# HG changeset patch # User Steve Losh # Date 1707089632 18000 # Node ID ac73155e84a8d56ba4e3ae5212fcf289dde86630 # Parent 7c104d1589c07747280bc1aa7be0ec5b029e3d96 Update diff -r 7c104d1589c0 -r ac73155e84a8 README.markdown --- a/README.markdown Tue Jan 30 10:19:17 2024 -0500 +++ b/README.markdown Sun Feb 04 18:33:52 2024 -0500 @@ -331,3 +331,87 @@ 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 +I modified yesterday. Wanted to push that to the git mirror but the hg-git +mapping was fucked again, so I needed to run that janky `remap-hggit-mapfile` +thing I wrote ages ago. But I needed to port *that* to Python 3 to get it to +run on this laptop. Did that and finally unwound the stack of yaks. Ugh. +Final process to run the remapping is something like: + + cd src/foo + cd .hg + git clone https://github.com/sjl/foo gitrepo + cd .. + remap-hggit-mapfile . .hg/gitrepo + remap-hggit-mapfile . .hg/gitrepo > .hg/git-mapfile + +BS522. + +BI529. Going to release the first homework assignment today. The assignment +was tricky today — I think there's a bug in the doctest and/or their +implementation of the Eulerian walk. + +Continued watching a couple of APL videos. + +## 2024-02-02 + +Started reading the journal club paper for next week, about prediction of CRISPR +off-target effects. It's not very well-written, unfortunately — I'm not even +a page in and there are multiple typos. + +BI545. Lecture plus interactive lab on Great Lakes. The lab was okay, but +quite rushed because the lecture took a long time. I'm pretty decent at CLI +stuff so it went smoothly for me, but I still didn't have enough time to finish +in class. + +## 2024-02-03 + +Watched some BI529 videos for next week. Still need to finish up the homework. +Next week is BWT, which always breaks my brain, so I think I should probably +have a poke around tomorrow just to get my head around it again. I wonder how +it would be to implement in APL. + +## 2024-02-04 + +Finished the BS529 homework. Wrote a bunch of stuff about the confusing parts +in the summary document only to realize there's a one page limit. Oh well, it +was cathartic for me at least. + +Started the BS522 homework, but I just don't have the willpower to deal with the +tedium of this today. I'll get it done tomorrow.