\u003e\nThis is despite almost never clicking on them!\n\u003c/small\u003e\u003c/span\u003e\nI have become convinced of the idea that, if you are not paying for the product, you are the product. From this assumption, it follows that anywhere I trust with my data that I am not paying for (like Google Drive, Google Photos, Dropbox, Facebook, Twitter) is using my data to earn money. We know that \u003ca href=\"https://www.theverge.com/2020/11/11/21559930/google-train-ai-photos-image-labelling-app-android-update\"\u003eGoogle uses the labels you add to Photos to train it\u0026rsquo;s AI\u003c/a\u003e, and \u003ca href=\"https://ai.facebook.com/blog/seer-the-start-of-a-more-powerful-flexible-and-accessible-era-for-computer-vision/\"\u003eFacebook uses (at least) Instagram photos to train it\u0026rsquo;s AI\u003c/a\u003e. For some, the value proposition of allowing a company to use your data for a useful service in return is an acceptable one. I find this to be a reasonable stance, but I took my growing interest in internet privacy as a chance to learn about how I can take control of my data.\u003c/p\u003e","title":"My selfhosting journey."},{"content":"N.B.: I hope to add screenshots for each of these eventually. For now, I hope links to each services\u0026rsquo; website will suffice.\nSeafile\nThis is a great tool for managing files. I moved to this from Nextcloud because I am of the philosophy that I would prefer services that do one thing excellently instead of many things well. Nextcloud is an incredible Office365 replacement, but I found myself using a fraction of what it was capable of providing. Enter Seafile. It is cloud file syncing with a robust encryption implementation, just what the doctor ordered.\nPhotoprism\nNextcloud\u0026rsquo;s implementation of photo management was a bit clumsy for my tastes, so I began on a hunt for a more feature complete option. I was very lucky to stumble upon Photoprism early on in my self hosting journey. I am a proud supporter of this project. It brings a ton to the table, and doesn\u0026rsquo;t leave me missing Google Photos one bit. It is also actively developed. For instance, as of 2022-07-02, there was a recent update that improved scrolling a ton, which was one of my remaining quibbles with it\u0026rsquo;s functionality. Some people complain that it doesn\u0026rsquo;t scale up for libraries of 10,000+ photos, but my 2000 photo library works swimmingly. On my phone, I use the Folder Sync app to automatically send any pictures I take on my phone to the Photoprism imports folder. Within 15 minutes of snapping a photo, it is there on my Photoprism instance. I highly recommend giving it a go.\nMealie\nI have to admit that the name leaves something to be desired. Fortunately, the service itself doesn\u0026rsquo;t fall short. Mealie is a recipe management application. It is able to parse your favorite recipe websites to create immortalized versions of the recipe. This helps fight detestable link rot that plagues the internet. It allows you to edit ingredient amounts, make comments about what you would change next time, and plan out your weekly meals. It helps that it is beautiful and intuitive to use. If only I could get my partner to use it\u0026hellip; I want to go on the record here and say that I think it is sensible that she doesn\u0026rsquo;t trust my self hosted services that much. In the early days of my self hosting journey, let\u0026rsquo;s just say that the up-time of my services were extremely finicky. I like to think they are more permanent now, especially because I am hosting everything on a VPS, but I certainly cannot compete with the stability of Google and Amazon. (Or pretty much any other paid service for that matter.) \u0026#x1f609;\nGitea\nGitea is a community managed, lightweight code hosting solution written in Go. I use it to manage my data analysis (using Private repos) and even host the source code for this very website! Using Gitea has given me the surface level introduction to the behemoth that is git. Fortunately, that is all I need. Once I have removed any sensitive data (like passwords, etc.) I will make my docker-compose file public. The docker-compose file is where I determine which services I pick to host, and how to configure them to my liking. Hopefully someone will find this useful.\nSyncthing\nIf I could only tell someone to self host a single service, I would have to pick Syncthing. It is a continuous file synchronization program, which means it keeps a specific file or folder the same between any device running Syncthing. I use it to keep my password database and my org-mode notes Now org-mode might be the biggest rabbithole of them all, and definitely the topic for another blog post. I use it to manage my TODO list, my lab notebook, my shopping lists, write this blog, and maintain my Zettelkasten note database. It is an immensely powerful tool. up to date between all of my devices. With Syncthing, all of my data is stored on my own devices and encrypted in transit.\nFreshRSS\nI keep up to date on the science in my field by subscribing to relevant RSS feeds. Yet another topic to write a post about. This really changed the game for my ability to keep on top of the latest research. 2022-07-14 Update: post complete! Check it out here. FreshRSS replaced Feedly for me, as I ran up against the number of feeds I could subscribe to on a free account. Also, when self hosting, I can save as many articles as my heart desires (even if I will never look at them again \u0026#x1f635; ).\nWallabag\nRemember Pocket for Firefox? (Yes, I know it still exists, okay?) Give Wallabag a spin, it is great for storing articles you want to read later. I set up FreshRSS to save articles to my Wallabag instance to keep for later.\nChangeDetection\nNow this is a fun one! ChangeDetection.io is a service that loads a webpage and checks to see if something has changed since the last time. This might not sound useful at first, but I recently used this to check for when a hot item for my new coffee roasting hobby was back in stock. I got an email the other day to let me know it was in stock. Pretty cool!\nHugo\nHugo is the static site generator I use to make this here blog! I was amazed at how much more response my site was using Hugo compare to when I paid a company to host a WordPress site. I\u0026rsquo;m sure WordPress could be fast, but I just wanted a barebones, pure html experience, and Hugo made it easy.\nCommento++\nYou may have noticed that I have some pretty snazzy comments sections on my site. I initially used Disqus, which you may recognize from a ton of sites around the internet, but didn\u0026rsquo;t like how it would serve ads through my comments section, and provided sign-ins using Google/Facebook/Twitter. I wanted to serve the simplest comments section I could, that still gave me the ability to migrate the comments to wherever I decide to keep my server. Go ahead and use the anonymous comment button, fill in your name, and you are off to the races.\nAuthelia\nThere are a few services I host that I really want to lock down. For these services, Authelia is great. It puts up a \u0026ldquo;Enter the 6 digit code on your phone\u0026rdquo; style 2 factor authentication in front of the services I choose. Or, if you follow the guide here, you can have it send you a DUO push, just like you are one of the big hitters out there. I feel much more secure with Authelia in front of Adminer, Traefik, and Portainer.\nBoring stuff that allows everything else to work!\nPostgreSQL database MariaDB database Traefik reverse proxy Umami privacy respecting site analytics Portainer for docker container management Redis in-memory data store Adminer database management traefik-socket-proxy to prevent pesky backdoors to my server! ","permalink":"https://www.zacharybillman.com/posts/zpb-current-selfhosted/","summary":"\u003cp\u003e\u003cem\u003eN.B.: I hope to add screenshots for each of these eventually. For now, I hope links to each services\u0026rsquo; website will suffice.\u003c/em\u003e\u003c/p\u003e\n\u003col\u003e\n\u003cli\u003e\n\u003cp\u003e\u003ca href=\"https://www.seafile.com/en/home/\"\u003eSeafile\u003c/a\u003e\u003c/p\u003e\n\u003cp\u003eThis is a great tool for managing files. I moved to this from Nextcloud because I am of the philosophy that I would prefer services that do one thing excellently instead of many things well. Nextcloud is an incredible Office365 replacement, but I found myself using a fraction of what it was capable of providing. Enter Seafile. It is cloud file syncing with a robust encryption implementation, just what the doctor ordered.\u003c/p\u003e","title":"What I'm currently selfhosting."},{"content":"My partner and I took a trip to the Mason Farm Biological Reserve the other day, and what a glorious day it was. This year, I\u0026rsquo;ve been quite busy in the lab, and missed a lot of the early spring warbler season, so I was very excited by the opportunity to check out the old stomping grounds.\nI brought the camera with me despite the fact we were going to be there around midday when the birds are much less active. I\u0026rsquo;m glad I did, because I got the best look at a common yellowthroat I\u0026rsquo;ve ever had. Normally these guys are flighty, staying close to the ground in small brush or tall grasses, but this one was putting on a proper show for the mating season. Even when you get a glimpse of one, it is usually just that, as they have jumped away before you can pull out the camera, taunting you with their iconic call. I was very pleased to capture a few choice shots of the bird. Hopefully there are more to come. While we were out, I also got a nice picture of a hermit thrush and a king snake.\nThese images have been compressed quite a bit for a lighter internet footprint. These have all been resized to 25% of their original size. If you would like the full sized images, let me know and I will send you a link!\n","permalink":"https://www.zacharybillman.com/posts/the-uncommon-yellowthroat/","summary":"\u003cp\u003eMy partner and I took a trip to the \u003ca href=\"https://ncbg.unc.edu/visit/mason-farm-biological-reserve/\"\u003eMason Farm Biological Reserve\u003c/a\u003e the other day, and what a glorious day it was. This year, I\u0026rsquo;ve been quite busy in the lab, and missed a lot of the early spring warbler season, so I was very excited by the opportunity to check out the old stomping grounds.\u003c/p\u003e\n\u003cp\u003eI brought the camera with me despite the fact we were going to be there around midday when the birds are much less active. I\u0026rsquo;m glad I did, because I got the best look at a common yellowthroat I\u0026rsquo;ve ever had.\n\u003cspan class=\"sidenote-number\"\u003e\u003csmall class=\"sidenote\"\u003e\nNormally these guys are flighty, staying close to the ground in small brush or tall grasses, but this one was putting on a proper show for the mating season. Even when you get a glimpse of one, it is usually just that, as they have jumped away before you can pull out the camera, taunting you with their \u003ca href=\"https://ebird.org/species/comyel#Modal-playlist\"\u003eiconic call\u003c/a\u003e.\n\u003c/small\u003e\u003c/span\u003e\nI was very pleased to capture a few choice shots of the bird. Hopefully there are more to come. While we were out, I also got a nice picture of a hermit thrush and a king snake.\u003c/p\u003e","title":"The (un)common yellowthroat."},{"content":"Welcome to my site! My name is Zachary Billman. I\u0026rsquo;m a UNC MD-PhD student in my 4th year of med school applying to pathology residency programs. I completed my PhD in Ed Miao\u0026rsquo;s lab. The curious reader may be thinking: \u0026ldquo;But Zach, Dr. Miao\u0026rsquo;s lab is at Duke, how did that come about?\u0026rdquo; What an astute question! Ed\u0026rsquo;s lab moved from UNC to Duke in early 2020, and I followed him down the street. My PhD was awarded by the UNC department of Microbiology and Immunology, but it just so happens that (nearly) all of my research took place at Duke. This move was quite a trial, especially when compounded with the onset of the pandemic. I suspect my research timeline suffered, though this is an extremely minor inconvenience compared to the tragedy the pandemic caused. This makes for very interesting basketball viewing parties with my Duke friends!\nMaybe having a diagram will make my training timeline make a bit more sense.\nFigure 1: An overview of my research training. I first began working for Dr. Sean Murphy in undergrad, then worked as a research scientist/lab manager for 3 years before heading to UNC for my MSTP training. During grad school, my lab moved from UNC to Duke, though my degree was awarded by UNC. The \u0026ldquo;Present\u0026rdquo; diamond was used on an older version of my CV and represents September 1st, 2025. Created using PlantUML.\nHopefully that can clear up the winding road I\u0026rsquo;ve taken a bit!\nMy research and scientific interests. I am broadly interested in innate immunology. I spent most of my time in graduate school studying the host-pathogen interaction between the intracellular fungus Histoplasma capsulatum and macrophages. There are many unstudied curiosities regarding the innate immune response to Histoplasma spp. and other intracellular fungi that I think are quite interesting. I also spent a considerable time thinking about the evolution of proteins involved in the programmed cell death pathway called pyroptosis.\nHobbies I may write about. Besides my science, I am interested in birding, baking sourdough bread (I swear I began years before the pandemic, though hearing of people baking bread brings me joy no matter when they first began!), board games, roasting coffee, and self-hosting free and open source software. Over the course of the pandemic, I have learned how to maintain a basic suite of services spread between a server I rent and a computer at home that have replaced my need for Google Photos and Google Drive. I\u0026rsquo;m hoping to be able to move away from these platforms entirely soon. I think they provide a great service, but at a substantial cost to privacy. Hopefully more to be said about my thoughts on FOSS soon! I also transitioned my old, (and quite frankly, embarrassingly slow) managed WordPress site with this lean, static site made in Hugo that I host myself. Now that I have mangled together some CSS to get my precious sidenotes up and running again, I\u0026rsquo;m ready to begin putting some ideas to paper. I love marginalia (the word to describe these notes on the side of this webpage). I\u0026rsquo;m not sure if this is unique to me, but I seem to get caught up in parenthetical / tangential thoughts very often, and I think using an Edward Tufte-esque sidenote is a great way for me to communicate in this way without distracting the reader too much. It seems marginalia such as this have been used throughout history, so perhaps it is normal, but most people can keep their thoughts focused better than me. The implementation I use is inspired by the Tufte CSS project and largely taken from this incredibly helpful post found at scripter.co. I\u0026rsquo;m quite proud of my progress in administering my server and self-hosting useful services.\nThe future of this site. On this site I plan to post updates about my journey through med school, grad school, and self-hosting I would like to share with the world. I have been helped immensely by many others\u0026rsquo; advice and I hope to impart similar tips to others someday. I suspect most posts will be about much lighter fare, like whatever hobbies tickle my fancy at the time.\n","permalink":"https://www.zacharybillman.com/posts/about-me/about-me/","summary":"\u003ch2 id=\"welcome-to-my-site\"\u003eWelcome to my site!\u003c/h2\u003e\n\u003cp\u003eMy name is Zachary Billman. I\u0026rsquo;m a UNC MD-PhD student in my 4th year of med school applying to pathology residency programs. I completed my PhD in Ed Miao\u0026rsquo;s lab. The curious reader may be thinking: \u0026ldquo;But Zach, Dr. Miao\u0026rsquo;s lab is at Duke, how did that come about?\u0026rdquo; What an astute question! Ed\u0026rsquo;s lab moved from UNC to Duke in early 2020, and I followed him down the street. My PhD was awarded by the UNC department of Microbiology and Immunology, but it just so happens that (nearly) all of my research took place at Duke.\n\u003cspan class=\"sidenote-number\"\u003e\u003csmall class=\"sidenote\"\u003e\nThis move was quite a trial, especially when compounded with the onset of the pandemic. I suspect my research timeline suffered, though this is an extremely minor inconvenience compared to the tragedy the pandemic caused.\n\u003c/small\u003e\u003c/span\u003e\nThis makes for very interesting basketball viewing parties with my Duke friends!\u003c/p\u003e","title":"About me. 👋"},{"content":"It\u0026rsquo;s over. My third year of medical school is officially behind me. I managed to get in a grand total of zero blog posts during grad school, so here\u0026rsquo;s to a new year with hopefully some more thoughts being shared. I have a lot to reflect on from the past year. It was wonderful. I wish everyone could experience what I did this past year. I think it goes without saying:\nI loved the third year of med school, but I do not want to do it again.\nA year of change. In the days leading up to my return to med school, I thought \u0026ldquo;Oh no, I really enjoy doing science, do I really have to go to med school?\u0026rdquo;. I also remember at the end of Step 1 and the first two years of med school thinking, \u0026ldquo;Oh no, I really enjoy med school, do I really have to do science again?\u0026rdquo;. I think I have a welcome problem of enjoying what I\u0026rsquo;m doing. The third year of med school is a shift. After years of memorizing and examinations, the doors to the promised land are finally opened. I have experienced nothing like it before It feels intentionally unsettling. You are thrown into the clinic with a modicum of guidance so you aren\u0026rsquo;t totally caught off guard, but you are thrown out to the wolves. I don\u0026rsquo;t mean this as a criticism of the system, it feels necessary. Third year medical students—commonly shorted to MS3s—have just one year to experience a broad swath of medicine and pick a specialty. So you had better be ready to dive in.\nTotal immersion I came to terms with my new reality quickly. Gone were the days of hitting the snooze button and going home when I pleased. I am now beholden to other people\u0026rsquo;s schedules. This came back relatively naturally. Maybe not hitting snooze. A regrettable personal failing of mine. I was, however, immediately faced with a new reality in the patient room. Patients come to the doctor for a number of reasons, but often seek relief. To get to the core of what ails them, they will tell you everything. I was not prepared for how vulnerable patients would be with me. I am not sure if this ever will feel natural. I hope it never does. I was told many stories of experiences living with scary diagnoses, and not knowing what to do with it. Family histories of all sorts. Personal details that were sometimes (oftentimes?) off the wall. I see all of these specifics as flailing, grasping at sand hoping that something could explain their pain. Sometimes it could. Usually it did not. But since I was in a white coat, I was privileged to hear it.\nI think my years spent in the lab have prepared me to face some of the challenges set before me. At the very least, having a few more years under my belt helped me approach the year with a bit of maturity. This seems to have paid off. I guess my recommendation is to simply get old before going to med school. Returning to studying The hospital is how I spent the majority of my time, but a new reality for me was also going back to daily studying. There is a strange dichotomy in medicine of \u0026ldquo;Oh, it doesn\u0026rsquo;t really matter\u0026rdquo; and \u0026ldquo;If you don\u0026rsquo;t get this class/score/grade then you won\u0026rsquo;t be able to be the kind of doctor you want to be, so you had better get your act together.\u0026rdquo; Simultaneously there are no expectations and immense responsibility for the looming specter of Step 2. I\u0026rsquo;m glad that studying regularly came back easily enough. I was concerned I would experience a studying whiplash. I\u0026rsquo;m glad it never came. I did UWorld and Anki nearly every day for a full year and felt alright.\nBecoming invisible I quickly learned I needed to change my understanding of my contribution to the team. Exiting grad school, people understood that they could come to me for help. I was a resource, a seasoned veteran of the lab. If someone needed an experiment done, I could do it, and be trusted to do it. In med school as a third year, I was nothing. A fly on the wall; a worm beneath the feet of the real doctors. In science, I felt like I was treated as a peer with even my committee members with multiple R01s. Even if I didn\u0026rsquo;t understand the science perfectly, I could contribute some different perspective. In medicine, sometimes not being recognized at all by my attendings was the best outcome. Which happened regularly. My role, was not as a contributor—as it was in science—it was simply to get in the reps. Once I understood that the expectations of me were below the ground, I understood that everything I did in third year was for myself. This is taken at face value by the team at times. I would spend 30 minutes working on a presentation, pre-rounding, the works, and at the end of my part, the intern would nod, then turn to the senior resident and say \u0026ldquo;I was thinking that we\u0026hellip;\u0026rdquo; without thinking of my work. This is perhaps a bit of cognitive restructuring, but recognizing this is what gave me the freedom to embed myself in the hospital flow, without a single worry about the outcome. Simply doing my best was the best thing I could do. Obviously. But this was not apparent to me at first. I needed more quality repetitions to develop good habits in the future. And also experience as much of medicine as possible to find what I want to do with my life. This permission allowed me to approach specialties I do not care about with the awe and respect they deserve.\nA year of wonder. Med school prepares you for the standardized tests. I think this is generally useful. The tests on aggregate are reasonable and evaluate your ability to think through common clinical scenarios. There will always be oddball questions that come out of left field, but I let these flow over me. No need to perseverate on the small stuff. The time for that can come later.\nWhat I didn\u0026rsquo;t realize is how much of the \u0026ldquo;classic\u0026rdquo; material we are fed in the first couple years of med school would come to the forefront. The \u0026ldquo;sandpaper rash\u0026rdquo; of scarlet fever really does feel like sandpaper. Nikolsky\u0026rsquo;s sign actually works. Tripoding for epiglottitis gets the physicians worked up. Don\u0026rsquo;t forget about von Willebrand\u0026rsquo;s disease when someone seems to be bleeding a bit too much. TB is out there, watch for hemoptosis. Night sweats, unintended weight loss, is cancer until proven otherwise. And yes, it really can be lupus.\nIn general, facing the unknown with a sense of earnestness was the way I felt best able to respect those who gathered and passed down the medical knowledge I am privileged to learn today. Sometimes, my excitement to see aspects of medicine would rouse a curious response from the residents. I project here, but I felt a sense of surprise, like that of a doting parent seeing their child experience something new, after forgetting the astonishment they once felt.\nEarnestness is next to med studentlyness.\nPerhaps what I\u0026rsquo;m getting at here is that I found it important to bask in the privilege of seeing the pathology I encountered in med school, and to remind the residents of this sensation. I felt childish at times—and perhaps overanimated—but I found this excitement was to my and my resident\u0026rsquo;s benefit.\nMy surgery rotation overflowed with examples of wonder of medicine. Partially because of the team I worked with, and the rest because of the undeniable coolness of surgery. The OR is a cool place. The orderliness and chaos ebb. The spans of steady, industrious work are interrupted with staccato notes of bedlam. The anatomy I learned in class was ever present, but the surgeons bemoaned \u0026ldquo;normal anatomic variation\u0026rdquo;.\nI was struck with wonder at the sight of human anatomy as it unfolded before me. What I was able to experience in the OR felt like the culmination of centuries of human curiosity. There is an ancientness to medicine that I catch flashes of—I could perform the physical exam on humans hundred of millions of years ago and interrogate the same pathologies as I do in the hospital today—and viewing the exposed anatomy is a pressure-bagged infusion of this collective wonder. To gaze upon the peristalsing of the small intestine, or steady beating of the heart is a sight to behold, indeed.\nA year of shame. It weighs upon me the circumstances that resulted in these transcendent experiences. Not one patient was in the hospital without reason. What to make of these patients with horrible pathology? I still feel unsettled about how the cause of their pain sparked wonder. How dare I gain, merely by the circumstance of having their care managed at UNC, Which, as a tertiary care center, layers on more complexity. Many patients end up at UNC because they have no where else they can go for help. And this signs them up for med students? For shame. from the very essence of their malady? I do not know what to do with my discomfort, but I think it is best that I dwell in it. With this, I respect the people before me in the hospital and recognize their humanity.\nBut I often complained of what I say here I was lucky to do. I find myself resentful of my future schedule; when was I supposed to learn that I will be working 13 hour days, 6 days a week for the rest of my life? And what of having a family? Medicine by necessity requires sacrifice. I happened to sign up for sacrifices years before I recognized how profound they were. How might I balance this dread and with the joy of practicing medicine? And why do I seem more concerned about this than others? Am I not grateful enough? Am I not capable of the sacrifices that others seem to offer so effortlessly? I don\u0026rsquo;t necessarily think this to be true, but these questions erode at my will to pursue medicine.\nPerhaps most shameful of all is how my understanding of the patient-provider interaction evolved over the year. It began as an exploration of an open book, a tabula rasa that held within it a diagnosis and how to best intervene. On my first day in the outpatient clinic, it was clear that this is not the case. My preceptor had only 20 minutes for me to ① interview the patient and perform the physical exam, ② present with a plan, ③ return to the room and do everything again, ④ write orders, educate, and get the patient out of the door. It simply is not amenable to the free form, personable, curious interview I hoped to perform. By the end of the year, I had optimized how I asked questions to keep patients from going off the rails. When prerounding in medicine, I was there to extract information and not much else. Small talk had to go, there was no time. I like to chat, so this came at a loss of who I think I am. I am not sure how to do this well, while still feeling like Zachary. And from what I gather from the interns, that may just come later in my career. I found myself questioning, \u0026ldquo;Is this the \u0026lsquo;patient interaction\u0026rsquo; that has been mythologized throughout my training?\u0026rdquo; The carrot at the end of the stick dangled before me with a \u0026ldquo;You are so lucky to be able to do this, so you had better not complain of any abuse that comes your way.\u0026rdquo; It wasn\u0026rsquo;t a genuine interaction as much as me leading the patient along to tell me what I wanted to know. Of course, I used open ended questions, but only open enough. Leave the door a bit too open and next thing you know, you are talking about their dog\u0026rsquo;s breeder while you constantly stare at your watch, imagining what your attending will say when you return. I feel like I am alone in missing the core human element that funnels sprightly youths into medicine. Or worse, finding it a façade.\nThe shame extends beyond the hospital. One aspect of my life that has changed most dramatically is the sheer amount of time I felt I needed to dedicate to medicine, whether at the hospital or at home. I spent all day basking in the wonder of medicine, then I would come home and study for hours. I relied on my partner for keeping our household together more than ever, because I spent all day—all year, rather—in a state of discovery. Her life was largely the same, with the normal challenges of being a scientist, with the added bonus of getting less help from me. The shame built over the year. Again, how dare I?\nA year of glad. This has been an undeniable year of growth and joy, with these quibbles. It is clear that I was happier than I was during grad school. I know this from within myself, and reinforced by my wife\u0026rsquo;s comments on my mood. The pace of the day, and immediacy of problem solving were a welcome change.\nI recall, during the very first days preparing for med school during xTAP, having to do a simulated patient encounter complete with patient presentation to an attending physician. We were told about this encounter days in advance. And yet, I dreaded it. And near the last day of my final rotation, I did 8 of these in a row without breaking a sweat. Progress!\nI think, in a word, what I\u0026rsquo;ve experienced in the third year of med school is gratitude. Gratitude to be privileged to learn what I am learning. Gratitude for the experiences in my life that brought me here. Gratitude for the support from my wife. Gratitude to be involved in people\u0026rsquo;s lives when they are fragile. Ever since reading Braiding Sweetgrass I think one could call me \u0026ldquo;gratitude-pilled\u0026rdquo;. I also selfishly enjoyed the gratitude from patients as I put on my best doctor performance. In reflection on the year, I have spent time thinking of a phrase that I heard a number of times throughout med school from residents, \u0026ldquo;The worst day of residency is better than the best day of med school.\u0026rdquo; I find this hard to believe. This year has been magical. It is hard to imagine a year filled with more wonder and joy of caring for those in need. I will have to rely on the experience of those who have walked this path and trust that the rest of my training has plenty of magic to spare.\n","permalink":"https://www.zacharybillman.com/posts/ms3-year-is-magical/","summary":"\u003ch2 id=\"it-s-over-dot\"\u003eIt\u0026rsquo;s over.\u003c/h2\u003e\n\u003cp\u003eMy third year of medical school is officially behind me. I managed to get in a grand total of \u003cem\u003ezero\u003c/em\u003e blog posts during grad school, so here\u0026rsquo;s to a new year with hopefully some more thoughts being shared. I have a lot to reflect on from the past year. It was wonderful. I wish everyone could experience what I did this past year. I think it goes without saying:\u003c/p\u003e","title":"The third year of medical school is magical."},{"content":"I, like many others, picked up a new hobby during the pandemic. Other people\u0026rsquo;s hobbies may bring them joy. This could be for many reasons. There is the joy of creating something from scratch. You can revel in your thriftiness. You can embrace the pride when you recognize that your creation is on par (or better!) than what you can buy. I feel like these are embodied in the sourdough craze that caught fire early on in COVID. Dare I say that I did this before it was cool? \u0026#x1f60e; I baked two loaves of bread almost every weekend through med school. Maybe I should bring that back, it\u0026rsquo;s been a while since I brought out the ole\u0026rsquo; starter. My pandemic hobby is similar, but different in that it often feels like a chore, costs more money, and often turns out worse than what I can buy. Of course, I am talking about how I\u0026rsquo;ve started roasting my own coffee at home.\nI\u0026rsquo;m not sure where this idea was planted into my brain. I don\u0026rsquo;t think I know anyone who roasts their own beans, and I certainly didn\u0026rsquo;t know how. I didn\u0026rsquo;t even drink coffee regularly until after college! I guess that extra time on the computer sent me down a rabbithole I have yet to emerge from.\nFirst, I want to preface the following with a disclaimer: This is not a detailed guide about how to roast your own coffee. If you are interested, I recommend checking out the How To Roast Your Own Coffee guide at Sweet Maria\u0026rsquo;s as a starting point. There is also the /r/roasting subreddit if that is your cup of tea. My only warning is there will be a lot of smoke. Roast your coffee outside, for Pete\u0026rsquo;s sake!\nIt all started with a trusty popcorn popper. There are a few things you want when you roast coffee:\nAir hot enough to roast coffee Remove the chaff from the beans Turns out that a classic popcorn popper fits the bill, as long as it has an upwards airflow and doesn\u0026rsquo;t let the chaff fall into the heating element. There is a bit of a cult following for the West Bend Poppery 2 model, but that one seemed a bit pricey, so I settled for a very capable popper from Nostalgia.\nFigure 1: I got a good bit of mileage out of my popcorn popper. If you are interested in roasting your own coffee I would give it a whirl.\nThings were simple back then. I still bought most of the coffee I drank, but I roasted enough to enjoy some freshly roasted coffee as an occasional treat. I ordered 10 pounds of green beans from Sweet Maria\u0026rsquo;s and life was good.\nThen I became a bit of a coffee snob.\nI could only roast 100 grams of coffee at a time in the popcorn popper, which is only enough for one pot of coffee in the morning for me. So it was time to upgrade.\nI bought the SR800 fluid bed roaster, which upped my roasting capacity and gave me finer control on temperature and airflow. Suffice to say my roasts improved a lot! At this point, I would consider my coffee good enough to sell at a farmer\u0026rsquo;s market to break even.\nIf you ever find yourself on a coffee roasting forum and bring up the SR800, someone is bound to bring up the famous RazzoRoasting extension tube. If you look for advice for how to use the SR800, I swear it\u0026rsquo;s assumed that you have this very specific accessory. \u0026hellip;And so I bought one.\nDon\u0026rsquo;t worry, that is the extent of all of my coffee spending (for now). I am a very satisfied coffee roaster now. Check out this quick series of images going from the green beans to a nearly finished product! I can spend about 45 minutes and go from nothing to nearly 2 pounds of roasted beans, enough for about a week and a half of coffee. Not bad! The only downside is that now I feel like I need to buy coffee from local roasters to get my fix. There are certainly crueler fates.\nAs a sign off, I will share something that surprised me about coffee roasting. When I roast coffee, the most important cue to determine if the coffee is roasted is the sound. That\u0026rsquo;s right, not the color, not the smell, but the sound. When heating up a coffee bean, the water trapped inside eventually bursts out of the bean in a rapid expansion. This is called \u0026ldquo;first crack\u0026rdquo;, and indicates that the coffee is roasted enough to be drinkable. The expansion also releases the chaff from the bean. If you continue heating up the bean, you will eventually reach \u0026ldquo;second crack\u0026rdquo;. I think a solid medium roast is taken out just before second crack, so I try to take my coffee out to this point and it hasn\u0026rsquo;t proved me wrong yet.\nHappy coffee-ing! \u0026#x2615;\n","permalink":"https://www.zacharybillman.com/posts/roasting-coffee-at-home/","summary":"\u003cp\u003eI, like many others, picked up a new hobby during the pandemic. Other people\u0026rsquo;s hobbies may bring them joy. This could be for many reasons. There is the joy of creating something from scratch. You can revel in your thriftiness. You can embrace the pride when you recognize that your creation is on par (or better!) than what you can buy. I feel like these are embodied in the sourdough craze that caught fire early on in COVID.\n\u003cspan class=\"sidenote-number\"\u003e\u003csmall class=\"sidenote\"\u003e\nDare I say that I did this before it was cool? \u0026#x1f60e; I baked two loaves of bread almost every weekend through med school. Maybe I should bring that back, it\u0026rsquo;s been a while since I brought out the ole\u0026rsquo; starter.\n\u003c/small\u003e\u003c/span\u003e\nMy pandemic hobby is similar, but different in that it often feels like a chore, costs more money, and often turns out worse than what I can buy. Of course, I am talking about how I\u0026rsquo;ve started roasting my own coffee at home.\u003c/p\u003e","title":"Roasting coffee at home. ☕"},{"content":"It is an age-old question: how can one keep up with the continuous output of science? I remember at the beginning of my PhD struggling to figure out how anyone found out when a new paper came out. \u0026#x1f635; Did they sit on nature.com and spam the refresh button? Did they know when each journal released their latest issue?\nBehold the power of RSS! Most websites have a page that contains information about each subpage in a computer-readable format called RSS (Really Simple Syndication). Mine has one right here! These pages can be parsed by a number of RSS feed aggregators. The way these pages are set up make it such that they add any new information hosted at that domain. This is useful in the science world because you can find the RSS feed of a given journal, subscribe to it, then have every new article published online be delivered right to you.\nThere are a plethora of RSS feed aggregators you can pick from manage your feeds. I have previously used Feedly and Inoreader, which are great free solutions, but have moved on to selfhosting my own instance of FreshRSS.\nAfter making an account at your friendly local RSS feed aggregator, you can add whatever feeds your heart desires. To find a journal\u0026rsquo;s rss feed, I often just search \u0026ldquo;$JOURNAL_NAME rss feed\u0026rdquo; and poke around until I find something that looks right. Most of the aggregators will test the feed out first to make sure that you are trying to add a legitimate one. Here are a few of the heavy hitters to get you started:\nhttp://feeds.nature.com/nature/rss/current https://www.science.org/rss/express.xml https://www.cell.com/cell/inpress.rss Nothing like a constant stream of Cell, Science, and Nature to make your project feel like a real winner, eh?\nHere is what my own site looks like.\nFigure 1: My current FreshRSS setup. On the left I have my feeds separated into folders. In the middle you can see the titles of papers that appear in my feed.\nAnd after I hit J to move to the first item in the feed.\nFigure 2: With a title selected, you can see the abstract and authors.\nAfter collecting all of your desired RSS feeds, you cannot forego your responsibility of actually reading them! Most RSS feed aggregators have shortcuts to move through titles quickly (Typically J to move on to the next one and K to move up.) They always seem to use vi keybindings. A bunch of computer nerds have really cornered the keybinding market. I have let them take over my computing life. Each morning when I get into the lab, I quickly set up something, then head to my desk to hit J until the counter reaches zero.\nBut what about my very specific field? You can subscribe to all of the journals you want, but that doesn\u0026rsquo;t make the papers with your specific interests pop out. Fortunately, the NIH has this exact circumstance in mind.\nWhen you make a new search on PubMed you might notice the \u0026ldquo;Create RSS\u0026rdquo; button. Give it a click, then you will have a personal link you can add to your favorite RSS feed aggregator.\nFigure 3: Somehow I never noticed this button until I needed it.\nThis changed the game for me for keeping up with papers. Unfortunately, it doesn\u0026rsquo;t solve the problem of library management, or actually getting around to reading the papers you care about. I will leave library management as an exercise for the interested reader. Here\u0026rsquo;s a tip, the best solution uses the Zotero citation manager. Bonus points for using Zotfile for renaming your PDFs and Better BibTex for Zotero. \u0026#x1f609; I hope this helps you get your eyeballs on that science you crave. If you have solved the problem of accruing papers to read faster than you read them, let me know.\n","permalink":"https://www.zacharybillman.com/posts/rss-feeds-to-find-science-papers/","summary":"\u003cp\u003eIt is an age-old question: how can one keep up with the continuous output of science? I remember at the beginning of my PhD struggling to figure out how anyone found out when a new paper came out. \u0026#x1f635; Did they sit on nature.com and spam the refresh button? Did they know when each journal released their latest issue?\u003c/p\u003e\n\u003ch2 id=\"behold-the-power-of-rss\"\u003eBehold the power of RSS!\u003c/h2\u003e\n\u003cp\u003eMost websites have a page that contains information about each subpage in a computer-readable format called RSS (Really Simple Syndication). \u003ca href=\"https://zacharybillman.com/index.xml\"\u003eMine has one right here!\u003c/a\u003e These pages can be parsed by a number of RSS feed aggregators. The way these pages are set up make it such that they add any new information hosted at that domain. This is useful in the science world because you can find the RSS feed of a given journal, subscribe to it, then have every new article published online be delivered right to you.\u003c/p\u003e","title":"Using RSS feeds to keep on top of science."},{"content":"My interest in self-hosting began in my with my interests in internet privacy. Plastered all over the internet are stories about how much Google, Facebook and Amazon know about you. I deleted my Facebook account years ago, and I\u0026rsquo;m too paranoid to go back to the site because there\u0026rsquo;s a real possibility that Facebook has cached my account, ready to spin it back up in case I try to login again. The ads served to me were too accurate for my liking. This is despite almost never clicking on them! I have become convinced of the idea that, if you are not paying for the product, you are the product. From this assumption, it follows that anywhere I trust with my data that I am not paying for (like Google Drive, Google Photos, Dropbox, Facebook, Twitter) is using my data to earn money. We know that Google uses the labels you add to Photos to train it\u0026rsquo;s AI, and Facebook uses (at least) Instagram photos to train it\u0026rsquo;s AI. For some, the value proposition of allowing a company to use your data for a useful service in return is an acceptable one. I find this to be a reasonable stance, but I took my growing interest in internet privacy as a chance to learn about how I can take control of my data.\nInitially, I lurked on forums like /r/privacy to learn what I could do to avoid big-tech\u0026rsquo;s watchful eye. There were numerous comments along the lines of: \u0026ldquo;The only way to be in control of your data is to self-host your services.\u0026rdquo; I had no idea what this meant! Hard to believe that less than a year later, I learned to use (and love) Linux as my primary OS, and have happily replaced Google Photos, Google Drive and other services with my own self-hosted alternatives. Self-hosting, I have since learned, is when you run useful programs from your own computer. By doing so, you have complete knowledge of where and how your data is stored and how it is being used. It has the additional effect of being a bottomless time sink.\nTo begin, I needed an always-on computer to run these useful programs. I began with a humble Raspberry Pi.\nFigure 1: My humble Raspberry Pi and its hard drive. This dude currently tirelessly runs the excellent Adguard Home and downloads a backup of my data every night.\nThese are tiny, but capable computers that are great for fiddling with. The projects people develop for these are amazing and diverse. With RPi in hand, I began with the ambitious project of replacing Google Drive with Nextcloud. After much frustration with a bare metal installation, I found the NextcloudPi project. Surprisingly, it went pretty okay! At first, I was intimidated by Linux defaults, but over time I grew to appreciate, and indeed, prefer Linux as an operating system. My decision to use Linux over Windows/MacOS is because it is free and open source software (FOSS). This is a topic for a different post, but I think using FOSS when possible is a moral imperative of sorts. I used Nextcloud strictly from my home for a few months, without the ability to connect to it from the internet, to test the self-hosting waters. My first true cloud replacement spun up once I decided to access this lil\u0026rsquo; guy from the internet. To do so, I purchased a domain (not the one this site is hosted on) and pointed it to the IP of my house. I forwarded the appropriate ports of my router to the RPi.\nThis is when the real exploration began. I was able to access my files and images using Nextcloud, but the photo viewing service left something to be desired. No problem, why not spin up an instance of Photoprism? I use RSS feeds to keep on top of the latest science in the journals relevant to my field using Feedly. Why not host my own RSS feed aggregator so I can subscribe to as many feeds as I desire?\nThis cycle continued, and I accrued many cool applications, but in the back of my mind I worried about opening up my home network to the internet. I also struggled to run some programs because the RPi uses the arm64 architecture, and most services are written with amd64 in mind. These two forces eventually convinced me to purchase a server where I could manage all of my services remotely. Some would say that not owning the hardware that is running your own services is not \u0026ldquo;true\u0026rdquo; self-hosting. I think this is needlessly exclusive. Let everyone self host, dangit! Someday, when I have more stable internet and a more permanent home, I hope to host everything from my own home, but until then, I\u0026rsquo;m extremely pleased with my current stack. And that is where I am now. I happily host numerous services on my virtual private server that entirely replace Google Photos, Google Drive and GitHub for me. Even better, there are specialized services that fill a need I never realized I had. What\u0026rsquo;s more, if I ever want to spin up a new service, all I have to do is add it to my to docker-compose file and it will be up within minutes. What a world!\nI thought about making this into a \u0026ldquo;guide\u0026rdquo; style post. I nixed that idea because, quite frankly, I feel like I don\u0026rsquo;t know what I\u0026rsquo;m doing. I am really happy with my setup, but I don\u0026rsquo;t feel like I have the authority to tell people how to administer their own services. If you are interested, allow me to point you toward the guide that really got me rolling: Ultimate Traefik Docker Compose Guide.\nFor those of you wondering what I am currently hosting, check out my current list at the link and let me know what you think!\n","permalink":"https://www.zacharybillman.com/posts/my-selfhosting-journey/","summary":"\u003cp\u003eMy interest in self-hosting began in my with my interests in internet privacy. Plastered all over the internet are stories about how much Google, Facebook and Amazon know about you. I deleted my Facebook account years ago, and I\u0026rsquo;m too paranoid to go back to the site because there\u0026rsquo;s \u003ca href=\"https://www.reddit.com/r/privacy/comments/6nmjfh/facebook_account_fully_recovered_3_years_after/\"\u003ea real possibility that Facebook has cached my account, ready to spin it back up\u003c/a\u003e in case I try to login again. The ads served to me were too accurate for my liking.\n\u003cspan class=\"sidenote-number\"\u003e\u003csmall class=\"sidenote\"\u003e\nThis is despite almost never clicking on them!\n\u003c/small\u003e\u003c/span\u003e\nI have become convinced of the idea that, if you are not paying for the product, you are the product. From this assumption, it follows that anywhere I trust with my data that I am not paying for (like Google Drive, Google Photos, Dropbox, Facebook, Twitter) is using my data to earn money. We know that \u003ca href=\"https://www.theverge.com/2020/11/11/21559930/google-train-ai-photos-image-labelling-app-android-update\"\u003eGoogle uses the labels you add to Photos to train it\u0026rsquo;s AI\u003c/a\u003e, and \u003ca href=\"https://ai.facebook.com/blog/seer-the-start-of-a-more-powerful-flexible-and-accessible-era-for-computer-vision/\"\u003eFacebook uses (at least) Instagram photos to train it\u0026rsquo;s AI\u003c/a\u003e. For some, the value proposition of allowing a company to use your data for a useful service in return is an acceptable one. I find this to be a reasonable stance, but I took my growing interest in internet privacy as a chance to learn about how I can take control of my data.\u003c/p\u003e","title":"My selfhosting journey."},{"content":"N.B.: I hope to add screenshots for each of these eventually. For now, I hope links to each services\u0026rsquo; website will suffice.\nSeafile\nThis is a great tool for managing files. I moved to this from Nextcloud because I am of the philosophy that I would prefer services that do one thing excellently instead of many things well. Nextcloud is an incredible Office365 replacement, but I found myself using a fraction of what it was capable of providing. Enter Seafile. It is cloud file syncing with a robust encryption implementation, just what the doctor ordered.\nPhotoprism\nNextcloud\u0026rsquo;s implementation of photo management was a bit clumsy for my tastes, so I began on a hunt for a more feature complete option. I was very lucky to stumble upon Photoprism early on in my self hosting journey. I am a proud supporter of this project. It brings a ton to the table, and doesn\u0026rsquo;t leave me missing Google Photos one bit. It is also actively developed. For instance, as of 2022-07-02, there was a recent update that improved scrolling a ton, which was one of my remaining quibbles with it\u0026rsquo;s functionality. Some people complain that it doesn\u0026rsquo;t scale up for libraries of 10,000+ photos, but my 2000 photo library works swimmingly. On my phone, I use the Folder Sync app to automatically send any pictures I take on my phone to the Photoprism imports folder. Within 15 minutes of snapping a photo, it is there on my Photoprism instance. I highly recommend giving it a go.\nMealie\nI have to admit that the name leaves something to be desired. Fortunately, the service itself doesn\u0026rsquo;t fall short. Mealie is a recipe management application. It is able to parse your favorite recipe websites to create immortalized versions of the recipe. This helps fight detestable link rot that plagues the internet. It allows you to edit ingredient amounts, make comments about what you would change next time, and plan out your weekly meals. It helps that it is beautiful and intuitive to use. If only I could get my partner to use it\u0026hellip; I want to go on the record here and say that I think it is sensible that she doesn\u0026rsquo;t trust my self hosted services that much. In the early days of my self hosting journey, let\u0026rsquo;s just say that the up-time of my services were extremely finicky. I like to think they are more permanent now, especially because I am hosting everything on a VPS, but I certainly cannot compete with the stability of Google and Amazon. (Or pretty much any other paid service for that matter.) \u0026#x1f609;\nGitea\nGitea is a community managed, lightweight code hosting solution written in Go. I use it to manage my data analysis (using Private repos) and even host the source code for this very website! Using Gitea has given me the surface level introduction to the behemoth that is git. Fortunately, that is all I need. Once I have removed any sensitive data (like passwords, etc.) I will make my docker-compose file public. The docker-compose file is where I determine which services I pick to host, and how to configure them to my liking. Hopefully someone will find this useful.\nSyncthing\nIf I could only tell someone to self host a single service, I would have to pick Syncthing. It is a continuous file synchronization program, which means it keeps a specific file or folder the same between any device running Syncthing. I use it to keep my password database and my org-mode notes Now org-mode might be the biggest rabbithole of them all, and definitely the topic for another blog post. I use it to manage my TODO list, my lab notebook, my shopping lists, write this blog, and maintain my Zettelkasten note database. It is an immensely powerful tool. up to date between all of my devices. With Syncthing, all of my data is stored on my own devices and encrypted in transit.\nFreshRSS\nI keep up to date on the science in my field by subscribing to relevant RSS feeds. Yet another topic to write a post about. This really changed the game for my ability to keep on top of the latest research. 2022-07-14 Update: post complete! Check it out here. FreshRSS replaced Feedly for me, as I ran up against the number of feeds I could subscribe to on a free account. Also, when self hosting, I can save as many articles as my heart desires (even if I will never look at them again \u0026#x1f635; ).\nWallabag\nRemember Pocket for Firefox? (Yes, I know it still exists, okay?) Give Wallabag a spin, it is great for storing articles you want to read later. I set up FreshRSS to save articles to my Wallabag instance to keep for later.\nChangeDetection\nNow this is a fun one! ChangeDetection.io is a service that loads a webpage and checks to see if something has changed since the last time. This might not sound useful at first, but I recently used this to check for when a hot item for my new coffee roasting hobby was back in stock. I got an email the other day to let me know it was in stock. Pretty cool!\nHugo\nHugo is the static site generator I use to make this here blog! I was amazed at how much more response my site was using Hugo compare to when I paid a company to host a WordPress site. I\u0026rsquo;m sure WordPress could be fast, but I just wanted a barebones, pure html experience, and Hugo made it easy.\nCommento++\nYou may have noticed that I have some pretty snazzy comments sections on my site. I initially used Disqus, which you may recognize from a ton of sites around the internet, but didn\u0026rsquo;t like how it would serve ads through my comments section, and provided sign-ins using Google/Facebook/Twitter. I wanted to serve the simplest comments section I could, that still gave me the ability to migrate the comments to wherever I decide to keep my server. Go ahead and use the anonymous comment button, fill in your name, and you are off to the races.\nAuthelia\nThere are a few services I host that I really want to lock down. For these services, Authelia is great. It puts up a \u0026ldquo;Enter the 6 digit code on your phone\u0026rdquo; style 2 factor authentication in front of the services I choose. Or, if you follow the guide here, you can have it send you a DUO push, just like you are one of the big hitters out there. I feel much more secure with Authelia in front of Adminer, Traefik, and Portainer.\nBoring stuff that allows everything else to work!\nPostgreSQL database MariaDB database Traefik reverse proxy Umami privacy respecting site analytics Portainer for docker container management Redis in-memory data store Adminer database management traefik-socket-proxy to prevent pesky backdoors to my server! ","permalink":"https://www.zacharybillman.com/posts/zpb-current-selfhosted/","summary":"\u003cp\u003e\u003cem\u003eN.B.: I hope to add screenshots for each of these eventually. For now, I hope links to each services\u0026rsquo; website will suffice.\u003c/em\u003e\u003c/p\u003e\n\u003col\u003e\n\u003cli\u003e\n\u003cp\u003e\u003ca href=\"https://www.seafile.com/en/home/\"\u003eSeafile\u003c/a\u003e\u003c/p\u003e\n\u003cp\u003eThis is a great tool for managing files. I moved to this from Nextcloud because I am of the philosophy that I would prefer services that do one thing excellently instead of many things well. Nextcloud is an incredible Office365 replacement, but I found myself using a fraction of what it was capable of providing. Enter Seafile. It is cloud file syncing with a robust encryption implementation, just what the doctor ordered.\u003c/p\u003e","title":"What I'm currently selfhosting."},{"content":"My partner and I took a trip to the Mason Farm Biological Reserve the other day, and what a glorious day it was. This year, I\u0026rsquo;ve been quite busy in the lab, and missed a lot of the early spring warbler season, so I was very excited by the opportunity to check out the old stomping grounds.\nI brought the camera with me despite the fact we were going to be there around midday when the birds are much less active. I\u0026rsquo;m glad I did, because I got the best look at a common yellowthroat I\u0026rsquo;ve ever had. Normally these guys are flighty, staying close to the ground in small brush or tall grasses, but this one was putting on a proper show for the mating season. Even when you get a glimpse of one, it is usually just that, as they have jumped away before you can pull out the camera, taunting you with their iconic call. I was very pleased to capture a few choice shots of the bird. Hopefully there are more to come. While we were out, I also got a nice picture of a hermit thrush and a king snake.\nThese images have been compressed quite a bit for a lighter internet footprint. These have all been resized to 25% of their original size. If you would like the full sized images, let me know and I will send you a link!\n","permalink":"https://www.zacharybillman.com/posts/the-uncommon-yellowthroat/","summary":"\u003cp\u003eMy partner and I took a trip to the \u003ca href=\"https://ncbg.unc.edu/visit/mason-farm-biological-reserve/\"\u003eMason Farm Biological Reserve\u003c/a\u003e the other day, and what a glorious day it was. This year, I\u0026rsquo;ve been quite busy in the lab, and missed a lot of the early spring warbler season, so I was very excited by the opportunity to check out the old stomping grounds.\u003c/p\u003e\n\u003cp\u003eI brought the camera with me despite the fact we were going to be there around midday when the birds are much less active. I\u0026rsquo;m glad I did, because I got the best look at a common yellowthroat I\u0026rsquo;ve ever had.\n\u003cspan class=\"sidenote-number\"\u003e\u003csmall class=\"sidenote\"\u003e\nNormally these guys are flighty, staying close to the ground in small brush or tall grasses, but this one was putting on a proper show for the mating season. Even when you get a glimpse of one, it is usually just that, as they have jumped away before you can pull out the camera, taunting you with their \u003ca href=\"https://ebird.org/species/comyel#Modal-playlist\"\u003eiconic call\u003c/a\u003e.\n\u003c/small\u003e\u003c/span\u003e\nI was very pleased to capture a few choice shots of the bird. Hopefully there are more to come. While we were out, I also got a nice picture of a hermit thrush and a king snake.\u003c/p\u003e","title":"The (un)common yellowthroat."}]
\ No newline at end of file
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       <title>About me. 👋</title>
-      <link>https://www.zacharybillman.com/posts/about-me/</link>
+      <link>https://www.zacharybillman.com/posts/about-me/about-me/</link>
       <pubDate>Sat, 27 Sep 2025 00:00:00 +0000</pubDate>
-      <guid>https://www.zacharybillman.com/posts/about-me/</guid>
+      <guid>https://www.zacharybillman.com/posts/about-me/about-me/</guid>
       <description>&lt;h2 id=&#34;welcome-to-my-site&#34;&gt;Welcome to my site!&lt;/h2&gt;
 &lt;p&gt;My name is Zachary Billman. I&amp;rsquo;m a UNC MD-PhD student in my 4th year of med school applying to pathology residency programs. I completed my PhD in Ed Miao&amp;rsquo;s lab. The curious reader may be thinking: &amp;ldquo;But Zach, Dr. Miao&amp;rsquo;s lab is at Duke, how did that come about?&amp;rdquo; What an astute question! Ed&amp;rsquo;s lab moved from UNC to Duke in early 2020, and I followed him down the street. My PhD was awarded by the UNC department of Microbiology and Immunology, but it just so happens that (nearly) all of my research took place at Duke.
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diff --git a/public/posts/about-me/about-me/index.html b/public/posts/about-me/about-me/index.html
index c9b29d7..e868907 100644
--- a/public/posts/about-me/about-me/index.html
+++ b/public/posts/about-me/about-me/index.html
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 My name is Zachary Billman. I&rsquo;m a UNC MD-PhD student in my 4th year of med school applying to pathology residency programs. I completed my PhD in Ed Miao&rsquo;s lab. The curious reader may be thinking: &ldquo;But Zach, Dr. Miao&rsquo;s lab is at Duke, how did that come about?&rdquo; What an astute question! Ed&rsquo;s lab moved from UNC to Duke in early 2020, and I followed him down the street. My PhD was awarded by the UNC department of Microbiology and Immunology, but it just so happens that (nearly) all of my research took place at Duke.
 
 This move was quite a trial, especially when compounded with the onset of the pandemic. I suspect my research timeline suffered, though this is an extremely minor inconvenience compared to the tragedy the pandemic caused.
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+  <meta property="og:description" content="Welcome to my site! My name is Zachary Billman. I’m a UNC MD-PhD student in my 4th year of med school applying to pathology residency programs. I completed my PhD in Ed Miao’s lab. The curious reader may be thinking: “But Zach, Dr. Miao’s lab is at Duke, how did that come about?” What an astute question! Ed’s lab moved from UNC to Duke in early 2020, and I followed him down the street. My PhD was awarded by the UNC department of Microbiology and Immunology, but it just so happens that (nearly) all of my research took place at Duke. This move was quite a trial, especially when compounded with the onset of the pandemic. I suspect my research timeline suffered, though this is an extremely minor inconvenience compared to the tragedy the pandemic caused. This makes for very interesting basketball viewing parties with my Duke friends!">
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 My name is Zachary Billman. I&rsquo;m a UNC MD-PhD student in my 4th year of med school applying to pathology residency programs. I completed my PhD in Ed Miao&rsquo;s lab. The curious reader may be thinking: &ldquo;But Zach, Dr. Miao&rsquo;s lab is at Duke, how did that come about?&rdquo; What an astute question! Ed&rsquo;s lab moved from UNC to Duke in early 2020, and I followed him down the street. My PhD was awarded by the UNC department of Microbiology and Immunology, but it just so happens that (nearly) all of my research took place at Duke.
 
 This move was quite a trial, especially when compounded with the onset of the pandemic. I suspect my research timeline suffered, though this is an extremely minor inconvenience compared to the tragedy the pandemic caused.
@@ -87,12 +87,12 @@ This makes for very interesting basketball viewing parties with my Duke friends!
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   "name": "About me. 👋",
-  "description": "Welcome to my site! ATTACH My name is Zachary Billman. I\u0026rsquo;m a UNC MD-PhD student in my 4th year of med school applying to pathology residency programs. I completed my PhD in Ed Miao\u0026rsquo;s lab. The curious reader may be thinking: \u0026ldquo;But Zach, Dr. Miao\u0026rsquo;s lab is at Duke, how did that come about?\u0026rdquo; What an astute question! Ed\u0026rsquo;s lab moved from UNC to Duke in early 2020, and I followed him down the street. My PhD was awarded by the UNC department of Microbiology and Immunology, but it just so happens that (nearly) all of my research took place at Duke. This move was quite a trial, especially when compounded with the onset of the pandemic. I suspect my research timeline suffered, though this is an extremely minor inconvenience compared to the tragedy the pandemic caused. This makes for very interesting basketball viewing parties with my Duke friends!\n",
+  "description": "Welcome to my site! My name is Zachary Billman. I\u0026rsquo;m a UNC MD-PhD student in my 4th year of med school applying to pathology residency programs. I completed my PhD in Ed Miao\u0026rsquo;s lab. The curious reader may be thinking: \u0026ldquo;But Zach, Dr. Miao\u0026rsquo;s lab is at Duke, how did that come about?\u0026rdquo; What an astute question! Ed\u0026rsquo;s lab moved from UNC to Duke in early 2020, and I followed him down the street. My PhD was awarded by the UNC department of Microbiology and Immunology, but it just so happens that (nearly) all of my research took place at Duke. This move was quite a trial, especially when compounded with the onset of the pandemic. I suspect my research timeline suffered, though this is an extremely minor inconvenience compared to the tragedy the pandemic caused. This makes for very interesting basketball viewing parties with my Duke friends!\n",
   "keywords": [
     
   ],
-  "articleBody": "Welcome to my site! ATTACH My name is Zachary Billman. I’m a UNC MD-PhD student in my 4th year of med school applying to pathology residency programs. I completed my PhD in Ed Miao’s lab. The curious reader may be thinking: “But Zach, Dr. Miao’s lab is at Duke, how did that come about?” What an astute question! Ed’s lab moved from UNC to Duke in early 2020, and I followed him down the street. My PhD was awarded by the UNC department of Microbiology and Immunology, but it just so happens that (nearly) all of my research took place at Duke. This move was quite a trial, especially when compounded with the onset of the pandemic. I suspect my research timeline suffered, though this is an extremely minor inconvenience compared to the tragedy the pandemic caused. This makes for very interesting basketball viewing parties with my Duke friends!\nMaybe having a diagram will make my training timeline make a bit more sense.\ntimeline.svg\nMy research and scientific interests. I am broadly interested in innate immunology. I spent most of my time in graduate school studying the host-pathogen interaction between the intracellular fungus Histoplasma capsulatum and macrophages. There are many unstudied curiosities regarding the innate immune response to Histoplasma spp. and other intracellular fungi that I think are quite interesting. I also spent a considerable time thinking about the evolution of proteins involved in the programmed cell death pathway called pyroptosis.\nHobbies I may write about. Besides my science, I am interested in birding, baking sourdough bread (I swear I began years before the pandemic, though hearing of people baking bread brings me joy no matter when they first began!), board games, roasting coffee, and self-hosting free and open source software. Over the course of the pandemic, I have learned how to maintain a basic suite of services spread between a server I rent and a computer at home that have replaced my need for Google Photos and Google Drive. I’m hoping to be able to move away from these platforms entirely soon. I think they provide a great service, but at a substantial cost to privacy. Hopefully more to be said about my thoughts on FOSS soon! I also transitioned my old, (and quite frankly, embarrassingly slow) managed WordPress site with this lean, static site made in Hugo that I host myself. Now that I have mangled together some CSS to get my precious sidenotes up and running again, I’m ready to begin putting some ideas to paper. I love marginalia (the word to describe these notes on the side of this webpage). I’m not sure if this is unique to me, but I seem to get caught up in parenthetical / tangential thoughts very often, and I think using an Edward Tufte-esque sidenote is a great way for me to communicate in this way without distracting the reader too much. It seems marginalia such as this have been used throughout history, so perhaps it is normal, but most people can keep their thoughts focused better than me. The implementation I use is inspired by the Tufte CSS project and largely taken from this incredibly helpful post found at scripter.co. I’m quite proud of my progress in administering my server and self-hosting useful services.\nThe future of this site. On this site I plan to post updates about my journey through med school, grad school, and self-hosting I would like to share with the world. I have been helped immensely by many others’ advice and I hope to impart similar tips to others someday. I suspect most posts will be about much lighter fare, like whatever hobbies tickle my fancy at the time.\n",
-  "wordCount" : "614",
+  "articleBody": "Welcome to my site! My name is Zachary Billman. I’m a UNC MD-PhD student in my 4th year of med school applying to pathology residency programs. I completed my PhD in Ed Miao’s lab. The curious reader may be thinking: “But Zach, Dr. Miao’s lab is at Duke, how did that come about?” What an astute question! Ed’s lab moved from UNC to Duke in early 2020, and I followed him down the street. My PhD was awarded by the UNC department of Microbiology and Immunology, but it just so happens that (nearly) all of my research took place at Duke. This move was quite a trial, especially when compounded with the onset of the pandemic. I suspect my research timeline suffered, though this is an extremely minor inconvenience compared to the tragedy the pandemic caused. This makes for very interesting basketball viewing parties with my Duke friends!\nMaybe having a diagram will make my training timeline make a bit more sense.\nFigure 1: An overview of my research training. I first began working for Dr. Sean Murphy in undergrad, then worked as a research scientist/lab manager for 3 years before heading to UNC for my MSTP training. During grad school, my lab moved from UNC to Duke, though my degree was awarded by UNC. The “Present” diamond was used on an older version of my CV and represents September 1st, 2025. Created using PlantUML.\nHopefully that can clear up the winding road I’ve taken a bit!\nMy research and scientific interests. I am broadly interested in innate immunology. I spent most of my time in graduate school studying the host-pathogen interaction between the intracellular fungus Histoplasma capsulatum and macrophages. There are many unstudied curiosities regarding the innate immune response to Histoplasma spp. and other intracellular fungi that I think are quite interesting. I also spent a considerable time thinking about the evolution of proteins involved in the programmed cell death pathway called pyroptosis.\nHobbies I may write about. Besides my science, I am interested in birding, baking sourdough bread (I swear I began years before the pandemic, though hearing of people baking bread brings me joy no matter when they first began!), board games, roasting coffee, and self-hosting free and open source software. Over the course of the pandemic, I have learned how to maintain a basic suite of services spread between a server I rent and a computer at home that have replaced my need for Google Photos and Google Drive. I’m hoping to be able to move away from these platforms entirely soon. I think they provide a great service, but at a substantial cost to privacy. Hopefully more to be said about my thoughts on FOSS soon! I also transitioned my old, (and quite frankly, embarrassingly slow) managed WordPress site with this lean, static site made in Hugo that I host myself. Now that I have mangled together some CSS to get my precious sidenotes up and running again, I’m ready to begin putting some ideas to paper. I love marginalia (the word to describe these notes on the side of this webpage). I’m not sure if this is unique to me, but I seem to get caught up in parenthetical / tangential thoughts very often, and I think using an Edward Tufte-esque sidenote is a great way for me to communicate in this way without distracting the reader too much. It seems marginalia such as this have been used throughout history, so perhaps it is normal, but most people can keep their thoughts focused better than me. The implementation I use is inspired by the Tufte CSS project and largely taken from this incredibly helpful post found at scripter.co. I’m quite proud of my progress in administering my server and self-hosting useful services.\nThe future of this site. On this site I plan to post updates about my journey through med school, grad school, and self-hosting I would like to share with the world. I have been helped immensely by many others’ advice and I hope to impart similar tips to others someday. I suspect most posts will be about much lighter fare, like whatever hobbies tickle my fancy at the time.\n",
+  "wordCount" : "697",
   "inLanguage": "en",
   "datePublished": "2025-09-27T00:00:00Z",
   "dateModified": "2025-09-27T00:00:00Z",
@@ -185,18 +185,26 @@ This makes for very interesting basketball viewing parties with my Duke friends!
     <h1 class="post-title entry-hint-parent">
       About me. 👋
     </h1>
-    <div class="post-meta"><span title='2025-09-27 00:00:00 +0000 UTC'>Saturday, September 27, 2025</span>&nbsp;·&nbsp;<span>3 min</span>&nbsp;·&nbsp;<span>Zachary Billman</span>
+    <div class="post-meta"><span title='2025-09-27 00:00:00 +0000 UTC'>Saturday, September 27, 2025</span>&nbsp;·&nbsp;<span>4 min</span>&nbsp;·&nbsp;<span>Zachary Billman</span>
 
 </div>
   </header> 
-  <div class="post-content"><h2 id="welcome-to-my-site">Welcome to my site! <span class="tag"><span class="ATTACH">ATTACH</span></span><a hidden class="anchor" aria-hidden="true" href="#welcome-to-my-site">#</a></h2>
+  <div class="post-content"><h2 id="welcome-to-my-site">Welcome to my site!<a hidden class="anchor" aria-hidden="true" href="#welcome-to-my-site">#</a></h2>
 <p>My name is Zachary Billman. I&rsquo;m a UNC MD-PhD student in my 4th year of med school applying to pathology residency programs. I completed my PhD in Ed Miao&rsquo;s lab. The curious reader may be thinking: &ldquo;But Zach, Dr. Miao&rsquo;s lab is at Duke, how did that come about?&rdquo; What an astute question! Ed&rsquo;s lab moved from UNC to Duke in early 2020, and I followed him down the street. My PhD was awarded by the UNC department of Microbiology and Immunology, but it just so happens that (nearly) all of my research took place at Duke.
 <span class="sidenote-number"><small class="sidenote">
 This move was quite a trial, especially when compounded with the onset of the pandemic. I suspect my research timeline suffered, though this is an extremely minor inconvenience compared to the tragedy the pandemic caused.
 </small></span>
 This makes for very interesting basketball viewing parties with my Duke friends!</p>
 <p>Maybe having a diagram will make my training timeline make a bit more sense.</p>
-<p><a href="/images/timeline.svg">timeline.svg</a></p>
+<p><a id="figure--timeline"></a></p>
+<figure><a href="./images/timeline.png">
+    <img loading="lazy" src="./images/timeline.png"
+         alt="Figure 1: An overview of my research training. I first began working for Dr. Sean Murphy in undergrad, then worked as a research scientist/lab manager for 3 years before heading to UNC for my MSTP training. During grad school, my lab moved from UNC to Duke, though my degree was awarded by UNC. The &ldquo;Present&rdquo; diamond was used on an older version of my CV and represents September 1st, 2025. Created using PlantUML."/> </a><figcaption>
+            <p><span class="figure-number">Figure 1: </span>An overview of my research training. I first began working for Dr. Sean Murphy in undergrad, then worked as a research scientist/lab manager for 3 years before heading to UNC for my MSTP training. During grad school, my lab moved from UNC to Duke, though my degree was awarded by UNC. The &ldquo;Present&rdquo; diamond was used on an older version of my CV and represents September 1st, 2025. Created using PlantUML.</p>
+        </figcaption>
+</figure>
+
+<p>Hopefully that can clear up the winding road I&rsquo;ve taken a bit!</p>
 <h2 id="my-research-and-scientific-interests-dot">My research and scientific interests.<a hidden class="anchor" aria-hidden="true" href="#my-research-and-scientific-interests-dot">#</a></h2>
 <p>I am broadly interested in innate immunology. I spent most of my time in graduate school studying the host-pathogen interaction between the intracellular fungus <em>Histoplasma capsulatum</em> and macrophages. There are many unstudied curiosities regarding the innate immune response to <em>Histoplasma spp.</em> and other intracellular fungi that I think are quite interesting. I also spent a considerable time thinking about the evolution of proteins involved in the programmed cell death pathway called pyroptosis.</p>
 <h2 id="hobbies-i-may-write-about-dot">Hobbies I may write about.<a hidden class="anchor" aria-hidden="true" href="#hobbies-i-may-write-about-dot">#</a></h2>
@@ -219,10 +227,10 @@ I&rsquo;m quite proud of my progress in administering my server and self-hosting
     <ul class="post-tags">
     </ul>
 <nav class="paginav">
-  <a class="next" href="https://www.zacharybillman.com/posts/about-me/">
+  <a class="next" href="https://www.zacharybillman.com/posts/ms3-year-is-magical/">
     <span class="title">Next »</span>
     <br>
-    <span>About me. 👋</span>
+    <span>The third year of medical school is magical.</span>
   </a>
 </nav>
 
diff --git a/public/posts/index.html b/public/posts/index.html
index ec3cc2d..a0dff46 100644
--- a/public/posts/index.html
+++ b/public/posts/index.html
@@ -143,7 +143,7 @@
 ...</p>
   </div>
   <footer class="entry-footer"><span title='2025-09-27 00:00:00 +0000 UTC'>Saturday, September 27, 2025</span>&nbsp;·&nbsp;<span>4 min</span>&nbsp;·&nbsp;<span>Zachary Billman</span></footer>
-  <a class="entry-link" aria-label="post link to About me. 👋" href="https://www.zacharybillman.com/posts/about-me/"></a>
+  <a class="entry-link" aria-label="post link to About me. 👋" href="https://www.zacharybillman.com/posts/about-me/about-me/"></a>
 </article>
 
 <article class="post-entry"> 
diff --git a/public/posts/index.xml b/public/posts/index.xml
index acea723..be0940e 100644
--- a/public/posts/index.xml
+++ b/public/posts/index.xml
@@ -10,9 +10,9 @@
     <atom:link href="https://www.zacharybillman.com/posts/index.xml" rel="self" type="application/rss+xml" />
     <item>
       <title>About me. 👋</title>
-      <link>https://www.zacharybillman.com/posts/about-me/</link>
+      <link>https://www.zacharybillman.com/posts/about-me/about-me/</link>
       <pubDate>Sat, 27 Sep 2025 00:00:00 +0000</pubDate>
-      <guid>https://www.zacharybillman.com/posts/about-me/</guid>
+      <guid>https://www.zacharybillman.com/posts/about-me/about-me/</guid>
       <description>&lt;h2 id=&#34;welcome-to-my-site&#34;&gt;Welcome to my site!&lt;/h2&gt;
 &lt;p&gt;My name is Zachary Billman. I&amp;rsquo;m a UNC MD-PhD student in my 4th year of med school applying to pathology residency programs. I completed my PhD in Ed Miao&amp;rsquo;s lab. The curious reader may be thinking: &amp;ldquo;But Zach, Dr. Miao&amp;rsquo;s lab is at Duke, how did that come about?&amp;rdquo; What an astute question! Ed&amp;rsquo;s lab moved from UNC to Duke in early 2020, and I followed him down the street. My PhD was awarded by the UNC department of Microbiology and Immunology, but it just so happens that (nearly) all of my research took place at Duke.
 &lt;span class=&#34;sidenote-number&#34;&gt;&lt;small class=&#34;sidenote&#34;&gt;
diff --git a/public/posts/ms3-year-is-magical/index.html b/public/posts/ms3-year-is-magical/index.html
index bfacdcf..f37915a 100644
--- a/public/posts/ms3-year-is-magical/index.html
+++ b/public/posts/ms3-year-is-magical/index.html
@@ -255,7 +255,7 @@ In reflection on the year, I have spent time thinking of a phrase that I heard a
       <li><a href="https://www.zacharybillman.com/tags/training/">Training</a></li>
     </ul>
 <nav class="paginav">
-  <a class="prev" href="https://www.zacharybillman.com/posts/about-me/">
+  <a class="prev" href="https://www.zacharybillman.com/posts/about-me/about-me/">
     <span class="title">« Prev</span>
     <br>
     <span>About me. 👋</span>
diff --git a/public/sitemap.xml b/public/sitemap.xml
index 8928026..5bac922 100644
--- a/public/sitemap.xml
+++ b/public/sitemap.xml
@@ -2,7 +2,7 @@
 <urlset xmlns="http://www.sitemaps.org/schemas/sitemap/0.9"
   xmlns:xhtml="http://www.w3.org/1999/xhtml">
   <url>
-    <loc>https://www.zacharybillman.com/posts/about-me/</loc>
+    <loc>https://www.zacharybillman.com/posts/about-me/about-me/</loc>
     <lastmod>2025-09-27T00:00:00+00:00</lastmod>
   </url><url>
     <loc>https://www.zacharybillman.com/posts/</loc>