2020: A different kind of year in review

Good evening, world. First of all, this is not exactly a review of the year 2020, but rather a review of a specific period roughly starting around mid-March 2020 and lasting till today, mid-March 2021. The “lasting till” part is not particularly meaningful, since as of today the future is not much more certain than it was a year ago, but it rather demarcates an amount of time I am willing to write about and feel the need to write about. As per usual I will try to break this down into sections for easier navigation, although this time the sections are likely to be chronologically rather than thematically ordered.

March-April 2020

Around beginning of March I was self-isolating in my apartment, so by the time WHO declared COVID-19 a pandemic and Rice University has suspended the classes (to be followed immediately by the Spring break) I was already settling into the realities of the work from home routine. I already have been working on SARS-CoV-2 sequence analyses for about 2.5 months by then, and was steadily getting deeper into the genome and variant analyses and related topics. By mid-April we have been working in collaboration with Baylor College of Medicine and Weill Cornell Medical College on the study of intrahost genomic variation in SARS-CoV-2.

Outside of the immediate research work this period was also full of the challenges of the schoolwork adjustment to the virtual environment. On my end most of these transformations were not particularly impactful, since in the spirit of good old college days I simply stopped attending most of the lectures opting for a 2x rewinds of recordings at convenient times. However, for the seminar-style classes the impact was noticeable. Giving a presentation into the void of a Zoom call felt eerie and rather disappointing, a feeling that hasn’t really left me ever since, but gained a new set of characteristics as the Zoom fatigue became more of a well-known phenomenon.

May-June 2020

By early to mid-May classes were mostly wrapped up, and to the credit of my instructors for this semester, I did feel that I managed to learn something new and exciting, even if a good chunk of the process had to be scrambled and re-built in less than two weeks. On the flip side, the Zoom call festival was just picking up. This time period was likely the busiest so far for me with respect to the number of Zoom calls I have been present on. In retrospect I can’t help but feel that in some way the work from home routine and initial panic about “social distancing” (which in fact really is more of a physical distancing) made a lot of people crave the meetings a bit more than they should. Nevertheless, a lot of the meetings I had attended in this period were instrumental for my work, and helped greatly in shaping the initial draft of the paper that we ended up submitting towards the end of June.

This two month stretch was also the most work intense part of the whole year and arguably that was in big part made possible by the work from home imperative. Without spending time on grocery shopping (we were rather panicked at that time and relied on Amazon Fresh…), bar hopping, museums, or pretty much any activities outside the apartment (except periodically joining for walking the dog), I could funnel all of my waking time into research, interspersing it with cooking and home-brewing to main an ounce of sanity. Needless to say, that was also only possible since the exhaustion from the said routine haven’t kicked me hard yet, and I could indeed focus for a solid 8 to 8 on a typical day. Well, you probably know what’s coming next.

July-August 2020: The swamp

First, I hate Houston summers! Second, I hate Chicago summers. Third, I am sure that I just genuinely do not enjoy summers, in all ways shapes and forms, since graduating high school. “The swamp” comes, of course, from the great humid and hot weathers of the bayou that I am living upon nowadays, but also from the general feeling I had throughout that period of time. The April-June push took it’s toll on me, and I was not in the best working mood for the rest of the summer. I mostly concerned myself with another collaboration, this time looking into the Influenza A virus. However, my overall progress was slow, and on certain weeks I could barely squeeze out 8-12 hours of solid work for the entire week.

Additionally, dropping out from a work only mindset made me observe the realities of the world a bit more clearly and with COVID-19 cases spiking in Texas and globally, racial injustices being brought up front and forward in the USA, and the relatively shaky situation with the visa policies those realities were not pretty. For people who might have had more energy at that point in time it might have been a time of action and/or reflection, for me it was mostly a time of sadness, discomfort and a general overwhelming feeling of “the swamp”.

September-October 2020

With summer being over the air in Houston became more breathable, but my exhaustion was still going strong. Beginning of classes helped alleviate that to some extent, and at some point almost re-energized me to the April levels of productivity. That period was relatively short. The month of September went by relatively uneventful for me, although I had to take care of a few things in the preparation for October.

October was hectic. My parents were visiting me from Moldova (a trip they booked way before the pandemic, and re-scheduling which would be an even bigger mess), so I had to figure out safe housing options and some form of an itinerary for their visit. On top of that, I was going to give a talk at a Ken Kennedy Institute Data Science conference mid-October, and that required some polishing and prepping. At the end of the day, both went smoothly, my parents were lucky to visit roughly in between two major COVID-19 waves in Texas, they took proper precautions, and most of their visit consisted of a road trip and hiking in the Grand Canyon/Sedona area (which I could not join, due to the aforementioned talk). The talk went by fine, as by that time I got accustomed to the practice of speaking into the Zoom void.

Towards the end of this period I felt more accustomed to the new life. Not the “dive into work” accustomed as in the beginning but rather routine accustomed. I had my balance of work and off-days, meetings I wanted or needed to attend and the ones that could be skipped, and some workable sense of interaction with the world through mostly digital means.

November 2020

Most of the November was consumed with responding to reviewers’s feedback on the SARS-CoV-2 paper, tying loose ends on other projects, and getting into the groove of wrapping up schoolwork. Importantly, I also finally got back to reading (no, scientific papers don’t count, even if I do enjoy a solid 60-75% of them). I finished my way through the I want to be a mathematician: An automathography by Paul Halmos, which was a nice and witty book and to a degree helped me in the process of recovering some of the energy and excitement about work. I also finally completed the reading of A Random Walk Down Wall Street, which while not extremely underwhelming was somewhat of a medium tier prose in my opinion. Also inspired by my parents adventures in the parks of Arizona I started planning a short retreat of my own into the wilderness.

December 2020

Classes were now officially done for the semester, revised manuscript has been submitted, and I was ready to take a week off. We have travelled West and South to a small town of Terlingua, TX, where we found a nice clean little motel. The two main attractions (both at about 20-40 minute drive from our base) were the Big Bend National and State parks. Both spots were amazing, with nice mountain hikes, desert views and scenic drives along Rio Grande it was a good way to let my eyes rest for a bit. The location was not busy with people making hiking in these places a much more insular and reflective experience (not to mention that it was also nice to travel without too much worry about COVID circumstances).

The rest of December went by fast and wasn’t particularly eventful.

2021

At the start of the new year I was getting back into the groove of things trying to spend a bit more time walking outside in parks and along the bayou. Work got into a steady and solid flow and with a new semester picking up, I got a few more things to work on, which brought a bit of fresh air into the workflow. I also continued with reading more, just finishing Hilbert by Constance Reid and setting my eye on a few fiction books, since I have been missing out on reading fiction for a while. I also had a great opportunity to give a talk at UChicago Center for Translational Data Science discussing the SARS-CoV-2 work we did over the past year. In general, even though in the global sense life is still far from stable, I am feeling like I have managed to find some local stability, which makes me somewhat optimistic for the next few months to come.

Other notes and miscellanea from past year

I heavily ignored personal projects throughout this period. Well, at the very least the ones I’d typically write about here. I did spend a lot of time cooking, had a long foray into home brewing mead, and dabbled in some music for a bit at different points in time. The closest thing to come to the personal projects scale was getting comfortable with ggplot2 and RShiny, but at the current moment neither really got beyond the level of purely professional engagement. I think that a rather sizable increase in screen time drove me away form my standard set of personal projects, since I got reasonably tired of spending time in front of my laptop with the regular work and study activities.

Talks in the Zoom age: Speak into the void and let the void speak back

I don’t think that this note warrants its own post, so I will tuck it in at the end of this review for those interested in my opinion on the Zoom talks.

At the start I felt discouraged by the Zoom talks. First, they completely remove the energy feedback loop between presenter and the audience, hence the “speaking into the void” claims. Not to mention, that the same problem of speaking into a device, also makes it somewhat physically uncomfortable for the presenter, since you need to maintain relatively same posture, limit hand gesturing and stare into the tiny dot of a webcam for the “engaging with the audience” feeling (to be precise, the feeling is not for you, it’s for the people watching the talk). Second, Zoom fatigue is very real, and concentrating on a speaking screen can be hard for some people (including me). Hence, “the void” is really often empty, with just a few people tracking with the presentation for limited blocks of time. In the meantime I developed some techniques that help me stay more engaged, including chat discussions, sidebar banter with friends attending the same talk, and paper and pen note taking. All of these help to a degree, but nevertheless the problem of fatigue still stands. Third, just as with the regular talks, when “the void” speaks back the questions are often disconnected form the talk, and without the clear prospect of the “taking it offline” it feels that some interesting in-depth discussion never end up happening.

However, with time and practice comes some form of acceptance. I ended up finding the positives in Zoom talks as I attended and given more of them. First, it really helps with boosting my confidence. People not asking questions or being disengaged doesn’t burn the same way when their cameras are off as they fall asleep or switch to watching TikToks. Second, for lectures (on the receiving end) Zoom or YouTube is great. You can play the recording at the speed you want, rewind, and replay the fragments as you need. Interactiveness takes a hit, but as long as there is some venue for asking more questions it is really convenient. Third, Zoom really opens up the possibility of attending talks globally. I’ve been to Berkeley, Chicago and a couple other places to attend the talks without the cumbersome process of getting onto a plane.

At the end of the day, I hope that some changes that we see Zoom bring into the world of lectures and talks are here to stay, since not all change is bad. Of course, I also hope that at some point later in the year, I will be able to grab a beer after a talk to discuss the finer points with the presenter (not over Zoom).

2019: A year in review

Travel

This year was quite eventful in terms of travel, both domestic and international. I started off with getting on a project in Connecticut, so starting the last week of January I was flying from Chicago to LaGuardia every Monday, and flying back out every Thursday. Of course this was a prime opportunity to rack up miles and hotel points, which came in handy later throughout the year. I also used my constant travel as an excuse to visit a few of my friends spread all across the US. I made stops in NYC, Philadelphia, Austin, and Boston. I also took a trip to New Orleans, which was a long standing bucket list item for me and my friend Cris. In between these fun trips, I also squeezed in a few more career related ones, including visiting Baltimore and Houston for graduate program weekends, and returning to Baltimore again for BPS’19.

The next major trip I undertook was going back home to Chisinau, Moldova for the entire month of July. It was a relaxing and fun time, and I mostly used it to unwind after a work intensive year. It also was an interim in my moving process from Chicago down to Houston. In the beginning of August, I flew back to Chicago, packed the last few suitcases (not really) and headed south.

I got to Houston mid-August, and the entire move-in process went extremely smooth thanks to my awesome roommate Robert, who helped organize common spaces in the apartment. I took another quick trip to Boston, to enjoy the last grill session of the (northern) season, and began my studies. I then also took two trips to Chicago, one for the autumn recess and one for Thanksgiving. Both trips were fun, and coming back to Chicago felt like coming home.

Finally at the end of this year I took a trip to Spain. It was an ambitious itinerary listing more than 5 cities and mostly organized and planned by Rachel. I pre-gamed the trip by spending a day in NYC, and then headed to Barcelona. From Barcelona we visited Girona and Figueres as day trips. Both trips were amazing, and I would totally recommend them to anyone spending some time in Barcelona. Then we took a train to Madrid. It was a packed schedule, and seeing Prado in one day is obviously a challenge, but we succeeded. The next stops were all in the south of Spain. Starting from Seville (with a day trip to Cordoba), onto Ronda and finally Granada, it was a route packed with great views and amazing foods. We rounded everything up by flying back to Barcelona and then in a day to NYC.

Thus, this year beings me into the great New York City! I will be heading back to Houston soon, but in the meantime, I am going to enjoy some bagels, pizza and public transport.

Work

I spent the first half of this year working on a project as a consultant with TruQua Enterprises, which involved quite a bit of travel and interactions with clients. It was an engaging opportunity to learn more about inner workings of a large business, and assist people by providing technological insights into their processes. I feel like I learned to be a better speaker and conversationalist, as well as, an attentive and active listener. Even if some days were slower or more heavy on the grunt work, I feel like I grew a lot through this experience.

In the second half of the year I have started my PhD in Computer Science at Rice University. My first semester was a combination of learning from courses and from peers in the lab. I took a great course on optimization taught by Tasos Kyrillidis. It was a mix of nice and fun math with solid practical motivation coming from the field of machine learning. I would absolutely recommend this course to anyone who has a chance of attending and is at all interested in anything mathematical or machine learning related. I also spent a lot of time working on a project in Treangen Lab, which was both stimulating and fruitful. I learned a lot of new material through this work, and strengthened some of my skills in data preparation and visualization.

Research

In the first half of this year I continued my work on the conformational transition pathways of insulin degrading enzyme and in early March I presented a poster on it at Biophysical Society Annual Meeting. It is an exciting project and it involved a lot of hours and effort both in learning and implementing simulations and analysis. I have continued this work by conducting more analysis, proposing a coarse grained model and starting out a set of swarm of trajectories simulations for determining the conformational transition dynamics of this protein. As the year progressed, I got busy with other projects and my current involvement with the project became minimal. I am currently finalizing some write ups and planning on handing over the project to the next students.

At Rice, I joined in on a project that involved graph theoretic analysis of metagenomic read data. It was my first research experience in genomics and metagenomics and I felt amazing about it. I was happy to contribute my knowledge of graph theory and general computer science to this exciting area. This project was developed in collaboration with Advait Balaji, a second year PhD student in Treangen lab. Throughout the entire process I had an amazing support from my mentors and our collaborators.

Overall, I’m happy to continue my work in the area of computational genomics and metagenomics. This is an exciting area, and I feel like I can both learn a lot and contribute significant work in the process.

As usual my research interests remain broad and lie at the intersection of mathematics, computer science and biology. I am looking forward to developing more work that can be directly applicable in both research and clinical environments, but of course that is a lengthy and complicated process.

Personal projects

This year not too many of my personal projects saw light, although I made a lot of progress on some. Overall, I feel that I carved out a few main directions for my personal work and I plan to strengthen and pursue those further in 2020.

First major initiative is exploration and adaptation of different data visualization techniques and tools. I have learned more about color pallettes and colorblind friendly design. I feel that this will make my subsequent projects more aesthetically pleasing and accessible. I also plan to round up a solid review of some basic data analysis pipelines and eventually release it as useful resource for my lab, as well as the community at large. Finally, I plan to finish up my “Where in the world” project, which was a foray into D3.js and geographic visualization.

Next, I am looking to reinforce my paper sorting and reading habits. I was meaning to organize my personal digital library for a while, but was falling short on convenient tools to do so. Therefore, I might eventually to settle either for a mix of practices and tools, or possibly write up some code myself to further streamline the process.

I haven’t worked much with Raspberry Pi or Arduino with the exception of Scav projects this year. While home automation appeals to me, I am not sure I’ll have enough time to invest into it next year, so I think most of these projects will remain on the shelf for a while.

Finally, this blog while not too active, will stay alive and will be an outlet for updates throughout the next year.

Thanks for reading, and see y’all in 2020!

Update on my whereabouts

Good evening world! Long time no see.

A lot of stuff has happened since I the last time I have updated this blog. I’ll go through most of it briefly while focusing on the things relevant for the blog content and my current plans for the upcoming few months.

I gave a super brief lecture on Fourier analysis to several first year students at the University of Chicago (non-math majors). The full write up for this lecture is long overdue, but I hope to finish it some time soon and post the full thing on here. As per usual, since I was trying to include several worked examples into the write up it got bloated very fast and as a result, I wasn’t able to finish it on time.

I have also developed a lot of new content for teaching basics of Python and programming in general. I plan to roll out those as a series of bi-monthly write-ups with Jupyter notebooks attached. The tentative idea is to post those on the first and third Sundays of the month.

I have finished up my job in consulting just a bit too shy of seeing the project go fully live. I had a wonderful time at TruQua Enterprises, and I am glad that my work made a meaningful contribution to the cause. I am not sure whether I’ll end writing up a note about my experiences and what I have learned while working in consulting, but if it happens I’ll share it here as well.

I also traveled back home to Moldova for a month. It was a relaxing experience and I got a chance to be a tourist in my own country visiting two wineries and touring their production and maturation facilities (with a tasting included). I also wrote up a set of problems for the IOI training camp, but due to the issues with creating enough testing sets, those were not used yet. Once the full set has been used by the team for the training purposes, I will make the contents of it, both problems and solutions available to the general public.

Last but not least, I moved to Houston, Texas and have started the PhD program in Computer Science. I am finishing up the orientation week activities and getting ready for an exciting semester ahead of me.

Cheers, and see you soon.

Biophysical Society Annual Meeting 2019

Evening world! ( I have rewritten this 5 times at this point)

My visit to the BPS AM’19 was very short, but nevertheless I am happy that I had the opportunity to travel to this conference. Those few days have been eventful, and I have met and talked with multiple amazing people . Below I would like to share some of my thoughts on the talks, presentations and posters I have seen and engaged with. Since I have left early Monday morning, I cannot comment on the most of the content presented, so take this as a short snippet of my thoughts and not a comprehensive review.

Style

I firmly believe that style and presentation are extremely important in scientific world, especially during conferences. Good content organization and clear, simple to follow figures greatly improve audience’s ability to engage with material. I also think that organizing your content in a parsable way is the minimal courtesy you owe your readers.

I will start with some positive notes and remarks. First of all, black backgrounds in presentations are great! Of course there is a caveat of choosing appropriate color schemes for your figures (which I bet will deter people from going this route, since who wants to spend time making two sets of figures: for your presentation and for the paper), but when done well black background makes the content shine. The few presentations that had black background at the AM, warmed my heart.

Next, I need to applaud the usage of space on the slides. I haven’t seen a single overcrowded slide (maybe I just got lucky). Spreading out plots and figures so that they are readable is absolutely essential. Space usage is something I’ll come back to when talking about posters (including mine).

Now, let me move onto my incoherent rambling about style. I am in the process of learning Beamer, and it is definitely on the list of things I plan to master by the end of the year. It seems that the usage of LaTeX and LaTeX based tools and packages at this conference is almost exclusive to people coming in from the theory angle. The only talk I have seen for which slides were coming in the Beamer generated fashion was a theory talk on the inverse temperature dependence. I am not too surprised that this is the case, for two reasons. On one hand, majority of the CS, Math, Physics theory people would learn and use LaTeX anyway, which makes copy pasting and rearranging stuff easier. On the other hand, picking up LaTeX just for the presentations, especially if they are not peppered with formulas all the way through, seems like an overkill. I do hold a firm belief that people working in STEM fields should have some basic LaTeX skill as a part of the undergrad experience or early professional, but I would not go as far as to claim that we need to build everything in LaTeX. This is mostly an observation, as I reserve my LaTeX evangelism for a different post and time.

One thing that I do not grasp at all is why in 2019 we still have Comic Sans being used in presentations. Honestly, there is a plenty of great fonts that can catch people’s eyes if you are going for catchy. I do not share the ridiculous disgust towards Comic Sans, but even if we look at the original design specs it is supposed to be informal, children oriented font. Of course great research typed in Windings, will be ridiculous to read through, but that won’t change the fact that the underlying work is important. However, the font choices like this scream lack of professionalism and absolute style illiteracy to me. Just to reiterate this point, your style choices affect my perception of your attitude and skill, they do not affect my perception of your research work. Please, stop the Comic Sans abuse at science conferences!

Whew, okay, now let’s move to posters. First of all, while still far from perfect, I am fairly satisfied with the way my poster turned out. My main concerns are the crowded middle region where I had to have partially overlapping plots, and some not properly cleared up VMD renders that I simply did not have enough time to redo due to the data availability. Modulo those nuances I was fairly happy with the color scheme and organization, including some accidental design features. Coloring both the protein renders from VMD, and the lines in the plots with the same color convention was definitely a good move, as it allowed for seamless parsing of the plots, and saved much needed space by reducing number of legends I had to carry. An accidental feature was positioning the initial question with the illustrations at roughly same horizontal level as the conclusions. Since both contain a very similar illustration, it was easy to visually grasp what is that thing that changed over the course of our work. I am not fully pleased with some of the text in the poster, and I definitely would want to have another 2-3 days of re-reading and editing it, but alas.

The vast majority of the posters I saw at the conference were great. Clear organization, good posting sentences, and clear figures that stood out from the distance. However, there were a few common issues that I have noticed, predominantly in undergraduate posters. First is simple lack of content, or rather overabundance of white space. I have seen one too many posters with 2 or 3 figures, 3-4 paragraphs of text, and a canvas large enough to fit at least 3 more figures. I assume that this problem partially stems from the poster size expectation. Hey, we all think of 36″ x 24″ poster, and how this is a standard. However, I’d rather see more 24″ x 18″ posters that are content packed than 36″ x 24″ full of wide margins. Worst thing is that sometimes a poster with huge margins will still overcrowd the plots in the middle of itself. No bueno. Spacing out and arranging stuff is a pain in the butt, I know this myself. Plots come in weird proportions, plotting software is a monster to tame, and things tend to look different on your screen vs matte letter print vs glossy/matte poster print. However, the grind against just going with “Egh, good enough” is essential step in improvement of style. My work on this poster taught me a good principle, that my PI learned from his PI, so let me pass it onto you.

Make your poster, then print it out on Letter/A4 paper. If you can read the main figures clearly, then it’s a good font and line size, and proper spacing. If you are having trouble making sense of it on this print, go back to the drawing board.

NS paraphrasing Esmael Haddadian paraphrasing someone else…

On the other hand, I was impressed by some of the very creative approaches to poster presentations. Namely, the poster on Structure of a Non-canonical Middle Domain in Protocadherin-15 by Brandon L. Neel had an interesting twist to it. In addition to the regular static imagery, there also was a tablet set up, so that the interested people could watch MD trajectories evolve over time. I think that with the technology we have at hand right now, people who go extra mile to get their point across and present data in new and informative ways are the people with the higher potential for an impact.

On this note, I will wrap up my discussion of the style and presentation choices and do a quick dip into some of the research related moments and ideas.

Research

An obligatory, I am not a biophysicist by training. I am a computer scientist, I code things, analyze how fast they run, and think about how math models can help us solve real world problems. Thus, the rant below is not necessarily driven by deep professional concerns from a biophysics angle, but rather by some common sense scientific practices and beliefs.

I have attended some talks by scientists from D. E. Shaw research group, and while the content was impressive, I do feel deeply troubled by the messaging and approaches. Let me elaborate a little bit. Science by a large degree consists of trial and error. Especially repeated trial and repeated error. This applies to both experimental and simulation based results. If you were to measure or simulate something once, you would not publish a paper claiming it as a result. (Well sure in some rare cases you would, but that’s a more involved discussion.) Repeatability and multiple data points are essential to any kind of result that you are willing to cite as evidence for your hypothesis. Now, let us take this one step further. If I say that I did 700 independent experiments, and 95% of them yield a certain result with error margin of epsilon, you probably will agree that this sounds like a solid dataset. However, what if I also tell you that at this point in time no other research group can replicate my results? Sure, that also happens, sometimes the machinery is too complex and in many senses unique to the experiment. I mean after all both LHC and LIGO are not easy to come by at every other lab. On the other hand, those are large projects open to multiple collaborators within the field. They are not exactly a proprietary system with limited access given only to the employees of a particular private company. I think you see where I am going with this.

Work done by D. E. Shaw group is marvelous. However, I do have an issue with irreproducibility of the results. Say someone really wants to push for a certain drug affecting catalytic cycle of a protein involved in a disease. Assume that someone has ability to simulate the said catalytic cycle at high resolution with appropriate timescale. Now, what if someone accidentally messes up the parameters of their simulation? We get a perfect proof of effectiveness backed up by 500+ simulations, which then turns into active drug development. If 3 years down the line we discover that this in fact is bogus and doesn’t work, well we have wasted 3 years. If we don’t then we have a new drug, which might still end up being not quite as good as promised.

This is a long stretch hypothetical, but it has some ground behind it. Datasets have been cooked before (the example I am thinking of is a very particular test/train split in a study on the effects of certain drug combinations in cancer treatment), especially when money is on the line, and when pharmaceutical companies are in play, there always will be money on the line. Thus, while I hope that the researchers are keeping level heads and cold judgement, I cannot simply dismiss the concern about exclusivity of the technology that makes the MD research at D. E. Shaw beyond the cutting edge.

I believe that we should strive for repeatability and cross-validation in science. There always will be obstacles on this path, and I do believe in intellectual property rights, patents and related concepts. However, I think that the balance shall be maintained, and tools could and should be shared. After all making the first hammer is an invention, but once we have one it’s about who can do the most with it.

Concluding remarks

I started writing this almost a month ago, so I am not sure how connected those pieces feel. This was a long ramble about random stuff, so critique away at it.

Cheers, ns.