# HG changeset patch # User Steve Losh # Date 1707858826 18000 # Node ID badccc49dcec0a2375ddbb5177daf3678020895b # Parent ae81801606d81d6d7e2945bca12bf8dfe1add900 Update diff -r ae81801606d8 -r badccc49dcec README.markdown --- a/README.markdown Sat Feb 10 16:53:16 2024 -0500 +++ b/README.markdown Tue Feb 13 16:13:46 2024 -0500 @@ -5,366 +5,6 @@ [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: - -* -* -* - -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: - - -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.