# HG changeset patch # User Steve Losh # Date 1706627957 18000 # Node ID 7c104d1589c07747280bc1aa7be0ec5b029e3d96 # Parent 8f8448c4dafe5aa7036a430cfe40bd13b1473c0d Update diff -r 8f8448c4dafe -r 7c104d1589c0 README.markdown --- a/README.markdown Fri Jan 19 16:16:58 2024 -0500 +++ b/README.markdown Tue Jan 30 10:19:17 2024 -0500 @@ -208,3 +208,126 @@ * 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. +