# HG changeset patch # User Steve Losh # Date 1707858836 18000 # Node ID 91d2c44772ef34ed266fc298a8eba68b22c3f302 # Parent badccc49dcec0a2375ddbb5177daf3678020895b Split diff -r badccc49dcec -r 91d2c44772ef 2024.markdown --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/2024.markdown Tue Feb 13 16:13:56 2024 -0500 @@ -0,0 +1,361 @@ +[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.