# HG changeset patch # User Steve Losh # Date 1710725282 14400 # Node ID da282038703d90f4359d4e9ae46044792ed7aa93 # Parent 899b6218714be79d0578651a981d66d487443dde Update diff -r 899b6218714b -r da282038703d README.markdown --- a/README.markdown Wed Mar 13 10:28:00 2024 -0400 +++ b/README.markdown Sun Mar 17 21:28:02 2024 -0400 @@ -399,3 +399,75 @@ ## 2024-03-13 Must have left my wireless mouse somewhere, need to try to find that today… + +Needed to update R to deal with bioinformatics backwards-incompatibility +garbage, the instructions at were +helpful. General process was: + +1. Add the GPG key for their Debian repo. +2. Add the repo line to `/etc/apt/sources.list`. +3. Update through `apt`. + +That worked okay. Then I had to update bioconductor to *its* latest version, +`BiocManager::install(version="3.18")`. Took a long time, but it seems to have +worked. + +That, of course, broke my nvim-r setup, because it started complaining about +`nvimcom` not being available for this version of R. Eventually I was able to +install the `nvimcom` thing from the `nvim-r` repo by running +`install.packages("devtools")` and then inside `nvim-r/R/nvimcom` running +`devtools::install_local()`. This *seems* to have worked and unfucked +everything, though I have no confidence that I haven't broken other things in +the process. R packaging does indeed seem to be pretty hellish, as I've heard. + +Found the mouse in BI545 class, thankfully. Now that I think about it, it's +probably worth buying a second copy of my Gamer Mouse™ at home to leave at the +lab. Attempted to do so and found that it's been recently discontinued, so +I have to pay a premium but thank god I can still find one. The hamster wheel +of backwards incompatibility turns ever on, even in the real world, I guess. + +Journal club class. Another machine learning tool for scRNA-seq. + +Watched 529 video for tomorrow. Guess we're starting on Profile HMMs. + +## 2024-03-14 + +BS522, over Zoom today. + +BI529, profile HMMs. + +Final PIBS504 session. + +## 2024-03-15 + +Had to use the core-imaged machine they gave us today (haven't used it since +the awful word doc writing for HG545). Took minutes to boot, then complained at +me to update teams (I've never used Teams on that machine). Then complained at +me to reboot, and when I said "Okay, reboot" it threw an "Error: can't reboot", +so I clicked start → reboot and it rebooted. Jesus. I guess I'll remember this +the next time Linux does something dumb. + +BI545. Lecture was on single cell data and ways to "integrate" it (I think this +just means ways to take multiple data sets and compare/contrast them, but it +wasn't super well defined). I mostly followed the general ideas, but there were +a lot of biology terms thrown in that weren't defined (although hey, I actually +did know what an astrocyte already is thanks to my rotation) and a lot of math +notation that was passed over too fast to really grok. + +## 2024-03-17 + +BI545 homework today, mostly implementing Baum-Welch. Looked around for some +resources on this, found which +really helped clarify the meaning of the forward/backward/forward-backward +values in my mind: + +* Forward (called α in the video): given the sequence we've seen so far, what's + the probability we're in this state? In their robot example, if I see blue + carpet I know I'm probably in my bedroom or den. +* Backward (called β in the video): given the sequence we're *going to see*, + what's the probability we're in this state? Continuing the example, if the + next state is a red rug I know I'm in the living room or the bedroom. +* Forward-Backward (called γ in the video): combine both forward and backward (α + and β) to find the most likely state. In the example, α says bedroom or den + and β lets me rule out the den. +