--- 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
+<https://james.fabpedigree.com/bwt.htm> 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 <https://www.ejmastnak.com/tutorials/vim-latex/intro/> 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.
+
--- 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
-<https://james.fabpedigree.com/bwt.htm> 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 <https://www.ejmastnak.com/tutorials/vim-latex/intro/> 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.
+