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.