# HG changeset patch # User Steve Losh # Date 1707406932 18000 # Node ID 55aa60130f5bfe2b485eb757d886e19067cda8df # Parent ac73155e84a8d56ba4e3ae5212fcf289dde86630 Update diff -r ac73155e84a8 -r 55aa60130f5b README.markdown --- a/README.markdown Sun Feb 04 18:33:52 2024 -0500 +++ b/README.markdown Thu Feb 08 10:42:12 2024 -0500 @@ -415,3 +415,55 @@ 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. + +Looked at some BWT transform videos. I think I understand it a little better +now, though not sure if I'll retain it. I need to write it down at some point +if I really want to remember it (is it worth it?). + +## 2024-02-05 + +Read part of the chapter on BWT in the Bioinformatics Algorithms textbook. +It's… really not great. They have a really weird way of presenting algorithms +that's long and rambly and does a lot of unnecessary work to actually explain +things. Sometimes they go on for a page about something trivial, and other time +gloss over major points. + +I think I need to find a better source to review for tomorrow. Found + which is actually pretty nice because it +shows how to *efficiently* do this, albeit with godawful terse C code. After +going through it and deciphering the stupid C programmer shortcuts… I think +I finally get it. At least the efficient compression and decompression side of +things. Took me a long time, but it feels good. + +BWT fried my brain, so I'm procrastinating the tedious BS522 homework til +tomorrow. Sorry, future self. + +## 2024-02-06 + +Slept late, missed BS522. Need to watch the VOD tomorrow. + +BI529 about BWT. Easy given that I figured it out yesterday, though there were +some new data structures that we'll need for string matching (which I still +haven't figured out — only the decompression). + +Had a stroke of luck with respect to the BS522 homework — they pushed the due +date back to Sunday (four more days) so I've got a few more days to deal with +it. That's a relief. + +BI545, about novel transcript identifications. + +## 2024-02-07 + +Spent a ton of time trying to decipher what the BI529 homework was trying to ask +for. Not fun. + +BI602. Paper was about using machine learning to predict CRISPR off target +scores for various sgRNA configurations. + +## 2024-02-08 + +BS522. Feels like we're moving incredibly slowly now, but the homeworks are +still painful. Very strange. + +BI529, BWT matching. Going to try to make sure I understand what's actually +happening here.