# HG changeset patch # User Steve Losh # Date 1710879128 14400 # Node ID 8f1af69d38e3e731beb94f504a13fb348af8b4de # Parent ae7af098ab4916d410a9a3e923eb1b0f83386231 Update diff -r ae7af098ab49 -r 8f1af69d38e3 2024.markdown --- a/2024.markdown Tue Mar 19 16:10:17 2024 -0400 +++ b/2024.markdown Tue Mar 19 16:12:08 2024 -0400 @@ -359,3 +359,297 @@ 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. + +# February 2024 + +## 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. + +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. + +BI545, hodgepodge of various topics (RNASeq contamination, GEO databases?). +Trying to install the R packages they told us to install at the beginning of +class using the cluster was an absolute mess, because 50 people all hitting the +login nodes and doing a ton of file IO slows everything to a crawl. I ended up +doing things locally, which was much faster. + +Started reading the paper for journal club next week, about prediction +transcriptional response to genetic perturbation. + +## 2024-02-10 + +Watched BI529 videos. + +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. + +BS522 lab. + +## 2024-02-14 + +Reading the paper for BI545 on Friday. They're trying to figure out the cause +of undiagnosed rare muscular diseases using RNA seq to look for alternative +splicing events. Noticed that figure S6 is confusing because they say in the +paper the median number of potentially pathogenic splice events per sample for +the "all genes" category is 190, but the S6 figure caption says 105, and the +figure itself looks like the median in the box plot is more like 250. So… which +is it? Finished the paper up to the methods section, will take a look at that +tomorrow I think. + +## 2024-02-15 + +BI529 in the morning. Managed to finish it in class at the end with some hints +from Alan. Wasn't too bad once I understood what they actually wanted. + +## 2024-02-16 + +BI545. This is the class where we had to read the paper about using RNA seq to +find novel splice isoforms in patients with undiagnosed muscular diseases. Also +getting some information about the group project. + +Figured out how to get R working with Vim. I should have done this months ago, +now that I've got it set up it's no longer nearly as painful to work in R. The +trick was realizing that base R running in a terminal, *on its own*, can open up +a plot window itself. So I don't have to do any horrible workarounds to get +plots visible, they just appear in a window that I can put wherever I want. +Maybe BS522 homework won't feel so painful now. + +## 2024-02-17 + +Did the BS522 homework. This one wasn't as mind-numbing as the last one, +thankfully. Only a tiny bit of R involved, but I can already tell I'm loving +the Vim setup with it. I can edit my code and LaTeX in the same editor, imagine +that. + +## 2024-02-18 + +Read some of the paper(s) for journal club this week. + +## 2024-02-19 + +A bunch of homeworks got rescheduled, and now everything is due on Friday. Ugh. + +Puttered around making a `reductions` function in the evening. Turned out to be +tricky if you want it to work like CL's actual `reduce`, i.e. supporting +`start`, `end`, `key`, `from-end`, and `initial-value` properly. I think I've +got something working, though it would also be nice to add a `result-type` +argument so you could ask for a vector directly though. + +## 2024-02-20 + +BS522. Another day on multiple regression, this time they mentioned continuous +vs continuous but otherwise it still just feels like treading water. I feel +like we got everything thrown at us in the first week and have been stalled on +the same stuff ever since. + +BI529. This week was much easier, maybe because I slowed down and read the +description more carefully first to try to + +* Try to figure out the biology behind what we're actually implementing. Way + too easy to treat the problems as a black box, but I'm actually getting to the + point now where the biological context *helps* me, rather than overwhelming + me. Progress? +* Identify which things they're going to handwave over in the implementation + (e.g. today we just compare *all* genes with *all* SNPs, not the ones near + them like you'd have to do in reality). + +Anyway, reading carefully at the beginning saved me going down a couple of +rabbit holes along the way. Need to remember to do the same next time. + +BI545. ChIP-seq. + +PIBS800, about funding after the PIBS year. Need to remember to register for +604 as soon as I'm able. + +* Figure out who the graduate coordinator is, check in with them once per term + about funding/appointment changes etc. + +Funding mechanisms: + +* Fellowship, etc. Paid through financial aid system. +* Training grants. Paid through financial aid system. +* Graduate Student Research Assistant (GSRA), paid through HR. +* Graduate Student Instructor (GSI), paid through HR. + +EdM stuff: + +* Need to be in PhD lab and program as of July 1. +* Make sure rotation 4 is done in EdM (I think we did this long ago). + +## 2024-02-21 + +Found and might sharpen +the LaTeX saw a little bit this morning before I dive back into stuff. I think +I'm pretty invested in LaTeX at this point, and aside from the snippets thing +I use almost everything there already, so it might be a good effort/reward +ratio. + +Went through the first part, about snippets. After some ridiculous yak shaving +(apparently the obvious, reasonable directory name `snippets` is special-cased +to be parsed as some *other* snippet plugin's syntax and so if you dare to name +the directory the obviously correct name it'll fail with a completely +inscrutable error) I got it working. Going to have a go and see if it's worth +adding snippets back into my life, at least for LaTeX — I haven't really used +them since the Textmate era. + +Journal club class. Paper was about deep learning for EEG data. + +## 2024-02-22 + +BS522 in the morning. + +BI529, about Markov chains. I've done these before so today was pretty basic. +Played around with some Python syntax to see if I could golf things down a bit. + +Finished up the BS522 and BI545 homeworks, no idea why it felt like pulling +teeth this time — they (mostly) weren't as bad as the previous ones. + +Also finished BI529 code (still need to do the writeup). Ended up being pretty +easy overall, a lot more straightforward than the previous homework, which was +nice. + +Finally got irssi set up on my new laptop. It's been months, I should have done +this before now. Oh well, at least it's done. + +## 2024-02-23 + +Cleaned up and submitted BI545. Going to review later today with folks and +maybe resubmit, but at least there's something up there now in case I forget. + +BI545, this time about ATAC-seq. I feel like it was a good introduction to the +assay, but am cautious about how in-depth the labs/etc will go. + +Journal club review. Last one for me, so I'm done with the reviews for the rest +of the semester, which is nice. + +Office hours to try to understand what the 545 homework wanted after submitting. +I still have no idea if I was correct. Oh well. + +Finished BI529 so I don't have to worry about it over the break. + diff -r ae7af098ab49 -r 8f1af69d38e3 README.markdown --- a/README.markdown Tue Mar 19 16:10:17 2024 -0400 +++ b/README.markdown Tue Mar 19 16:12:08 2024 -0400 @@ -5,297 +5,6 @@ [TOC] -## 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. - -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. - -BI545, hodgepodge of various topics (RNASeq contamination, GEO databases?). -Trying to install the R packages they told us to install at the beginning of -class using the cluster was an absolute mess, because 50 people all hitting the -login nodes and doing a ton of file IO slows everything to a crawl. I ended up -doing things locally, which was much faster. - -Started reading the paper for journal club next week, about prediction -transcriptional response to genetic perturbation. - -## 2024-02-10 - -Watched BI529 videos. - -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. - -BS522 lab. - -## 2024-02-14 - -Reading the paper for BI545 on Friday. They're trying to figure out the cause -of undiagnosed rare muscular diseases using RNA seq to look for alternative -splicing events. Noticed that figure S6 is confusing because they say in the -paper the median number of potentially pathogenic splice events per sample for -the "all genes" category is 190, but the S6 figure caption says 105, and the -figure itself looks like the median in the box plot is more like 250. So… which -is it? Finished the paper up to the methods section, will take a look at that -tomorrow I think. - -## 2024-02-15 - -BI529 in the morning. Managed to finish it in class at the end with some hints -from Alan. Wasn't too bad once I understood what they actually wanted. - -## 2024-02-16 - -BI545. This is the class where we had to read the paper about using RNA seq to -find novel splice isoforms in patients with undiagnosed muscular diseases. Also -getting some information about the group project. - -Figured out how to get R working with Vim. I should have done this months ago, -now that I've got it set up it's no longer nearly as painful to work in R. The -trick was realizing that base R running in a terminal, *on its own*, can open up -a plot window itself. So I don't have to do any horrible workarounds to get -plots visible, they just appear in a window that I can put wherever I want. -Maybe BS522 homework won't feel so painful now. - -## 2024-02-17 - -Did the BS522 homework. This one wasn't as mind-numbing as the last one, -thankfully. Only a tiny bit of R involved, but I can already tell I'm loving -the Vim setup with it. I can edit my code and LaTeX in the same editor, imagine -that. - -## 2024-02-18 - -Read some of the paper(s) for journal club this week. - -## 2024-02-19 - -A bunch of homeworks got rescheduled, and now everything is due on Friday. Ugh. - -Puttered around making a `reductions` function in the evening. Turned out to be -tricky if you want it to work like CL's actual `reduce`, i.e. supporting -`start`, `end`, `key`, `from-end`, and `initial-value` properly. I think I've -got something working, though it would also be nice to add a `result-type` -argument so you could ask for a vector directly though. - -## 2024-02-20 - -BS522. Another day on multiple regression, this time they mentioned continuous -vs continuous but otherwise it still just feels like treading water. I feel -like we got everything thrown at us in the first week and have been stalled on -the same stuff ever since. - -BI529. This week was much easier, maybe because I slowed down and read the -description more carefully first to try to - -* Try to figure out the biology behind what we're actually implementing. Way - too easy to treat the problems as a black box, but I'm actually getting to the - point now where the biological context *helps* me, rather than overwhelming - me. Progress? -* Identify which things they're going to handwave over in the implementation - (e.g. today we just compare *all* genes with *all* SNPs, not the ones near - them like you'd have to do in reality). - -Anyway, reading carefully at the beginning saved me going down a couple of -rabbit holes along the way. Need to remember to do the same next time. - -BI545. ChIP-seq. - -PIBS800, about funding after the PIBS year. Need to remember to register for -604 as soon as I'm able. - -* Figure out who the graduate coordinator is, check in with them once per term - about funding/appointment changes etc. - -Funding mechanisms: - -* Fellowship, etc. Paid through financial aid system. -* Training grants. Paid through financial aid system. -* Graduate Student Research Assistant (GSRA), paid through HR. -* Graduate Student Instructor (GSI), paid through HR. - -EdM stuff: - -* Need to be in PhD lab and program as of July 1. -* Make sure rotation 4 is done in EdM (I think we did this long ago). - -## 2024-02-21 - -Found and might sharpen -the LaTeX saw a little bit this morning before I dive back into stuff. I think -I'm pretty invested in LaTeX at this point, and aside from the snippets thing -I use almost everything there already, so it might be a good effort/reward -ratio. - -Went through the first part, about snippets. After some ridiculous yak shaving -(apparently the obvious, reasonable directory name `snippets` is special-cased -to be parsed as some *other* snippet plugin's syntax and so if you dare to name -the directory the obviously correct name it'll fail with a completely -inscrutable error) I got it working. Going to have a go and see if it's worth -adding snippets back into my life, at least for LaTeX — I haven't really used -them since the Textmate era. - -Journal club class. Paper was about deep learning for EEG data. - -## 2024-02-22 - -BS522 in the morning. - -BI529, about Markov chains. I've done these before so today was pretty basic. -Played around with some Python syntax to see if I could golf things down a bit. - -Finished up the BS522 and BI545 homeworks, no idea why it felt like pulling -teeth this time — they (mostly) weren't as bad as the previous ones. - -Also finished BI529 code (still need to do the writeup). Ended up being pretty -easy overall, a lot more straightforward than the previous homework, which was -nice. - -Finally got irssi set up on my new laptop. It's been months, I should have done -this before now. Oh well, at least it's done. - -## 2024-02-23 - -Cleaned up and submitted BI545. Going to review later today with folks and -maybe resubmit, but at least there's something up there now in case I forget. - -BI545, this time about ATAC-seq. I feel like it was a good introduction to the -assay, but am cautious about how in-depth the labs/etc will go. - -Journal club review. Last one for me, so I'm done with the reviews for the rest -of the semester, which is nice. - -Office hours to try to understand what the 545 homework wanted after submitting. -I still have no idea if I was correct. Oh well. - -Finished BI529 so I don't have to worry about it over the break. - ## 2024-03-04 Back in Ann Arbor. Need to get in touch with the 545 group so we can get the @@ -515,3 +224,4 @@ Did some more StumpWM yak shaving between classes, fixing up broken mode line/sensor support, etc. +