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[TOC]
-# January 2024
-
-## 2024-01-08
-
-Back from break. Started a new rotation (classes don't start for another
-couple of days). Feels good to be back.
-
-## 2024-01-09
-
-Another day of rotation before classes start. Getting my laptop set up to do
-actual work again.
-
-Looked around a little bit in Canvas. One of my classes doesn't seem to have
-posted anything yet, but I'm definitely registered so I think I should be good.
-
-Did a couple of tasks to get ready for classes tomorrow (though they don't
-*really* start til Thursday).
-
-Need to remember to bring things into the lab tomorrow:
-
-* Something to put my laptop on to raise it.
-* Headphones.
-
-## 2024-01-10
-
-Cleaned up my schedule and sketched out my TODO list, found all the rooms for my
-classes. Got one new building to find/learn: USB, the "Undergraduate Science
-Building". I think I've seen it before, never been inside though.
-
-First day of journal club. Main things I'll need to do are:
-
-* Ask two questions during the semester.
-* Two review sessions for particular papers.
-* Read over the rest of the papers.
-
-## 2024-01-11
-
-First two actual classes.
-
-BS521. Fairly straightforward. 8:30 AM sucks. Tried to change lab sections to
-something that works better with my schedule, but the class registration system
-is awful and won't let me swap things out for some reason, despite there being
-open seats.
-
-BI529. Need to watch videos (and do the embedded quizzes) before classes.
-Really awful high-pitched whine from something in the ceiling in the spot I sat
-in the room — need to move around and find a spot that isn't going to destroy my
-ears. Got both Great Lakes and my VM set up with Jupyter (I think) and
-accessibly by SSH port forwarding (e.g. `ssh -NAL 8888:localhost:8888
-slosh@gl1234 -J gl`) so we'll see how this goes during the next class I guess.
-
-Poked around at running `make docs` in a Lisp project with my new laptop and
-something in `d`'s Python dependency shitpile broke since I last built it, so
-I had to screw around with the guts of `d` to get it rendering again. I really
-need to rewrite `d` in a sane language.
-
-Attempted to set up printing in the lab, but of course it doesn't work on Linux.
-
-Downloaded the first 3 papers for journal club. Need to print them and start
-reading soon, at least for next week's.
-
-After going back and forth with someone about the BS522 lab section stuff, they
-realized they needed to grant me permission for that section. Once they did
-that I was able to swap it, so that's all set now.
-
-Read through chapter 1 of the BS522 textbook. It's… meh.
-
-## 2024-01-12
-
-Reinstalled Figlet and the `figlet-fonts` repo yet again on this new computer.
-Finally got around to writing a script to do the stupid install so I don't have
-to manually do it every time.
-
-Reinstalled ABCL on the new machine. Changed my scripts so they invoke `java
--jar /usr/local/bin/abcl.jar` directly instead of requiring
-a `/usr/local/bin/abcl` wrapper for no reason, so now all I have to do is
-download the binary distribution and move the two jars to `/usr/local/bin/`.
-
-Reinstalled ECL on the new machine. Trivial thanks to my notes, except the git
-tagging convention switched from `ECL-1.2.3` to just a bare `1.2.3`. My kingdom
-for consistency.
-
-Downloaded the textbook and marked down important dates for BI545 today so I'll
-be prepared for class.
-
-Running some of my project tests on the new machine resulted in `make: time: No
-such file or directory` because… apparently Debian doesn't include
-a `/usr/bin/time` by default? Wow. `apt install time` to get it.
-
-Read chapter 2 of the BS522 book. Mostly meh again.
-
-One thing I'd like to do some weekend that's been on my mind for a while is
-a small proof of concept web app with Lisp and HTMX. Would be good to poke
-around at it and see if I can make something reasonably easy to get up and
-running, in case I want to do something like that in the future. Stuff I'm
-probably going to need to choose:
-
-* Web server (almost certainly just boring old Hunchentoot)
-* Router
-* DB interface (probably Postmodern)
-* DB migrations (will write my own)
-* Template library (Djula is the obvious choice but has a shitload of deps)
-* Monocss style
-
-Also really need to write a simple FASTQ parser and bio seq library in Lisp, so
-I don't have to do everything with janky UNIX tools. Name idea: `skein`,
-because it's for strings that are a tangled/knotted mess. Should probably try
-to separate interface and implementation pretty well here so I can potentially
-plug and play different implementations in the future.
-
-Found my way to the BI545 classroom. These MSC/MSRB buildings are laid out like
-someone's first Dwarf Fortress build.
-
-First BI545 class. Mostly reading the syllabus and going through Molecular
-Biology 101. Feels quite basic after HG545 last semester, hopefully things will
-pick up as the course gets going.
-
-## 2024-01-15
-
-Tried to modify Pubmed search subscriptions but it looks like logging in via UM
-Oauth is broken, sigh.
-
-Finally got around to setting up keyboard shortcuts for a couple of my most
-commonly used `pass -c` commands. I should have done this months ago.
-
-Need to make a last-minute slide for myself for PIBS 800 when I get home.
-
-## 2024-01-16
-
-BS522 early. Mostly review of stuff from BS521 today.
-
-BI529. Most of the time spent getting Jupyter working and the data all
-downloaded. Need to find a better workflow here.
-
-BI545:
-
-* Slurm account: `bioinf545w24_class`
-* Scratch: `/scratch/bioinf545_w24_class_root/bioinf545w24_class/`
-* Turbo: `/nfs/turbo/dcmb-class/bioinf545`
- * `gsi/`: GSI's stuff
- * `sec001`: directories for each student
- * `shared`: read-only, shared data and stuff.
-
-Now basic UNIX/bash scripting stuff.
-
-Slurm `.sbat` script tidbit: use `my_job_header` for debugging info.
-
-Method for raw-dogging batch mode execution instead of writing an sbat: `sbatch
--c4 --mem=32G foo.sh`. Not sure I'll use that much, but good to know it's an
-option.
-
-Ate lunch during my short break today. Tuesdays are going to suck.
-
-Looked around again for how to integrate Jupyter and Neovim and found nothing
-good. Maybe I'll just suffer through using Jupyter for a class and not try to
-shave this yak.
-
-BS522 lab. Pretty simple, but gave lots of advice for the homework which will
-come in handy when I get to that. Sketched out a LaTeX file for it, but
-I really really need to get around to modularizing my LaTeX situation at some
-point — the copy/paste is getting untenable.
-
-## 2024-01-17
-
-Finished BS529 exercise. Looked at the solutions to figure out some of the
-fiddly bits, like the 1-based indexing from the GFF (I was right) and the GFF
-entry type (`CDS`, I was also right). The problem was I was dumb and forgot to
-reverse in the reverse complement. Welp.
-
-Went through the videos for BI529 tomorrow.
-
-BI602. Didn't get a chance to ask questions — this is going to be a very
-annoying part of the class.
-
-## 2024-01-18
-
-BS522. Started talking about simple linear regression. Mostly still review at
-this point.
-
-BI529. Talking about transcription factor binding sites, and fuzzy-matching
-motifs using Positional Weight Matrices (PWMs).
-
-Went to a lecture by my grandPI about the human skin microbiome, especially
-mapping the distributions of various populations across the topology of the
-human skin.
-
-Wrapped up BI529 after getting the clarification email. Today was more
-straightforward than the last class, probably in part by not having to mess
-around with Jupyter setup.
-
-Did a first pass at a read of the journal club paper for next week. It's an
-older ML paper whose results are… meh?
-
-## 2024-01-19
-
-BI545. The next few classes will be mostly RNA-seq data, especially focused on
-QC. Need to watch 2 videos in the slides before next time. Mostly a review for
-me at the beginning. Need to look into:
-
-* Ribodepletion as an RNA selection step.
- * This just means using probes with magnetic beads to select and pull out ribosomal RNA so it doesn't get sequenced.
-* Strand-specific library prep for RNA seq.
-
-## 2024-01-22
-
-Tried to watch the BI529 videos but they kept cutting out. Will retry later.
-
-Started the Biostat 522 homework. So far it's… meh. Still trying to find
-a Latex font setup I like. Going to try XCharter this time, it seems… slightly
-better than Stix? Really with I could use Rotation, but foundries gonna founder
-I guess.
-
-BI529 videos are still cutting out. Ugh.
-
-Watched the BI545 videos. Those were on Youtube, so that worked reliably.
-
-## 2024-01-23
-
-The roads and sidewalks are one giant sheet of ice today. This sucks.
-
-BS522. More linear regression stuff. He really rushed through the last few
-topics far too fast in the last couple of minutes of class — I think I need to
-review those slides myself to make sure I got what he was trying to cover.
-
-BI529. Gibbs sampling. Thursday will also be this topic, so if we finish today
-we can skip that day if we want.
-
-BI545. QC and such for RNAseq. Lots of various things to consider, but felt
-like a bit of a grab bag of topics.
-
-Read through the journal club paper again for tomorrow. Some ideas on
-questions:
-
-* How does the performance of their tool compare to a human doctor?
-* How robust is their data? E.g. what if someone has a heart attack outside of
- the hospital, could that be counted as a control?
-
-PIBS800.
-
-BS522 lab.
-
-## 2024-01-24
-
-Finally learned about `View > Panes > Console on Right` in R. Should have found
-this months ago.
-
-Reread the paper for BI602. Being forced to ask synthetic questions sucks
-a lot, but oh well.
-
-BI602.
-
-## 2024-01-25
-
-BS522. Many slides with walls of text and notation.
-
-BI529. Mostly done already, so just relaxing for a change.
-
-Started reading the paper for BI602 review session tomorrow.
-
-Poked around a little at implementing some of the 521 stuff in Common Lisp. It
-was trivial to port the first class, but I've now hit two stumbling blocks.
-
-Naive parsing of bioinformatics files like FASTAs is slow when you have a stream
-sandwich of a flexi stream wrapping a gzip stream wrapping a Lisp stream. Can
-likely live with this for now, and writing a real parser for some of the common
-formats (which would probably work directly with the binary and avoid the slow
-flexi stream layer) has been on my list for a while, so this isn't an
-insurmountable obstacle.
-
-The other snag I hit is the lack of Numpy. There are a bunch of linear algebra
-libraries in CL and they're all lacking. Oddly enough the one that seems to
-have the most promise for me is April, even though it would have the steepest
-learning curve at the beginning. I've poked around with it a bit before but
-maybe this is a good time to actually give it a real try. Need to go through
-some/all of:
-
-* <https://xpqz.github.io/learnapl/intro.html>
-* <http://archive.vector.org.uk/art10011550>
-* <https://microapl.com/APL/tutorial_contents.html>
-
-At least I shaved the input yak the last time I looked at it, so I can dive
-right in (as if I don't have enough other shit to do, but at least this is
-computery so it's actually fun to learn).
-
-## 2024-01-26
-
-BI545. More RNA seq lectures, talking mostly about how to normalize and account
-for non-biological variability when doing differential gene expression.
-
-BI602 review session. Was pretty fun and chill and cool. By far the best part
-of the class so far.
-
-Continued one of the APL tutorials. Pretty basic stuff, pretty much just
-getting my fingers used to the keyboard shortcuts to type basic stuff.
-
-## 2024-01-27
-
-Found a series of videos about using APL to build neural networks, which might
-be a fun thing to go through:
-<https://www.youtube.com/playlist?list=PLgTqamKi1MS3p-O0QAgjv5vt4NY5OgpiM>
-
-Watched the BS521 videos for Tuesday. Starting assembly with De Bruijn graphs
-which is going to be fun. Need to find those papers I read a while back that
-had a good summary of the process.
-
-## 2024-01-28
-
-BI545 homework. Long. The first two sections (biology/computer stuff) were
-easy, the last (experimental design) was rough.
-
-Started the BS522 homework. Going to finish it tomorrow I think.
-
-Went through some more of those APL videos. I'm actually liking it (and April)
-quite a lot. I feel like I might be actually motivated to learn this time
-because I can see things I would use it for now, as opposed to years ago when it
-was just a fun novelty.
-
-## 2024-01-29
-
-Finished BS522 homework. That was *tedious*. The inconsistent notation in this
-class is… not fun.
-
-## 2024-01-30
-
-BS522. Started multiple linear regression, mostly review for now.
-
-BI529. Today's assignment was pretty trivial after reviewing De Bruijn graphs
-last night, presumably it'll get more difficult when we actually use it on
-Thursday. We also figured out what the high-pitched whine in the room was
-coming from (one particular bank of lights), thank god.
-
-Spent some of the spare time to create a bug report for April and the April guy
-responded pretty quickly that I had indeed ran into multiple compiler bugs. If
-I could ever just use a computer and have it reliably work I would be so happy.
-
-BI545 on Zoom, mostly talking about how to measure the false discovery rate in
-a variety of different ways.
-
-PIBS800, about posters.
-
-Watched the BI529 video. It suggested we read the Velvet paper, which is funny
-because I already printed it out the other day intending to reread it.
-
-Did one or two more of the APL videos, now that I've confirmed I'm not crazy and
-it was a bug in APL. Got the forward pass working, though I need to learn to be
-even more precise than usual in APL I guess. When all your variables are like
-`ws, bs, w, b` then `1↓ ws` and `1↓ w` is an easy mistake to make, and I guess
-because everything is an array and every operator works on any shape of array
-that could even be conceivable for convenience you won't get any type errors to
-help you realize you did something stupid.
-
-## 2024-01-31
-
-Read the Velvet paper for BI529 tomorrow. Seems like what I remember, though
-I think I actually understand it better now. There are still a few bits I'm not
-100% clear on, but I think I get the general idea.
-
-BI602. This is the paper I reviewed the presentation for, and I asked something
-last week, so I think this week I really have nothing to do.
-
## 2024-02-01
Tried to commit my dotfiles this morning and had to commit to a subrepo
@@ -484,3 +124,30 @@
Finally did the absolutely mind-numbing homework 3 for BS522. Truly, truly
miserable. Result was eleven pages, much of which was manual plug n' chug
algebra to verify that R can, in fact, do math correctly. Very unpleasant.
+
+## 2024-02-11
+
+Did a chunk of the BI545 homework. Otherwise not super productive today,
+unfortunately.
+
+## 2024-02-12
+
+Finished BI545 homework.
+
+## 2024-02-13
+
+BS522. This class is too early. Spent all class talking about the special case
+of binary interaction variables, which felt like it didn't need a whole entire
+class just for that.
+
+Forgot to charge my laptop last night, so I'm at 50% in BI529. Welp. Managed
+to finish all but the last function, though the documentation was not
+particularly clear and I think they didn't expect us to handle certain edge
+cases they gave us. Finished that last bit of 529 right before 545 started.
+
+BI545. Another grab bag of stuff, none gone into a lot of depth, lots of magic
+incantations for how to perform analyses in R without explaining what everything
+is. Oh well. Checked my work with some folks after class and feel a bit better
+now.
+
+PIBS800, training grant fair.