Usually I tend to write long winded posts with many side topics, but today is not the day. The circumstances of our current days are not the happy ones, so I wish to share something that is dear to my heart (and recent to my memory).
I visited Chicago (again) from March 11th to 20th in the year of 2022. My wife was attending APS March meeting and I was just tagging along for a fun visit. The weather was more pleasant than I usually recall from March in Chicago (thanks no thanks global warming). It was a fun trip, less so on the sightsee side (due to the busy schedule), and much more so on the social side, since I finally reconnected in person with my friends.
The feeling of being back in the city was amazing. The CTA, albeit being slower due to worker shortages, was lovely. Food and bar scene was great as always. I was sad about the closure of Lost Lake, and even more so about my favorite mezcal bar Todos Santos going out. However, Three Dots and a Dash was still a shining spot with all the usual buzz, and even though I didn’t end grabbing a spot at Havana Grill I am glad it’s still around. I finally made my way into the Aviary (with many thanks to Carter Grieve and Hana for actually pushing though on this), and it was a lovely experience.
I didn’t catch any museums this trip due to my stupid stomach acting up for a few days in a row, but I still caught a few murals and architectural pieces in my free time.
All in all, I am just happy to share a few photos, that capture some of the highlights of the trip, and I hope I’ll be back to more regular blogging some time in the near future.
One day I might have something intelligent to say about the world and what we are doing in it, for now however I will stick to being happy about having wonderful friends and sharing great memories together.
Good (local time option) world! I am back with another year in review. This time we are back to thematic groupings, since time ceased existing (not really but something like that). The intro won’t be long because either (a) you also lived through 2021 and are probably quite tired OR (b) you are doing some sort of history research; in both cases let’s not waste too much time.
Two major trips this year, one back home to Chisinau, Moldova, and one to Paris, France. Let’s start with Chisinau.
I went back to Chisinau around May 20th, which meant that I got to spend my birthday back home for the first time since 2014. Now, if you know me, you will realize that this fact actually meant nothing in particular, since I am not the biggest fan of my birthday. However, having home cooked meal that I didn’t even have to cook, I’ll take that as a solid option. Other than that my visit was quite routine: some paperwork here and there, some bars (mostly in the city center), and a missed opportunity to see Morgenshtern live. On the brighter side I got a personal tour of some artworks by @e.art.n and got to hang out with two adorable beagles for a bit.
Paris was amazing. That’s it. I had a good time being a tourist, as expected the food was great and weather cloudy. Versailles was quite interesting, gave me flashbacks to Hermitage. Louvre was also quite cool, and just as expected Mona Lisa is way too overhyped. Musee d’Orsay was sadly somewhat disappointing due to subpar room organization and endless flocks of people. Musee de l’Orangerie was the highlight of the trip. However, not due to the water lilies, but due to a temporary exhibit of Chaïm Soutine’s works. Say what you want about my taste in art, but now I have a nice bœuf magnet on my fridge (pic of the original below).
You thought I was done with the trips? Nope. Minor trip time: Denver, Colorado and Yosemite, Sacramento and Berkeley, California. Both Rocky Mountain and Yosemite National Parks were great. Outdoors with beautiful views, long (apparently they were labeled as strenuous) hikes, and nice animal spotting episodes (skunk, pika, marmot?, elk, and a black bear cub). Sacramento and Berkeley allowed me to reconnect with some of my friends who I haven’t seen in a very long time. It was nice to see familiar faces accompanied by the reminiscence of days past.
This year I have read the following books:
Hilbert by Constance Reid
The end of everything by Katie Mack
Flash boys by Michael Lewis
You look like a thing and I love you by Janelle Shane
What is life? by Paul Nurse
The statue within by François Jacob
Sadly all of the above are non-fiction books, since my two attempts (The servant by Fatima Sharafeddine, and Slaughterhouse-five by Kurt Vonnegut) at reading some fiction failed at various points in the corresponding books. I am planning to actually read both, but that is a job for 2022.
Overall my reading pace and habits were sporadic. I read What is life? in a single evening (the book is short), and I binged The statue within for a bit shy of 11 hours on the flight back from Paris. At the same time after my return from Moldova (where I finished The end of everything) I had a two month hiatus, which got interrupted by reading spree of August, which then gave way to desolation of September-October.
All six books make it into my recommendations list, but if I had to only pick one it would be What is life?. The book is brief, crisp and extremely inspiring. Ideas explained in the book hit a great balance between simplicity and profoundness. Finally, I guess since I am myself somewhat involved in biology, I think this book gives a great in on the modern view of life.
Besides books I have discovered a wonderful world of Thelonious Monk‘s music, and got extra excited about long awaited new album from Oxxxymiron. In the realm of TV shows I picked up and binged Expanse after returning from France, and earlier in the year watched Dopesick and Arcane. Also for the first time since the beginning of the pandemic I went to the cinema to see Dune and it was amazing.
It’s been a busy year for work. For a quick summary you can check my Google Scholar profile, but the main focus this year has been on the wastewater monitoring. Long story short: SARS-CoV-2 sheds into human waste, so by screening wastewater we can get insights into what’s happening in a region (e.g. which variants of concern circulate around) [1, 2, 3, 4, 5].
I’ve felt that my overall rate of paper reading went down in 2021. My suspicion is that I suffered from what I’ll call “COVID research fatigue”. High pace of anything that has to do with SARS-CoV-2 research meant that every week I got an extra set of 5-10 open tabs added to my never ending life of 4 browser windows. Thus, reading non-SARS-CoV-2 papers was much more exciting, but due to the energy expenditure and limited battery in my brain it also was less frequent. Overall I think I’ve been keeping up with most of the stuff I was interested in, but I wish I had those extra 4 hours every day just for reading.
Classes wise this year has been aggressively meh, with the sole exception of Information Theory (ELEC 535 @ Rice) course by Ashutosh Sabharwal. It was a delightful course, which while only covering the basics still managed to inspire me, and as a result led to me going doing down a few lengthy rabbit holes of reading (maybe one day I’ll write more on that).
Finally, I spent 6 weeks this summer working as a Research Mentor at the Summer STEM Institute (fully online). I have mixed feelings about the experience, since on one hand I learned a lot about trying to lead multiple independent research projects, but on the other hand the end results could have been more impressive. Overall, I take this experience as an exercise in management, which pointed out to me some weak spots I plan to address in the future.
The social life in 2021 was full of ups and downs, as we were navigating the world after the vaccination, but with re-emerging threats posed first by Delta and then by the Omicron variants of SARS-CoV-2. One constant presence in my social life was the D&D campaign in the (heavily customized) world of Ixalan led by the long standing DM of our group Diego Bejarano. Ability to escape the world for 4 hours every week and explore dense jungles, tall mountains, and vast oceans (and rivers), while RPing as a devil from Hell turned into a giant pug (named Pugmeister) or Jinx from League/Arcane is definitely something that helped me stay sane otherwise.
Overall it’s been an incredibly busy year that had some good and some bad in it. I don’t think I managed to write up a particularly exhaustive review, and it definitely ended up being more biased towards the end of the year. I guess my memory does some sort of exponentially moving weighted average over the experiences, so that’s what I end up with without a weekly journal.
As is customary, I will try to write more on this blog, and most likely I won’t. See you in a year or so!
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.
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.
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.
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.
I am traveling to Baltimore, MD this weekend for Biophysical Society Annual Meeting. I will be presenting my research on the insulin degrading enzyme (IDE) as a part of the poster session on Sunday at 1:45pm. Feel free to stop by and say hi, and/or inquire more about my research. [doi: 10.1016/j.bpj.2018.11.301].
Hopefully, I will also have some free time to roam around the conference and the city.
I will be presenting tomorrow in the Exhibit Hall C, stand B13. Drop by to say and chat about research!