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+
+# 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.