Negative

I assumed from the lack of electronic message that my coronavirus test was positive, but I called the health center this morning and it turns out they just forgot to send the results. Viral RNA was not detected. I've been provisionally cleared to return to campus, though I should call the specific provider who tested me for the final decision. The timing is good because I was starting to run out of food in the house and would have needed to pay for delivery if I were to stay isolated. But I was able to go shopping today and am now restocked.

No Facebook app ads

Earlier this week I created a Facebook ad campaign for my app and got blocked pending verification. I filled out the reactivation(?) form at the time, but I got a response a couple days ago informing me that my ad account was disabled for a terms-of-service violation, which was not specified. After looking through the terms I noticed that it might be a problem that my app's logo has the same shape as a play button, but I'm not sure that was the reason. Anyway, I will apparently not be advertising on Facebook.

First day of graduate classes

Today was the first day of instruction at UT Knoxville. I would have had two classes to attend in person, but due to possible infection I attended virtually through Zoom. The genetics/genomics course launched into an introduction to rice plants. Overall this university seems to have a much stronger emphasis on plants than UIUC and I may need to do some reading to shore up my plant biology knowledge. The first biochemistry lecture was mostly class organization. After classes I spent the afternoon doing the first genetics assignment in its entirety to have it done.

I still haven't received results from the coronavirus test yesterday. Symptoms are roughly unchanged, still just a mild sore throat with occasional headache and cough.

Self-isolating

I woke up this morning with a minor cough, headache, and possibly sore throat. I had planned to stop by campus again today, but as the self-screening tool reminded me, these are all symptoms consistent with COVID-19. After filling out the appropriate form from the screening tool, I was advised by a university response team to get tested. I went to the Student Health Center; they took a quick nasal swab (not the super invasive kind) and a throat sample (for a strep test). The strep test already came back negative, but I won't know the viral RNA detectability results for another day or so. Until then I will attend class remotely to be safe.

Graduate orientation begins

Early this morning was the start of the Graduate School's online orientation. It mostly focused on professional development opportunities and campus resources. I learned about a center for refining teaching/learning methods, which sounds very helpful since I'll be TAing in the spring. I signed up for a 1-credit online class this semester called Best Practices in Teaching Biology. Tomorrow is the graduate teaching assistant orientation, again an all-morning online event.

Undergraduate research archived

 Today I attended an online lab meeting of the research group I was in back at Illinois. My mentor presented my recent figures and new work he did in lab. To preserve my tools in case someone needs to extend some work I did, I tidied up and cataloged all the files in my "lab work" folder. I exported my electronic notebooks from Benchling, added them to the archive, zipped the whole thing up, and stored it in a lab Box folder. This concludes my work for that lab.

Relocated to Knoxville

Today I spent 13 hours in transit from the Quad Cities to Knoxville. All the stuff got unloaded pretty quickly but is currently in a big mess around the house. Tomorrow I'll start unpacking for real and take care of things like getting Internet installed.

Registration complete

The online registration system was giving me some trouble, but with the assistance of university staff I have now successfully registered for all the core first-semester courses in my graduate program. I checked the bookstore's web site but textbook information doesn't seem to be available for fall yet. I will keep an eye on that and order books as soon as possible.

Another app workaround

Today while testing the app features I added yesterday, I noticed that my bus app was completely failing to display departure information. The bus company's server is currently returning empty departure lists for all stops, and very slowly at that. I had a workaround ready to go for when that server doesn't provide departures, but the slowness in response was causing my server to give up before reaching the fallback plan. I reorganized the error handling and my app can now use a fallback for all routes' information.

Yet more app improvements

I spent today making several more improvements to my bus app before more students (?) arrive back on campus next month. I started by making it possible to switch off the display of specific information on the trip list screen in case it was too dense for people. I went to finally finish the half-done vehicle lookup feature but then noticed a serious problem: the trip information as called up from departure details was often for the wrong trip. This seems to have been caused by a recent change to code that loads data from the bus company into the database. After fixing that, I did complete the vehicle lookup feature, filling in the missing UI. Finally, I fixed the longstanding strange behavior of navigation directions displaying the bus's whole route shape. The server now tells the app which shape points are associated with stops so that the app can draw just the subsection of the trip that's relevant to the user.

Revisiting ENCODE data

Last year I wrote scripts to do a big search of the ENCODE Project data for proteins that could affect the one we're focused on. We identified one that happens to be a member of a family of proteins. My task is now to search the data for relationships between that regulatory protein family and the family to which our protein of main interest belongs.

More app tweaks

Today I addressed a handful of tiny inconveniences in my app, mostly surrounding the route trip listings. Those listings now require less jumping around when trying to learn about a route that isn't currently running. I also adjusted some of the "landmark" stops used in the new trip summary feature. Once the bus company releases the full data set in August I will probably need to add a few more landmarks to display the (numerous and arcane) school district diversions in a helpful way.

App improvements for fall

UIUC is planning to have some in-person classes in the fall, so some students will likely use the bus system. I want new students to have a good experience with my bus app, so I spent yesterday and today making some improvements. I finally fixed a longstanding issue where the app's main screen failed to identify the user's location. I then added a new feature to display a "fingerprint" of each trip in the route trip listings so the user can tell apart variations on and brief diversions from the common route.

Degree awarded

Today I received an email notifying me that my official transcript from the University of Illinois has been sent to the University of Tennessee's graduate school as I requested a couple months ago. Since the transcript was set to be released after degrees appear on transcripts for that semester, that indicates that my degree has been fully awarded.

Left Champaign

This morning I packed up the few remaining things I needed for my stay in my apartment last night and quickly vacuumed a couple spots I missed yesterday. There was no caffeine left unpacked from last night, but I had a bag of cereal to eat from for breakfast. I then drove directly back to the Quad Cities. I've vacated my apartment and will not need to return to Champaign for anything.

Staying to clean apartment

I drove back from Indiana today and planned to continue all the way home after a stop to pack up everything from my apartment. But cleaning and packing took much longer than I expected and it started to rain intensely, so I'm staying here in my apartment tonight. I also spent some time trying in vain to get into buildings to return my keys. I'll load the last of my stuff into the car and leave tomorrow morning.

End of Indiana trip

Today was my last full day vacationing(?) in Indiana. We ended the day roasting marshmallows on a small fire. Tomorrow morning I'll head back home through Champaign.

Turkey Run State Park

I spent most of today with a friend at Indiana's Turkey Run State Park. It has a network of hiking trails of varying difficulty. We did the most rugged one - involving numerous stone stairs, tricky slopes, and rock paths through creeks - then a long loop to see some landmarks. My favorite was Falls Canyon with a slippery path up to a little waterfall.

Visiting Indiana

This afternoon I arrived in Indiana with a friend. Tomorrow we'll visit the Turkey Run State Park. After a couple days I'll return to Champaign to clean out my apartment.

Last stay in Champaign

I returned to campus today for a visit and to clean out my apartment. I'll stay about a week and vacate the apartment when leaving. I also need to return my keys to various places.

Preliminary home setup done

After making some improvements and storing a few items in the new house yesterday, we all made the drive back to Illinois today. I'll stay around there for the rest of the summer and fully move to the new house a couple weeks before graduate school officially starts.

House deal completed!

This morning I met the realtor I had been working with remotely. We did the final (and first in-person) inspection of the house. Almost everything was in excellent condition. We all went to the title company to deliver the check and sign the final paperwork. After brunch, my family and I spent the day making some home improvements. In the afternoon a member of the HOA board stopped by to welcome me to the neighborhood.

Ready to close

I've sent all the appropriate documents regarding the house purchase to the people who need them. The termite inspection was done and showed no problems. We should all be ready for closing tomorrow!

Arranging research rotation

In the first year of graduate school, I will "rotate" through three different labs, doing projects of a couple months to see if each lab is a good fit for me. I have reached out to two professors working in computational biology. One has space in his lab and seems interested in me rotating there, so it looks like I have my first rotation just about set.

Graduated!

This afternoon I watched the university's brief commencement livestream with family, followed by a video from the School of Molecular & Cellular Biology. Transcripts that are waiting for degrees to be awarded will be sent next month, so I assume the diploma will be sent in the mail around then too.

I didn't accomplish much the rest of the day, but I intermittently looked into some things that I'll need to handle this summer for starting grad school.

Empty to-do list

This morning I went over my last take-home exam, noticed one mistake, fixed it, and submitted. I then spent the rest of the day finishing documentation of the projects I worked on for the class I was on staff for. It was a lot of writing, but I finished everything I had planned to do. Tomorrow I just need to wake up and watch the virtual graduation ceremony.

Lots of documentation

I've spent the last couple days writing as much documentation as I can for one of the tools I created. My outline calls for six "chapters" and five shorter "appendices." Along the way I realized a small issue with the tool itself and corrected that. After writing 68 KB of prose and code, I just have one chapter and three appendices to go. I have two days to finish those and a (hopefully shorter) explanation of my part of another project.

One last week

Today began my last week as a student at UIUC. I made good progress on my last paper for an MCB class. I'll wrap that up over the next two days. There is one more take-home exam later this week that I'll have a day to complete. Other than that, I'll work on documenting all my work for the class I was on staff for. Graduation is Saturday: 6 days.

Last day of undergrad instruction

Today was the last official day of instruction for my last semester at UIUC. I didn't actually have any class meetings because my only class on Wednesdays had no lecture or activity this last week. Instead, I had some time to put together some more figures for the lab, attend a meeting for my job, and then present my lab work to the lab group.

Last deadline night

Instruction ends for the semester in two days. The students in the class I'm on staff for are wrapping up their final projects to present tomorrow in their (online) lab sections. Though I have some writing work I need to get done for a class I'm taking, I wanted to be available for one last deadline night. As expected, there were some last-minute tricky issues, but we got them sorted out. Now to hammer out another paragraph of a research paper.

Online research symposium ongoing

Today was the opening of the entirely online Undergraduate Research Symposium. My video is available for viewing and people can ask questions in the forum. I answered one this afternoon. It's nice being able to compose a response rather than needing to answer verbally on the spot.

Learning to visualize proteins

My grad student suggested I start experimenting with tools for protein structure visualization. Protein structure is a Very Big Deal in biology, so I should definitely get comfortable manipulating it. Today I spent some time tinkering with PyMOL on our protein of interest.

Documenting for handoff

Since I'll be graduating this semester, it's important that my fellow course staff understand the systems I worked on so they can continue development and maintenance. Over the summer I contributed some complicated features to a project. This semester I periodically met with the project's maintainer to explain and clarify the code. We finished going over the last of it today.

Decided on grad school

Yesterday I collected my thoughts about future plans and decided to commit to the Genome Science & Technology graduate program at the University of Tennessee Knoxville. I notified the coordinator of my decision and created my account in their system. They suggest that I get moved in during the first week of August.

Highly distinct

A month ago, I finished and submitted my undergraduate thesis to the MCB department as part of an application for research distinction. I have now received an email notifying me that I received Highest Distinction in Research based on my thesis and the poster I presented last year. Soon after, I received another email saying I've received Academic Distinction in the department based on my GPA in the major.

Remote lab work

This evening I started doing some of the remote computational lab work discussed last week. After a good deal of fiddling with alignment tools, I produced a figure (well, a block of monospace text) showing the equivalents in other species of the protein region skipped by one of our splice variants. There are indeed commonalities in that region.

Keeping the app running

Virtually all students are out of campustown, but the bus system is mostly still running as usual. A couple days ago the company published a partial data update that seems to be inconsistent with some of their other systems, causing a lot of departure information to vanish again. This has happened several times before, so I was prepared and able to work around it enough to get basic departure information. Interestingly, by AdMob metrics, app use didn't completely flop last month despite the lockdown.

Hiring freeze

I did some looking around on the Internet today and found reports of a hiring freeze at numerous companies. That seems to include John Deere, where I applied. I probably won't be hearing from them for quite some time. That's unfortunate; I'll need to think about other plans.

Back to class, kind of

Today was the first day back from break, but with entirely online classes. I only had one class today, but tons of other meetings and things to handle. The class I'm on staff for is mostly alright for now. We released another (pretty easy) segment of the semester-long project this evening, so I'll keep an eye on that tomorrow.

Thesis submitted

This afternoon I submitted the final version of my thesis. I'm now back in the Quad Cities for spring break and will hopefully return to lab work next week.

UTK visit day 4

This morning all the GST visitors, hosts, and some faculty went to brunch at a nice place with a great view:

Some mountains near South Knoxville

The program director said they would start sending offers around mid-March, so I'll probably hear something within two weeks. After the meal, my host showed me a bit of downtown Knoxville and then dropped me off at the airport.

I managed to do a little useful work while waiting and flying, but I still have a lot to catch up on.

UTK visit day 3

I got up early this morning to go tour some of the bioinformatics- and genomics-related facilities on the main University of Tennessee campus. After lunch, the actual interviews were held. They had matched each visitor up with a faculty member doing related research. Each 30-minute conversation went at least reasonably well, especially the first. That professor is doing purely computational work, though it is very interesting and I might want to look more into her lab.

After interviews, we got to attend the GST retreat, a poster session and mini-symposium held in partnership with the biochemistry/molecular/computational biology department. I saw many interesting posters and spoke briefly with a handful of faculty. The two departments had dinner together - a lot of people! In a few minutes I'll go to a GST grad student social event, the last part of the day.

UTK visit day 2

Today was full of tours. In the morning we were shown select parts of the (extremely large) Oak Ridge National Laboratory. Their Spallation Neutron Source was offline for maintenance, so we were able to visit the facility. A beam of neutrons produced by hitting mercury with accelerated protons powers many different lab instruments.

Part of the top floor of the SNS

We then saw the Summit supercomputing facility, which provides a huge amount of computing power mostly in the form of GPUs. The sentence "we're installing a 40 megawatt line" was spoken. We visited several labs, both at ORNL and the University itself. UTK has a large focus on agriculture even in the Genome Science & Technology program, so they have sophisticated greenhouse facilities.

At dinner we were joined by some GST faculty. Tomorrow we'll have the official interviews.

UTK visit day 1

I got up at 3:55 AM this morning to make sure I could board my flight in time. I had scheduled an Uber to the airport ahead of time, but for a few minutes the app was trying to schedule my trip but no drivers were online. (To be fair, it was 4:30 AM.) Fortunately, one driver did eventually appear and picked me up as planned. The original flight was through Dallas to Knoxville, but due to weather in Dallas the connecting flight would have been delayed, so I was reassigned an earlier connection into Chicago. (Good thing I got to the airport early!) After a few hours of flight I safely arrived in Knoxville.

A current graduate student in the program - my "host" - picked me up from the airport. We ate lunch together, featuring some awkward silence because I'm very quiet. I was then dropped off at the hotel, where I spent the afternoon doing some work. I took a break to walk around outside a little. Campustown is very nice and clean. I saw this interesting scene:

Could be a Myst scene. What's up with the devices in the middle of the drainable river?

In the evening all the recruitees and their hosts went to dinner together. I think the original plan was for some faculty to be there as well, but none were. I got more comfortable with everyone and overall had a good time. Tomorrow we're all off to Oak Ridge National Laboratory.

Hackathon day 3

After a nap of ~2 hours this morning I freshened up and went back to work on the hackathon project. There was just one remaining problem: the web UI for our application no longer connected to the server. Fortunately it got solved pretty quickly. A change to the data structure had made the UI's requests invalid, which was made more difficult to debug due to the environment we ran in.

With the work time over, we went to the atrium of one of the event's main buildings to display the project. A steady stream of people talked to us and seemed to like the project. At the closing ceremony we were awarded second place in the judges' selections. We left satisfied and exhausted. I'm now going to try to catch up on the sleep.

Hackathon day 2

I've now been awake for about 20 hours. Yesterday and overnight we made a lot of progress. I'm still not used to the language this project is written in, but I've been getting a little faster. I made a system to send email and then extended a teammate's code to support authorization. Submissions will close in a few hours.

Hackathon day 1

After my class and a lab meeting today, I packed up my stuff and went to meet my project partners at the hackathon venue. We discussed alternative project ideas, then settled on the one that was already the most fleshed out. The tech stack doesn't use any components I know well, so I got a slow start, but I'm making some progress. Energy is less of a problem than I expected - I was more tired at 10 PM than I am now at almost 3 AM despite not getting any extra caffeine. We'll all get some sleep and come back tomorrow to keep working.

Preparing for assignment relaunch

The major assignment of the class I'm on staff for will be released early next week. It would be good if students got the development environment fully set up in advance, so I held extra office hours today. A couple students attended and we got them set up as much as possible. During downtime, I worked on tweaking one infrastructure program that supports the assignment.

Got an interview

Today I received an email from the University of Tennessee Knoxville inviting me to visit and interview there. The trip will also involve a visit to the Oak Ridge National Laboratory, with which the Genome Science & Technology program is affiliated. I'm very excited about the trip and program!

Last application finished

Today I finally finished my statement of purpose for Knoxville and compiled all my application materials. I will probably receive instructions tomorrow on how to submit everything into their system how they like.

Interestingly, I didn't hear anything from Boulder. They might have sent their interview decisions via physical mail rather than email. My application status in their system still says "submitted"; no news could be good news.

Possible decision tomorrow

With Boulder's committee meeting last Friday, it's likely that they'll send their decisions this week, possibly tomorrow. In the meantime, I made a little progress on my last application's last document, which I should finish tomorrow.

App data issue

I just checked on my app this evening and noticed that all the cached information on trips' stop times was gone. This normally happens whenever the bus company publishes a data update, but I checked and that hadn't happened recently. Trying to look at those trips failed; my server thought it already had the information on them but the relevant data table was empty. Strangely, only that table was empty. (This is somewhat fortunate, since it would be much more difficult to clean up if two certain tables were lost.) I cleared the server's notes of what trips' data was downloaded and it's being refetched now. This is strange and somewhat concerning, but I will have to wait to investigate further.

The month for grad school interview decisions

At least two of the graduate schools to which I have already applied will release interview decisions in January. Boulder sent me an email with a specific admissions committee date (January 10!); Stanford said interview offers will go out starting the week of January 6 until the end of the month. I suspect that in eight days I'll have my first result.