Crashes mostly eliminated

I thought I had fixed all crash bugs in my app, but I got one report in Google Play a couple days ago. Interestingly, it doesn't mention any of my code, so it's difficult to know what part of my app is involved. Fortunately there only seems to have been that singular report, no reoccurrances even for the same user.

App fixes appear to be working

After releasing an update to my app last week, I still have received zero crash reports from the new version. The fixes appear to have been successful.

App crashes reduced

The recent problems with the town's bus system's API revealed some rare issues with my app. Yesterday I examined all the crash reports, tweaked the code to address each, and published an update. Many devices installed the update and I haven't seen any crash reports from the new version in Google Play.

Got an online interview

This afternoon I received an email from Caltech informing me that I've been selected for an online interview. It will be a 15-minute videoconference early next week (!) with two professors in the department. My understanding is that if this interview goes well I'll be invited to a recruitment/interviewing weekend on Caltech's campus in the spring. This is a good start!

App works when others don't

The bus company's API hasn't been returning information for several routes this weekend. Without that, most bus apps for the town cannot display departures for those routes. Fortunately, there is an undocumented API endpoint that provides limited information but is still working. I was able to include data from that endpoint into my server's database, allowing my app to keep functioning reasonably well.

Lecturing again

The professor of the CS class I'm on staff for invited to me to talk to the class again on Monday. The students are working on their final projects, so I'll discuss the process of developing a few-weeks-long project into a real deployed app.

Immunoprecipitation retry results

Yesterday in lab I finished up the western blot of my immunoprecipitation retry from before break. Unfortunately the images were not clear. The one that I was most interested in had inconsistent results between my new immunoprecipitation products and the original ones, though that might have been because I didn't have much of the old ones left. If the results are accurate, only the full-length protein - none of my tested splice variants - interacts with a certain protein, which is fine and interesting, but it's very difficult to tell with the images I have.

Western blotting again

I spent this afternoon doing most of a western blot for the last immunoprecipitation attempt. So far it's going better than last time - the transfer from gel to membrane was decent from a visual inspection. I'll finish that up tomorrow afternoon so I can include my results in my presentation on Friday.

Break is for applications

I spent most of today working on grad school applications. I filled out some application components, but it's going somewhat slower than I hoped. Tomorrow I should email some professors at the universities to introduce myself and inquire about their research.

Graduation paperwork submitted

Registration opened for me this morning. There are restrictions on CS registration as usual, but I was able to add the three classes I need to graduate. I need that one last CS class for my CS minor and will be able to attempt registration for it in December. Since all requirements will be satisfied by the classes I could enroll in, I submitted the application for graduation!

App earned $100

Last month my bus app crossed the $100 line in ad revenue. That's the first payment threshold, so I'll actually get paid! The number of users has also been growing somewhat, crossing 700 recently.

Looking for grad schools

While still very busy with regular work, I now need to do some serious planning for grad school. I'm currently looking at University of Colorado Boulder and University of California San Diego. Caltech and Stanford are on my list, though those are very prestigious and probably very competitive. Most application deadlines are December 1, so I do have some time, but do need to get working.

Surprise! Graduating this year

While looking over my remaining class requirements on Thursday, I realized that I can fit them all in next semester. So I'll graduate next semester - seven months from now! This means I need to get graduate school applications or a job hunt done ASAP so that I can start next summer or fall.

App almost reached a payment threshold

Google AdMob only pays advertising revenue in chunks, once a payment threshold amount has been reached. Somehow my app earned over $30 last month alone. It's now just a couple dollars from the first threshold, so after over a year I'll almost certainly receive my first payment at the end of this month!

Lectured!

The professor for the CS class I'm on staff for is out of town, so I delivered the lecture this morning! (This class is, if I remember correctly, still the largest at the university: ~900 students.) On Friday I went over the auditorium setup with him to be as prepared as possible. This morning I arrived early to set up as much as possible backstage during the previous lecture. I struggled a bit with the audiovisual equipment (where are the plugs again?) but managed to get the display on in time. The microphone was more challenging - I got it turned on but it couldn't be heard unless I held it very close. That was unfortunate, but once I began the lecture it went along well. I realized after the end that I missed a couple extra notes I wanted to touch on, but I covered everything on the slides. Packing up also took a little longer than expected, but that was mostly done backstage out of the way of the next lecturer. Overall it could have gone smoother but I got the job done.

Time for a lot of office hours

This is the first weekend students have to work on the major semester-long project we just released. The professor is out of town for a few days, so to make sure things are going smoothly, I and some other senior course staff will be spending a lot of time in office hours tomorrow. I plan to be there for all eight hours of them.

App passes 600 users

The beginning-of-year surge has continued: my app surpassed 600 active installations this week. I recently made a change to try to fix a semi-rare crash that I can't reproduce on my own device; the update is in automated testing now.

Moved in for the new semester

After an all-day training session, I got settled into my new apartment this evening. It's quite nice. We did notice, though, that no coaxial cable was provided with the modem one of my roommates brought, so I'm doing a quick Walmart run to get it. In other news, I just tonight detected that the main hard drive in my desktop computer is in the process of failing, so I'm copying the data over to the other drive. Unexpected things, but all manageable.

App hits 500 users

A few new students have arrived on campus already. I'm not sure how they heard about my app since I don't have ads going yet, but the Google Play console stats show that it's surpassed 500 installations!

I'm trying to get Facebook ads up, but it's constantly locking me out of my account and requiring extra security checks. Strangely, the Facebook page I made using Facebook's advertisement creation wizard was immediately flagged as spam (i.e. advertisement?) by Facebook and unlisted. I appealed it and it was restored, but as soon as I went to the page's settings to add appropriate disclaimers I was locked out again and cannot log in now. Hmm.

App updates rolled out

New students are moving into campus this week, so a lot more people may be interested in my bus app. I didn't have time this summer to implement all the additions I wanted, but I did make some updates which I published this morning. Before I go back to campus I'll try to get Facebook ads up to inform more people that the app exists.

App still growing, somehow

Despite most students being off campus for the summer, and despite my total lack of marketing, my transit app has been steadily gaining users. It passed 400 a couple months ago and is now a little under 450.

Working on supporting infrastructure

With the assignment I wrote out for test to other course staff, I've turned my attention to developing tools related to the grading process. We want students who didn't complete previous segments on time to still be able to work on the current segment, so there needs to be a way to use a known-good solution for past segments. That needs to be done without distributing source code so we can reuse the assignment next semester. I started a tool at the beginning of the summer to make this possible, but it will need more work to be able to support what the assignment has become.

Working from home

I spent this morning packing my belongings and cleaning my apartment. I'm now back in the Quad Cities and will resume working tomorrow (since I didn't get any work done today). I have a little less than three weeks to finish my project before the semester starts.

Last day in the office

Even though my full-time appointment continues until the semester starts, I need to move back to the Quad Cities due to my summer lease ending. Today was my last day working in the same physical office as the other summer course staff. I finished documenting my project for the testers and started working on infrastructure that will be involved in grading the assignment. Tomorrow morning I'll finish cleaning my apartment and move out.

Making the project easier

The programming assignment I wrote for the introductory CS class is currently out for test to a few other course staff. Initial feedback, along with my own concerns, indicates that there's too much work at the beginning. One of the handful of functions for students to implement is very finicky and somewhat long, so much so that I'm inclined to split out parts of it into helper functions. Today I decided to just provide that function in the starter code since there's enough other stuff to work on in the segment. As I continue writing up more detailed specifications I'm finding that the later segments are also a lot of work. They might need to be trimmed back as well.

Cleaning started

I'll be moving out of my summer apartment and leaving campus at the end of the week. I hear the landlords on campus tend to be very eager to charge cleaning/maintenance fees, so I want to make sure everything is as clean as possible before leaving. Conveniently, there was a vacuum in the apartment when I moved in, so I started with some vacuuming.

Project out for testing

Yesterday I finished the first draft of the test suites for the assignment students will complete in the fall. I spent today adding explanation and hints to the starter code so students will have an easier time getting acclimated on the first segment. I then wrote some quick documentation for the first two segments and released it to initial testers! Next week I'll work on more complete documentation and start the module management system.

First draft done

Today at work I wrote the last of six test suites for the assignment students will work on over the course of the fall semester. Despite checking the simplest behavior, it was one of the more complicated test suites because the logic implemented by students in its segment gets refactored/rearranged later, so the tests need to be able to find and invoke the student code appropriately. Tomorrow I plan to heavily comment the starter code and put together enough instructions for other course staff to start testing it.

Close to a viable product

Today at work I finished the fifth of six test suites for the fall's project. Since I'm working in the opposite direction students will, the segments get simpler as I go on - this one took only about a day total. Tomorrow I'll at least mostly complete the tests for the very last (first) segment. At every step along the way, I remove the solution code to my last tested segment to create the starter code. Once that's done for this next segment, I'll just need to add documentation and helpful hints, then we'll have a usable assignment.

Not much time left in the summer

My two-month stay on campus for the summer has less than two weeks left. Before I leave, I want to get an early but usable version of my project out for testing. The sub-project of writing the assignment's test suites is almost half done. If I can keep up the pace, all the tests should be finished before the end of July. My full-time appointment continues until the Saturday before classes start, so that's three weeks working from home. During that time, other course staff will be testing the assignment; I'll be tweaking it based on their feedback and working on a system to make sure students who fall behind aren't completely sunk.

Making progress on the main project

A while back, I finished the reference solution to the assignment I'm preparing for a CS class. This week I started in earnest on writing the test suites, which automatically test and grade student submissions. The assignment is broken up into six segments. Two segments now have test suites, including a very significant one that wraps up a lot of work. (I'm working backwards starting from the completed assignment so that I can produce "starter" code for each step as I go along.) That leaves four segments to go, but they're smaller and (hopefully) easier to test.

Now to handle the main project

When writing a programming assignment as I am for the fall, I first write the reference solution, then a set of test cases to make sure a student submission works properly. Quite a while ago I finished the reference solution for the fall's major assignment. The professor returned from vacation today and approved my plan for what aspects to test. I had been working on various other things during his absence, but now I should complete my main task of writing these tests.

Disruption in the routine

This morning I received a text from the apartment company stating that power would be intermittent today. Between when I drink my morning tea and when I make my coffee to take to work, the power did indeed go out. Without coffee to bring along, I bought some at lunch from the bagel shop on the ground floor of the building I work in. When I got back in the evening, the power was still out. I didn't want to open my fridge and I couldn't cook anything anyway, so I walked over to McDonald's for dinner. Some time after I returned, a buzzer started sounding: the fire alarm. Several fire trucks arrived, and after consulting with the electrical workers, they learned that the alarm was just because the fire system ran out of battery. They were able to silence it temporarily, but it's still going now, though everything is fine and people are back in the building. Amid the alarm the electricians got power restored. Fortunately my frozen items seem to be still frozen solid.

Progress at work

My main job as course developer this summer is to prepare the app/assignment students will work on over the course of next semester. The app (our solution) as originally planned got done yesterday; today I started on an extra feature added in order to introduce students to machine learning. I'll be helping with a coworker's project tomorrow, but I may be able to finish this section of mine, after which I can start writing test suites and turning it into an actual assignment.

Walking more

This afternoon I went out walking again. Rather than trying to finish the northeast region without sidewalks, I went west past some nice residential areas. Unfortunately my phone (which I use to keep track of where I've visited) ran low on battery, so I had to turn around a little earlier than planned. Since there isn't direct bus service between that area and my apartment on the weekend, I walked the full round trip, for a total of eight miles. I've now visited 60%~ of the bus stops in town.

Office upgrade

When I got to work this morning I saw that some unrelated equipment had been brought into our room. Soon after I got started, a faculty member asked when the room would be available - apparently it had been reserved for an activity for high schoolers. Two more such events were planned for later in the month. When our professor arrived he spoke with building administration and got us a nice conference room to work in. So we moved all our stuff from the basement up to the third floor. We now have windows (with a great view!), nicer chairs, and a projector.

Yet more walking

It was a reasonable temperature this morning, so I went out walking on my quest to visit all the bus stops in town. I had previously finished all of Urbana except the north, so I went there to start cleaning up the remaining stops. Even getting to unvisited places from my current residence was a long walk - by the time I got there, it was getting noticeably warmer. More problematically, there are very few sidewalks and the stops are very spread out. So I had to turn back, but I got a few more stops and have now visited 58% of them all. That particular area may require a bicycle.

First full week of work

This week was my first week of full-time work on campus. I've wrapped up one of my projects and made a little progress on another. I spent a lot of time helping with some tricky aspects of another developer's project. The professor approved my plan for my main project, so that can start Monday.

App made a profit

At the beginning of every month, the AdMob console shows an updated earnings amount. At the beginning of June my app just crossed over the amount I paid to publish it. Eighteen cents of profit!

Settling into the apartment

Today was my first full day in an apartment. My first task was to go to Walmart to buy a pillow because I forgot to bring mine. I then spent much of the day moving my desktop computer setup into the office (again via the bus system) and installing needed updates so I'll be ready to go tomorrow. After relaxing in the apartment a bit I went for a little walk to visit a small collection of bus stops I missed on my previous trip in that direction.

Moving to work

For the past two weeks, I've worked nearly full-time on CS course development from home. On Monday the professor will arrive in town and all staff will be colocated. I'll depart tomorrow afternoon and move into my apartment. Full-time work will resume Monday.

Full-time work begins

The time tracker for my full-time summer appointment opened yesterday. I did a bit of work then, but put much more time into it today. So far I've nearly completed my first task, which is to rewrite and improve a piece of the grading infrastructure. At this rate the summer should be extremely productive.

App hits 400 users, somehow

Despite the university being on break and most students leaving town, my bus app's install count has continued growing. It recently hit 400 users!

Clearing the backlog

Now that I'm back in the Quad Cities, I have some time to work on things I had previously deferred due to academics going on. Today I implemented an update to one of my programs that had been requested a few weeks ago. I'll see about deploying it tomorrow.

Summer development work begins

Yesterday I started doing some CS 125 development work. Even though my full-time appointment won't begin for a couple weeks, this semester's appointment is still in effect and there's some small items I can look into. So far I've tested out some possibilities for autograder infrastructure.

Assembly mostly worked

Sequencing results for my last batch of plasmids came in yesterday. Most of the new ones worked, but a couple have extra mutations and one failed to sequence, indicating that the assembly probably failed. Nevertheless, 7 or 8 of the 10 are ready to go.

Out of the dorms

This morning I packed my remaining items together and left campus. That's the end of my two-year stay in University Housing - I'll move into an apartment this summer and a different one in the fall.

Preparing to leave

I spent pretty much all of today moving stuff around in preparation to move out of University Housing tomorrow. The CS 125 professor is letting me store some stuff in our future workroom, so I hauled my appliances into there, one at a time, using the bus system. The current occupants of my summer apartment let me store a bit more stuff, so I hauled over my large computer equipment using a similar method. That should make it much easier to move out and, later, in to my apartment since I won't have to manage as much stuff in transit.

Miscellaneous work

Today was one of two full days on campus between my end of finals and departure. In the morning I went to lab to set up the sequencing for nine of my plasmid purifications. Results from those should come in tomorrow evening. Then I met with the CS 125 professor to discuss work related to our summer projects. In the time in between, I worked on some data analysis for a graduate student in the lab. Finally I picked up my apartment key and arranged to store some of my equipment there in my absence from campus.

Finals done

This evening I took the MCB 252 final exam. With that, I'm finished with all class work for this semester. In the remaining time before I depart campus, I need to stop by the lab to organize some things, get the keys to my summer apartment, meet with the CS 125 professor, and possibly find a space to temporarily store some stuff.

Free time for app development

With the long space between final exams, I currently have very little academic work to do. So I took some time yesterday and today to work on my bus app a bit. I made the stops list show a short summary of what routes serve each stop and improved its existing display of the new few departures for favorited stops. I also added an in-app feedback form so users could conveniently send thoughts and suggestions.

Half of exams done

Today I took the MCB 253 and MCB 300 final exams. Both went well, though I was very tired after the second. After handling a few emails and a bit of studying for my CS 233 exam tomorrow, I went walking on my quest to visit all the town's bus stops. On this trip I covered 8.6 miles. I've now visited over half (51.7%) of all the stops.

Busy Reading Day

Today was Reading Day, the day on which neither final exams nor classes are held. Despite the break, I was busy. In the early afternoon I helped judge the CS 125 project fair. Immediately after that I attended a get-together for a University committee I'm on. Then I went back to the dorm to study and process emails. Tomorrow morning and afternoon I have exams.

Assembly worked at last

Today in lab I did a miniprep of yesterday's cell pellets using a completely different purification kit. The new procedure was straightforward and went well overall. (The handbook even gave me a new tip on easily resuspending cells.) I was relieved to find that the results had great DNA concentrations relative to the volume I eluted in. The cultures grown in small tubes had lower yield as expected, with one set on the edge of useful concentration, but the purification clearly worked. Sometime next week we'll send these plasmids for sequencing.

Fourth assembly attempt continues

I think I'm now on my fourth attempt at cloning and purifying DNA for my last five splice variants. Today I stopped by the lab to take yesterday's liquid cultures off the shaker and pellet them. We ran out of our normal culture tubes so I had to use small ones; those didn't yield as large pellets but it should be sufficient. Tomorrow I'll use a completely different, new purification kit to attempt the DNA harvest.

Harvest failed again

Today I did another DNA preparation from last Friday's frozen cell pellets. It started off well - the cells were easy to resuspend - but when I finished and measured DNA concentration I got the same poor results. I started liquid cultures (again!) from the last set of plates. I'll pellet them tomorrow and probably harvest them with a different miniprep kit on Wednesday.

The last week begins

Suddenly there are only three days of instruction left in the semester. Tomorrow is pretty regular, but then there's a deluge of meetings, presentations, events, then final exams.

CS registration might not be possible

Next semester I'm hoping to take CS 241, System Programming. Like many CS classes, it's restricted by major/college for a time, in this case becoming generally available this coming Monday. Unfortunately, the only one of its two lectures I can attend (due to time conflict from a one-lecture core MCB class) is now full. I'll keep an eye on it in case someone drops, but I might not be able to take it next semester. There may be other interesting, non-core, CS classes available to me, though - I'll look into that.

Reassembly continues

Today between class and the start of a lab meeting I quickly pelleted the liquid cultures I started yesterday evening. All fifteen had growth, so on Monday I can try harvesting DNA again.

Reassembly going smoothly so far

This afternoon I stopped by the lab to check the plates I started for redoing plasmid assembly. There were numerous colonies (more than was convenient to count) on each plate except the negative control, which is all as desired. I started some liquid cultures immediately - without refrigerating the plates like I did last time - and will turn those into cell pellets tomorrow.

Trying assembly again

Since my last attempt at assembling plasmids for my last batch of splice variants failed, I tried again today. Just in case my last Gibson assembly was bad, I redid that this time and transformed into freshly purchased competent cells. Tomorrow after class I'll go in and see if colonies grew.

Helping more in lab

Another person in my lab needs to do some moderately tricky data analysis, so I volunteered to help. The task is well-defined, so it will be easier to make progress than with my previous collaboration. (Which I should spent more time on after exams end, hmm.)

Yet more exams

In the less-than-two-weeks prior to the end of instruction, CS 233 is holding two non-final exams. One was tonight: its one and only paper exam, known for being very difficult, which it was indeed. The other is this coming weekend, covering similar material but in short answer and multiple choice format.

Walking again

After several hours fiddling with a CS project this morning, I decided to take advantage of the beautiful weather and go walking again on my quest to see all the bus stops. There was a run of stops out east remaining, so I went that way out to the Urbana Walmart, then back along a slightly different route to pick up a few straggling stops I didn't get to on my last venture that direction. Since no buses ran today due to the Easter holiday, I had to go the entire way back on foot, for a total of 9.6 miles, my longest venture so far. In all I've now visited ~520 stops (47.2% done).

Many projects

With the end of the semester approaching, I'm currently handling several different projects. CS 233 has a contest involving assembly programming, its honors section has the FPGA final project, and MCB 253 has a final paper and poster. There's also a couple projects I'd like to make progress on for CS 125 development before the summer. Lots of work!

Undergraduate Research Symposium

This morning I presented my poster at the Undergraduate Research Symposium. I was assigned to the earliest session, so there was only a modest amount of people there, but a few wandered by to talk to me. One was a bioinformatician who was considering using Pac-Bio sequencing - the sequencing method that produced that data I worked with - so we discussed considerations for its use. After my session ended, I rolled the poster back up and stored it in the lab, where we'll put it up tomorrow.

Further plasmid problems

My second attempt at plasmid purification for my last five splice variants again yielded very poor results. Today I did a PCR on the results to see if there's any relevant DNA in those tubes at all. This is somewhat confounded by using a different (cheaper) polymerase with which I have no experience - hopefully I picked a reasonable annealing temperature - so a previous high-concentration tube was used as a positive control. We'll find out Friday or Monday, depending on when I have time to run the gel.

Housing for the fall

I've decided to leave the dorms in favor of an apartment, starting this fall. My group of four guys has selected a place on the west side of campus, approximately the same distance to class as my current dorm. I'll have time over the summer to adapt to apartment life before classes begin again.

Poster printed

When I got up this morning, I saw an email informing me that the poster I submitted last night had been printed. So after class today, I stopped by the printing facility to pick it up. It looks very sharp. Conveniently, it came in a clear plastic roll so I can safely transport it even if there's rain.

Poster done!

Today I finalized by poster by improving one figure and finagling some tiny alignment details. After sending it to my grad student for another quick review, I submitted it to the printing service!

Poster feedback

Today I showed my poster draft in a lab meeting and practiced explaining it to people. I learned some details of the sequencing method involved, in case people ask about that. We also identified some adjustments which I will make tomorrow. Overall it's going very well!

Poster practice

Tomorrow in lab meeting I'll show a draft of my poster to the group for feedback. To facilitate this I've printed out handout-sized copies of it (for annotation) and created a slide deck with one figure per slide for easy visibility. I should probably submit the final poster for printing by Monday so it can be ready for the symposium Thursday.

Retrying transformation

This afternoon in lab I restarted the process of getting plasmids of my last five splice variants. Fortunately I had kept the Gibson assembly mixes, so I didn't have to go all the way back to that step. I transformed bacteria, plated them, and will check for growth tomorrow morning.

Exams over for now

Tonight I finished this run of three exams by taking an MCB 252 midterm. Tomorrow is going to be a long day from regular-ish work and events, but then I get to relax for a while.

Delay in getting plasmids

This afternoon I went into lab to harvest DNA for my last five assemblies. Everything went mostly as normal until I measured concentration afterward and found very little DNA. There's probably some there in four of the five cases, but not even enough to sequence. Fortunately I kept the Gibson assembly mixes so I can easily transform some more bacteria and try again on Wednesday.

Series of exams

This week I have three exams in a row: CS 233 earlier today, MCB 300 tomorrow morning, and MCB 252 Tuesday evening. CS was straightforward as expected. After the MCB exams, I have a lot of things going on Wednesday, but after that I get to relax for a while.

Further poster development

Yesterday I continued working on my poster by applying some layout suggestions from my grad student mentor. Whitespace is much more consistent now and I think it looks much better. I sent a draft to the PI for review.

Mostly registered for next semester

Fall registration opened Monday for me, so I went ahead and added all the classes in my plan. The MCB ones all went through, of course, but the CS one is still closed to non-majors. I'll have to wait until the end of the month for that one. So far I've been able to get the seats I need - hopefully that will continue.

Preparing the rest of the plasmids

Previously I assembled, grew, and purified a batch of five plasmids. The other batch of five has been assembled and I'm now working on growing it in bacteria. There was the hiccup of some plates producing no colonies earlier this week, but I redid those yesterday and now have a few colonies for each plasmid.

Sublease confirmed

Previously I found a good deal on an apartment sublease for the summer, since I'll be spending a lot of time in town for a job. I viewed the apartment and signed the lease.

More poster progress

Last night I put together all necessary information into my poster and sent the draft to my grad student mentor for review. I got feedback today, implemented as much of it as possible, and sent the revised draft back. The layout is now much more comprehensible, but there's still a ways to go.

Yet more walking

Yesterday it was nice out and I had finished all necessary work, so I went out walking on my quest to visit all bus stops in town. This time I went east almost until the edge of the town, past some residential areas. I then doubled back and went north to visit a few stops left behind by previous trips. When I was done, there was no nearby bus to take me back to campus - it being near the end of daytime service on Sunday - and I had to walk a ways more to encounter any active route.

 The entire southeast quadrant of the map is now clear of unvisited stops. I've visited 494 stops (44.5%) so far.

Got a summer job

This week I received an offer to work full-time as a CS course developer for 10 weeks over the summer. I accepted and started making arrangements to stay in town. I found a very good deal on an apartment sublease and began filling out the paperwork with its tenant.

Assignment development done for the semester

Yesterday, the CS class I'm on staff for released its last autograded assignment of the semester. It's mostly a rerun from last semester, so the office-hours course assistants should be well equipped to help students. My work as assignment maintenance developer therefore seems to be done. Soon I'll see what other projects I can help out with.

Poster progress

The last couple days, I started putting together the poster I'll present at the Undergraduate Research Symposium in mid-April. I collected some figures, wrote a bit of explanatory text, and put it into a rough layout. There's still more to add, and I fortunately have the space for it.

Planning for next semester

Yesterday I worked out a possible class schedule for this fall. It contains four classes for a total of 13 credit hours: Biochemistry, Cell Structure & Dynamics, Experimental Microbiology, and System Programming. Biochemistry and System Programming are known to be tough, so I think staying at 13 hours is reasonable, especially since I'll continue a couple credits' worth of work in the research lab. I'll be able to register for all except the CS class on April 1.

Back to lab

This afternoon I went into lab. Sequencing results came in a while back for my Gibson assembly products, so I examined those. A couple seem to have worked perfectly fine, but not all. On one plasmid, the region of reliable sequence didn't quite reach the region of interest, so I don't know for sure whether my desired deletion was achieved. On another, the deletion was perfect but a random single-base change happened to produce a stop codon, which would terminate the protein early. Even the good plasmids had one or two single-base changes, but nothing catastrophic.

Back to walking

After arriving back on campus this afternoon and doing a little work, I took advantage of the nice weather to go walking again on my quest to visit all the town's bus stops. Long-term reroutes created two new stops on campus, so I started out by going directly to them. Illinois Terminal, a central passenger terminal, was somewhat nearby, so I proceeded to visit that area. Then I went west into Champaign mostly along one road, headed back east to the Terminal along another parallel road, and took a bus back to the dorm. On foot I covered about seven miles. I've now visited >450 stops total, 41% done.

Break is over

On my last day of break, I finished up a little course development work. This last autograded assignment should be about ready to deploy, over one week in advance of its release to students. Other than that I didn't do a lot of school-related work, so there are some things to take care of when I return to campus tomorrow.

One more day of break

Today I took care of my last business-related appointment for the break and did a bit more CS course development work. Tomorrow is my last full day in the Quad Cities before I return to campus Sunday. I'd like to get a draft of my Undergraduate Research Symposium poster mostly done before then.

Assignment development almost done for this semester

This semester, my primary duty on CS class course staff has been to prepare programming assignments for students. There's now only one more autograded one left to run. My part in it is nearly done: it's been converted to our new format and I only need to polish a couple things, which I may get done tomorrow. Once it's done, there will probably be a different kind of project for me to work on the rest of the semester.

Work over break

I got to mostly relax the last two days, but now I need to start handling all the work I had planned for the break. Today I went to the office to take care of several IT-related things. Tomorrow and Thursday I'm going to teach chess, then on Friday I have another IT consulting meeting. Sometime this week I need to prepare a poster to present at the symposium in April.

Back for spring break

After lectures as usual today, I packed up some items and headed back to the Quad Cities. I've been back for a few hours now and have just relaxed so far. During break I have a lot of work to handle: chess tutoring, IT consulting, and preparing a poster for presentation.

Quick run

Today was very warm compared to recent weather, so after class I took the opportunity to go walking. I mostly went down Urbana's Main Street, past some shops and residential areas. As I was going along, I remembered that one trip per day of a common campus bus route is special in that it transmutes into a different route mid-trip. I wanted to see exactly how that happens, so I reversed direction and went back towards the start of that trip, but to get there I had to move decently quickly. After a bit of a run, I arrived at Lincoln Square with 5 minutes to spare. Sure enough, the bus had a different headsign - "Illini Union only" instead of "FAR/PAR only" - and changed its displayed route mid-trip as I rode it back to the dorm. I've now visited 400~ (36%) of the bus stops in town.

Sequencing the results

Today in lab we placed the sequencing order for the plasmids I purified Monday. The order turned out to be complicated because the different plasmids' regions of interest were all over the place, so I needed to provide eight distinct primers for the five plamids so that each plasmid could be sequenced in two directions. Results should come in sometime on Friday, but I will be on spring break then, so I'll see them in a couple weeks.

First batch of plasmids ready

Today in lab I harvested the DNA from the bacteria that were growing the first five of my ten desired new plasmids. I had grown three liquid cultures of each, for a total of 15 tubes. Happily, all 15 seemed to work - every tube had a usable amount of DNA and most had quite high concentrations. The only downfall is that the one box I've been using for tubes related to this project is now too full to hold all of them!

Quick continuance of assembly

Today after lab meeting, I briefly stuck around to move some bacterial colonies from yesterday into liquid cultures. That will provide many more identical bacteria from which the desired plasmids can be harvested.

Assembly good so far

This morning I stopped by the lab to see if my transformed bacteria had grown. They did indeed, on all five plates, suggesting that the assembly of those five plasmids worked correctly. Tomorrow I'll use those colonies to start producing large amounts of the plasmids.

Assembly begins

Today I put together the Gibson assembly reactions for five of the ten plasmids we're interested in. I then transformed the resulting (hopeful) plasmids into bacteria and started growing them on agar plates. I'll see tomorrow morning if things worked.

Assembling soon

This afternoon in lab, I checked the concentrations of the PCR purification products from last Friday. The purification worked; there's plenty of DNA. I did another quick processing step and planned out the procedure to assemble the pairs together. That will happen Wednesday and the final plasmids should be ready early next week!

Still preparing assignments

Tomorrow the CS class I'm on staff for will release its next two-week assignment. This one didn't require as much from me as the previous because it already had the Android app ready. I just wrote the Android test suite and rearranged the project files for the current autograder version. I got a head start on updating the final autograded assignment, which is a rerun of the one I helped write new last semester.

Exam week

This coming week is going to be intense. I have a CS 233 exam tomorrow - not so hard - but then MCB exams Tuesday evening and Wednesday morning. Tonight I briefly reviewed MCB 300 and will continue doing so tomorrow.

Almost time to assemble

Today in lab I purified the PCR products from Monday. I did not have time to measure their concentration, but I will do that next Monday. Once I make sure that I actually have all the fragments needed, I can start putting together the halves of the ten new plasmids.

Course development plans expanding

This morning I met with the professor of the CS class I'm on staff for. The class is going to be changing over the next few semesters, especially in the assignment department (which I've been working on this semester). That means there's a very large new project for me that will be very important for next semester. Exciting!

Presenting in April

Today I got an email from the Office of Undergraduate Research informing me that my application to the Undergraduate Research Symposium was accepted. At the symposium in April, I'll be presenting a poster about my research. I'll need to have a draft ready soon - the lab scheduled a practice talk for me in March.

Possible summer plans

The lab asked me about summer research fellowships - they suggested that I stay around and do research this summer. We investigated a bit and found that the normal biochemistry student research fellowships aren't an option because I'm not yet far enough along to have taken the core biochemistry class. I have, however, found another grant possibility through the university's Office of Undergraduate Research, which I may apply for. If that works out, I might be staying on campus this summer.

Plasmid assembly continues

Last week's production and purification of the first half of my desired plasmids worked well. Today I started making the second half by running another 30-tube PCR. On Wednesday I'll run a gel to see if the PCR worked. The full plasmids could be ready by sometime next week.

Another assignment's development begins

The current two-week assignment in the class I'm on staff for is now in its second week. So we've started planning for the next assignment, which is a modest update of an assignment from the semester I took the class. I did the simple rearrangement parts of the update today and will begin adding the new parts soon.

Walking in the rain

Today seems to have been the last day of reasonably warm weather before it gets cold for a long time again, so despite the rain I took the opportunity to go walking. I went directly east for a while through places I had been before, then went south past some shopping centers, then further past some residential subdivisions. I covered 5.7 miles today and have now visited 35% of the bus stops in town.

Assignment correction

The latest CS assignment I helped update was released to students on Monday. It looked like it came out quite nicely. But tonight I was helping a student with an issue and I realized that I made a small mistake in the autograder. My intent was to allow a certain part that would usually be dependent on another student-written part to be tested in isolation, but for one test the dependency remains. It's not a huge deal, but it would have made students' lives a little easier, and it can't really be fixed post-release. Oops.

App hits 300 users

The Android app I made about the local bus system jumped above 300 installs recently. Before it was hovering around 260, but earlier this week the bus company's API had some temporary problems, which my app can handle better than most others.

Other MCB exam went well

Earlier today, scores came out for the microbiology exam I took earlier this month. I got 100% - a good start to the semester's exams!

Exams going well so far

The first MCB 252 exam's results came out a couple days ago: 97%. MCB 300's isn't graded yet, but I think it went well. Tomorrow I have the second CS 233 exam in the computer-based testing facility.

Primers here

All 20 primers we ordered Monday arrived yesterday. Today in lab I started a Gibson assembly by doing half the PCR reactions we'll need. On Monday I'll see if they all worked as intended.

Primers ordered

This morning I went into the lab and reviewed all my proposed primers with my supervisor. I found an error in the step prior to primer design, so I corrected that and adjusted the affected primers. Then we placed the order. They should arrive by Friday!

FPGA class starting

The CS 233 honors section (the one with the FPGAs) is up and running. Last week I met with my project partner at the computer center to do the introductory lab. Labs are now happening weekly. I did a preparatory worksheet for this week's lab tonight and will meet with my partner again soon.

New lab project starting

At the very end of last semester, my computer analyses suggested two new splice variants of the protein we're studying in lab. My supervisor suggested preparing plasmids of those and several other known splice variants. I've started some design/preparations for that and will probably begin the project this week!

Exam season begins again

It's now the fourth week of the semester, so exams are starting up in earnest. (CS 233 uses a different schedule of more exams that are smaller, so I had one of those already.) Tomorrow MCB 300 will hold its first exam during lecture time, so it will only take 50 minutes. Next Tuesday MCB 252 has a standard evening exam.

Warm weather walking

After an exam yesterday, I decided to take advantage of the warm weather by continuing my quest to visit all the town's bus stops by foot. The exam center was already on the north end of campus, so I continued north by a small park, following one route through a residential area until it crossed the territory of another whose stops I had mostly finished. That route has a loop served only a few times during the day, going by some industrial areas. I've now visited 360 stops (32% done).

Warming up

This week was very cold - so remarkably cold that the university canceled class on Wednesday for safety. Thursday was chilly too, but the next several days will feature highs in the 40s and 50s. That will give me an opportunity to continue my walking tour of all the bus stops in town.

Possibly presenting research

UIUC holds an Undergraduate Research Symposium every spring. My lab supervisor suggested that I present my bioinformatic work, so with his help I wrote an abstract and applied to present a poster. The symposium isn't until April, so I have plenty of time to put the poster together.

Course development up and running

This semester, I'm continuing on the course staff of an introductory CS class. My role is now officially the maintenance/development of auto-graded programming assignments. The first such assignment, written by the professor using a new testing approach I demonstrated, was released to students yesterday. There have been a couple snags, but they seem to be resolved now. The remaining assignments will be reruns from previous semesters with some polishing that I'll handle.

Not so light

I thought this week would be pretty light because of MLKJ day, but lab work has made up for that. I was in the lab yesterday between meetings and today after class. Over the last few days, we did a Western blot on cells containing the plasmids I prepared last semester. Although not perfect, the resulting images are the best I've gotten so far.

Added a class

My schedule is pretty light in credit hours this semester, so I decided to add the CS 233 honors section, which covers various extra topics and has a few extra labs. Notably, the final project involves Field-Programmable Gate Arrays. The first homework assignments covered error detection codes and CMOS logic. Very neat so far!

Light week

Today being Martin Luther King Jr. Day, there were no classes. Since there were no classes today, courses that hold some discussion/lab sections on Mondays cancelled them for the entire week. I therefore have no classes tomorrow or Thursday. That leaves plenty of time for lab work, which I did this afternoon and will continue tomorrow.

App use increasing

Last semester I released an Android app for the campustown bus system. For much of last semester, it hovered around 200 users. I noticed earlier this week, though, that it recently jumped to more than 230. I haven't been advertising it, but I did look a bit into Facebook ads and might deploy a few of those eventually.

Course staffing resumes

Tonight was the first meeting of the CS 125 course staff, which I joined last semester and will continue on this semester. It was mostly training for course assistants (people holding office hours and managing labs) but also had an overview of the assessments that will be given. The two-week assignment I helped write will be run again. A couple major assignments will be brushed up a bit and run again - hopefully I'll get to help maintain them.

Back up to speed

Classes started up again yesterday. I only had three then, but it was a moderately intense day anyway. CS 233 offered a visual/spatial skills test for extra credit, but the only times it was available were during class or my lunch break, so I took it instead of eating. The classes were mostly introductions instead of material, which is good because the ice makes it dangerous to get from one class far up north back down to another back on the main quad in 10 minutes. Fortunately I was only a minute late. After classes, I went to the lab to briefly discuss plans for the semester.

Another semester begins

I returned to campus this afternoon. I unpacked all my clothes and, after a while getting my dorm computer back up to date, went to the bookstore to pick up my textbooks. Then I went through the course startup checklist sent out for CS 233. That class has a collection of pre-lecture videos and a quiz for each lecture. I did the one for tomorrow (a brief introduction to logic gates and Verilog) and found it very interesting - the course should be a good time, though perhaps a lot of work.

Despite the semester starting tomorrow, I've heard nothing about my application to join the CS 225 course staff. I did some searching: apparently staff won't be finalized until the end of the first week.