# HG changeset patch # User Steve Losh # Date 1700073682 18000 # Node ID 665b6ddcdfd5e4ea0c72bf55355d2a2a7acba196 # Parent e2e3eb42c4300cee0e636d1109379b7181b505ae# Parent 4bd223543cdcdb3a3d8cc81bc0d64ebfbcf447a3 Update diff -r e2e3eb42c430 -r 665b6ddcdfd5 2023.markdown --- a/2023.markdown Tue Nov 14 16:16:35 2023 -0500 +++ b/2023.markdown Wed Nov 15 13:41:22 2023 -0500 @@ -1884,3 +1884,605 @@ and my calendar/TODO list was extremely tedious. I think I've got it all mapped out now though. +# October 2023 + +## 2023-10-01 + +Put up a bunch of stuff for sale on the PIBS list. Need to declutter my +apartment now that I've mostly moved in. + +Did a few hours of work on Lab 1 for BS521. Too much unproductive screwing +around in R trying to figure out how to get decent fonts. Should be able to +finish it up tomorrow though. Random notes jotted down from the process follow. + +Side-by-side figures in LaTeX: + + \begin{figure}[h] + \begin{minipage}[t]{0.48\textwidth} + \includegraphics[width=\linewidth]{figures/bp-histogram} + \caption{Distribution of blood pressure among participants.} + \label{fig:bp-histogram} + \end{minipage} + \hfill + \begin{minipage}[t]{0.48\textwidth} + \includegraphics[width=\linewidth]{figures/bp-nqq} + \caption{Normal QQ plot of blood pressure values.} + \label{fig:bp-nqq} + \end{minipage} + \end{figure} + + +Reasonable quantile plot in R: + + qplot <- function(filename, data, label, main, ...) { + n = length(data) + plot(((1:n - 1)/(n - 1)), sort(data), + type = "l", + main = main, + xlab = "Quantile", + ylab = label, + ...) + } + +QQ plot with the damn line in R: + + nqqplot <- function(data, ...) { + qqnorm(data, ...) + qqline(data) + } + +Reading in a CSV with specific column types: + + data <- read_csv("EPID_521_lab_data.csv", col_types="iddfiffdffdd") + +Note that this seems to give you a "tibble", whatever the hell that is. Some +kind of tidyverse thing? It's very confusing that everywhere you look there's +a hairball of a mess of base R, tidyverse, and ggplot2 and everyone just assumes +you understand which is part of what. + +Reordering levels: + + data <- mutate(data, diet=factor(data$diet, levels=c("Poor", "Fair", "Good", "VeryGood", "Excellent"))) + + +Removing rows with `NA`s for e.g. the `cot` column: + + data <- data[complete.cases(data$cot),] + +Histograms with specific bin widths, rather than a number of bins: + + hist(data$age, breaks=seq(from=15, to=90, by=1), main="", xlab="Age") + +Multiple box plots in one image: + + boxplot(bmi~sex, data=data) + +Marking and/or filtering on a boolean condition: + + data$locot <- data$cot <= 0.011 + locot <- subset(data, cot <= 0.011) + hicot <- subset(data, cot > 0.011) + +## 2023-10-02 + +HG545 review this morning. Need to go back and review the first module again +tomorrow since it's been a while. + +Finish BS521 lab 1, finally. That was a lot more work than I expected. + +Met with a professor about possible rotation. Need to chat with my advisor to +see if there's special paperwork I'll need. + +## 2023-10-03 + +BS521. Confidence intervals. + +BI500. Research writing. + +Finally got around to splitting my Vimrc into minimal and extra files, so I can +sync the minimal one to servers and not hate myself when trying to edit. There's +some jank involved around the colorschemes and `set termguicolors` but I think +have have something that should work. + +PIBS800. Mentor/mentee relationships. + +## 2023-10-04 + +Advising meeting. Need to do a couple of things in EdM and register for 602, +but I'm currently blocked on both by other folks so I'm good for now. + +HG545 exam. + +## 2023-10-05 + +Finished the HG545 exam last night. That was… deeply unpleasant. + +BS521. Hypothesis testing. + +BS521 reading. + +Read the paper for HG545. I get the general idea, and it seems like a pretty +clear experiment. I wonder how much we'll stick to the paper vs going off topic +this time. + +Needed to convert some PDF graphs to PNG to put in a presentation, but `convert` +was whining about some security crap: + + ><((°> convert n50.pdf n50.png + convert-im6.q16: attempt to perform an operation not allowed by the security policy `PDF' @ error/constitute.c/IsCoderAuthorized/421. + +Turns out there was a bug in ghostscript, which was fixed, but convert still +doesn't trust it so won't convert stuff. Great. Have to edit +`/etc/ImageMagick-6/policy.xml` and comment out these lines to make it behave: + + + + + + + + + +Skimmed through the slides for HG545 tomorrow. It's nice to be able to get +a preview of things again. + +## 2023-10-06 + +HG545, class was about splicing. I feel much better about this module thanks to +being able to prepare a bit with the preview last night. + +## 2023-10-07 + +Installed — might come in handy here and +there. + +## 2023-10-08 + +Reread the paper for HG545. It's… a little clearer now? Though honestly it +wasn't too bad before compared to the other papers. Just a lot of acronyms. +Got a list of things to ask. + +## 2023-10-09 + +HG545 this morning, about co/post-transcriptional modification. The downside of +having slides is that people put a ton of things on them and you can't take +notes fast enough. Need to go back over the slides and write down things once +I get home so I don't forget them. + +## 2023-10-10 + +BS521, hypothesis testing, p values, t distribution. + +BI500, code quality tips. Checked with Prof. Sartor and submitting a LaTeX PDF +for the references homework is fine. + +Pinged a few students in a lab I'm interested in to see if they're willing to +chat about their experience. Just need to nail down my third rotation and then +I'll be all set. + +Ordered a used copy of the Grammar of Graphics book. I've read enough in the +ebook copy from the library that I know I want the entire thing, even though +it's quite expensive. + +Read chapter 4 of the book while the straggler genomes finish in the last batch, +about variables and basic transformations on them. The book uses the ridiculous +terms "homoscedasticity" and "heteroscedasticity" to mean "homogeneous variance" +and "heterogeneous variance", which I *think* is the same idea as Cleveland's +"monotone spread" (or possibly a more general version of it). + +I really wish the book wouldn't omit the axis-drawing code from the diagrams +— it makes it unclear where each piece of the output is coming from. I think +I *mostly* understand it, but would prefer if it were all explicit (even if it +would make things a bit longer). + +Read chapter 5 too, on algebras. This was much, much more confusing and would +have been much clearer with more explicit examples. Need to read this at least +one more time to get it, I'm sure. + +Going back to take some notes for HG545 while they're still (vaguely) fresh in +my mind. First: notes from the class on splicing. + +The "R-loop" terminology is confusing. It's inspired by the name "D-loop", +which notes how DNA will unzip to show a loop when it's being duplicated (and +there's a complementary strand bound to one side). "R-loop" *also* refers to +the loop *in the DNA* when it's bound *to RNA* (e.g. when it's being +transcribed). Again: the actual loop in an "R-loop" is a loop of DNA. + +An RNA molecule has 3 relevant sites when considering splicing: + +``` + 5' exon | intron | 3' exon + ======AG|GUAAGU============================YNYURAY====Y₁₁NCAG|G============== + ↑ + 5' Splice Site Branch Site 3' Splice Site +``` + +Note that in this case the branch site is specifically an adenine. That's +important (reason comes later). + +One important aspect of RNA that allows it to be spliced (contrasted with DNA) +is the hydroxyl group on the 2' carbon in RNA, which is not present in DNA +(that's why it's *deoxy*ribose). That hydroxyl group is what attacks the +phosphate bond at the 5' splice site and cleaves it apart (after being brought +close to it by the spliceosome). That leaves a hydroxyl group exposed hanging +off of the 5' exon, and in the next step *that* group is brought close to the 3' +splice site and attacks it. Once that bond is broken the intron (as +a lariat-shaped thing) floats away, and the exons are spliced together. + +The chemistry of the breaks is called "transesterification": two +phosphodi*ester* bonds are broken (at intron/exon and exon/intron boundaries), +and two more are created (one in the lariat, and the splice between exons). + +(Of course like everything in biology, in reality it's all a giant mess and there +are multiple kinds of splicing, including self-splicing.) + +The spliceosome is a giant thing made of a bunch of different proteins and also +5 RNAs that mediates splicing. The RNAs are important because those are what +recognize the splice and branch sites through complementary pairing, e.g. at the +5' splice site we have: + + ____________ + / U1 \ U1 component of spliceosome + \ / + \__CAUUCA__/ + ┆┆┆┆┆┆ + ==GUAAGU== RNA + +In a similar way, the U2 component binds to the branch site, but the binding +sequence specifically skips the adenine at the site, which "extrudes" it from +the RNA a little bit: + + extruded adenine + ↓ + A + ======U A C U A C======= RNA + ┆ ┆ ┆ ┆ ┆ ┆ + .——C A U U C A——. + / \ + / U2 \ U2 component of spliceosome + \___________________/ + +Alternate splicing is also a big deal, because it allows the creation of many +different mRNAs from the same gene by bringing together different exon/intron +boundaries to be spliced instead of always splicing the closest one. + +Of course there's other complications too, like splicing enhancers and silencers +that can recruit/block the splicing machinery. + +Skimmed over tomorrow's HG545 slides so I don't have to go in blind again. Seems +pretty reasonable, though the end seems pretty rushed and I *think* it's +relevant to one of the questions in the homework. Need to pay attention at the +end. + +PIBS800, how to read a research paper. I feel like I've had three versions of +this presentation by different people at different times at this point. + +Started BS521 homework 5. A bit more confusing than the previous homeworks, and +it's been a week or so since I touched LaTeX so I once again have to fight it +every step of the way. + +## 2023-10-11 + +HG545 this morning, about translation. + +VA onboarding after that. Took a couple of hours, but I now finally have +a badge. + +Been reading the GoG book during some spare free minutes here and there. +Skimming over a lot of the formalism, I still feel like this could be much +improved by showing some full examples with everything laid out. + +Sketched out some answers to HG545 questions. + +Finished BS521 homework 5, turned it in. + +Cleaned up HG545 answers. Need to do one final pass tomorrow. + +## 2023-10-12 + +BS521, started talking about two-distribution t tests. + +Finally got around to swapping my search engine on my phone to Kagi. The +degoogling continues. + +I really need to figure out a decent way to do proper pivot tables in Postgres. +From reading the docs it looks *surprisingly* janky for what I'd expect from +Postgres. + +Read up on index operator classes, which was preventing Postgres from using an +index when searching for a prefix of a string, e.g. `SELECT name FROM foo WHERE +name LIKE 'pref%';`. Fixed by telling Postgres this index will be used with +text patterns by e.g. `CREATE INDEX i__foo__name ON foo(name +text_pattern_ops);`. + +## 2023-10-13 + +HG545 discussion. + +## 2023-10-14 + +Fall break. + +## 2023-10-15 + +Did the BIOINF-500 homework on reference management/citation. Figured out how +to get Latex set up to do references. Lots of jank, but I think I've got it +working now. JabRef produces a `.bib` file as its database. Then in the Latex +document, add a preamble: + + + \usepackage[ + backend=biber, + style=nature, + sorting=ynt + ]{biblatex} + \addbibresource{sjl.bib} + +Cite things with `\cite{foo}` and `\cite{bar,baz}`. Then `\printbibliography` +to put the references section into the paper there. + +This is complicated by the fact that you have to run `biber` between runs of +`pdflatex`, so I kludged together a `mklatex` script that does something +horrifying like `pdflatex; biber; pdflatex; pdflatex` to actually make the damn +document. Gross. + +I really need to get my latex stuff into a set of files, rather than +copy/pasting everything into every single document. + +## 2023-10-18 + +Back from fall break. Time to get back into the swing of classes. + +HG545 this morning, starting the section about transposable elements. The +professor put up slides, videos, and a narrative document in advance which is +really great — I was able to prepare and not be completely lost. + +Read over animal ethics stuff for tomorrow. Need to consider if I want to +really do a rotation with animal subjects. I'm a little less sure now. + +## 2023-10-19 + +BS521 this morning. The second half of the class has a different lecturer, +starting today. Talked about paired t-tests (which are essentially just doing +a one-sample t-test on the difference of the paired values) and ANOVA for +many-sample t-testing. + +First PIBS503 discussion section. This is (I think) the only one that's in +person, and it's in the middle of goddamn nowhere on the North Campus. +I managed to find my way there, but dear god are these buildings confusing. + +BISTRO at 4. Topic: HMMSTR, using HMMs for tandem repeat copy number detection +from ONT reads. + +Need to remember to ask Alan if he has any suggestions on reading material +I should look at over the weekend before I start with him on Monday. + +## 2023-10-20 + +HG545. More on transposable elements, this time about LTR retrotransposons. + +Met with Bob about rotation paperwork. + +Last day of my first rotation! I think it went well. Looking forward to trying +out more things in the next few rotations, but this one was great! + +## 2023-10-21 + +Finished reading the HG545 paper, finally. It was long, but a lot more clear +than the other papers thanks to the supplementary material actually *explaining* +things. So even though it was a little tedious to get through with so many +abbreviations, I think I preferred it overall to the other papers so far. + +Finally got around to hooking up a keyboard shortcut for `switch-yubikeys` +since I find myself actually using it a lot again, now that I'm not working from +home full time. + +Sent my lab notebook to the PI, which is my last official act of the rotation. + +Swapped out a fresh VM for my next rotation. Keeping the old one around for +a few weeks in case I end up needing anything from it. Glad I've got everything +scripted up around this — much easier to do it this time. + +Started BS Lab 2. Not going to do the extra credit this time, I just don't have +the spare time at the moment. Too much going on all at once. + +Installed Weechat+wee-slack and irssi on my laptop. Going to give irssi a try +for a while as an IRC client, which would let me reserve Weechat (which I don't +really like all that much) for Slack. Irssi config was a little janky, but +I think I got something dogfoodable for now. + +Installed the Python lib for the next rotation on the VM in a venv. + +## 2023-10-22 + +Finish BS lab 2. Didn't go the extra mile on this one either, still trying to +catch up from break. I'm getting there though. + +Figured out some travel/break logistics for between semesters. + +Finished BS homework 7. I should be all caught up on stuff for that class +(aside from reading, which goes quick) for a while now. Next big thing for it +is the exam on 11/02. + +Got a couple of LaTeX snippets to remember after all the biostat stuff. First, +often worth making shortcuts for frequently used stuff in a given assignment: + + \def\h0{\textbf{H}_0} + \def\hA{\textbf{H}_A} + \def\tstar#1{t^\star_\textit{#1}} + +Adding spacing between equation lines with `\jot`: + + \begin{equation*} + \setlength{\jot}{10pt} + \begin{split} + T & = \frac{\bar{X} - \mu_D}{s/\sqrt{n}} \\ + & = \frac{-0.545 - 0}{8.887/\sqrt{200}} \\ + & = \frac{-0.545}{0.6284058} \\ + T & \approx -0.867 \\ + \end{split} + \end{equation*} + +Started HG545 homework, just sketching out notes. Burned out before getting too +far, will have to actually get a rough draft done tomorrow (then cleaned up on +Tuesday). + +## 2023-10-23 + +HG545, about the L1 transposition assaying and Alu. + +First day of the new lab rotation! Set up `black` on the laptop since I'll be +doing Python. Ended up installing it into a venv and symlinking to the binary, +which seems to have worked okay. + +Need to figure out how to get Irssi to autoload scripts properly and set up +e.g. `/toggle awl_viewer` on startup so I don't have to do it by hand every +time. + +Got a first draft of HW5 90% done. Will finish tomorrow. + +Did some reading for BS521. Still have a little left for Thursday. + +## 2023-10-24 + +BS521 today. Got another intuitive explanation of ANOVA (which was nice) and +talked about categorical CIs/hypothesis testing. + +BI500. Presentations by faculty who are looking to recruit students: + +1. Statistical/online bioinformatics. +2. Cell lineage trees via imaging + ML. If only there was a way to kludge + something into mitosis that would tag descendant genomes ala service request + ID tagging (or even just e.g. a plasmid that would mutate quickly as + a clock). +3. Head/neck cancer and ALS research via multiomics and large cohort studies. +4. How molecular/biological clocks work. +5. How cell cell signaling controls cell fate in human pluripotent stem cells. +6. Exercise, multiomics, and wearables, cell communications and differential + expression with ML. +7. Wearable and multiomics data to identify biomarkers for early + detection/prevention of disease. + +Should also look into the additional ones who couldn't be fit into timeslots to +present. + +Lunch at Maizie's. + +PIBS 800 about grants, e.g. + +which can be done as a pre-candidate *and* candidate. I think I should get Cat +to explain this to me in idiot terms so I can figure out all the stuff I'm +missing. + +Met with study group for HG545 homework. I feel like I understand everything +very well, but trying to fit a coherent explanation into the line limits of the +homework is absolutely miserable. + +Finished HG545 homework. Walking unsteadily as I emerge from the prose-gutting +facility covered in texual viscera and stinking of article blood, my filleting +backspace key dull in its socket. + +## 2023-10-25 + +HG545 discussion this morning. Chatted about a bunch of stuff, nothing too +groundbreaking. + +Spent the rest of the day in the lab. + +Put together my new table at home. Looks nice. + +Reviewed the files for the next two 503 discussions this week. Nothing +really surprising here. + +Did the BS521 reading for tomorrow. + +## 2023-10-26 + +BS521 class this morning. + +I've got the 503 discussion thing at 2, need to figure out a good place to take +that Zoom call. Maybe the study rooms at the top of THSL? Need to figure out +how to reserve those at some point. + +PIBS 503 discussion class zoom meeting. + +Started reading the next HG545 paper and glanced over the slides. I wish we had +lectures recorded like the last module. + +## 2023-10-27 + +HG545 lecture. New module starts today, on replication. + +There's more than just one DNA Polymerase. Three main ones are called α, δ, and +ε. Roughly, α starts, then hands off to δ. On the lagging strand, that's all +it has time for before it falls off and the process starts again for the next +Okazaki fragment. But on the leading strand, δ has time to hand off to ε, which +is much more stable and can continue along the strand. + +Proofreading and mismatch repair are both very important. The initial +polymerization process has an error rate somewhere around 10⁻⁶. Mismatch repair +happens *in-line* with the replication process: DNA Pol doesn't like continuing +from a mismatch based, so most of the time it will pause for a bit and the +proofreading machinery that's also in the replication complex will chomp off the +bad base, then DNA Pol will continue. Mismatch repair happens separately: one +protein recognizes the mismatch and recruits another protein that excises the +match *and a big chunk of the downstream strand*, and that whole chunk gets +resynthesized. + +Another PIBS 503 class discussion zoom meeting. 3 down, 4 to go. + +## 2023-10-28 + +Started digging into the HG545 paper. I hate that we only have 2 classes for +this one, it feels far too rushed. + +## 2023-10-29 + +Finished the second readthrough of the paper. I feel a little better now, but +am still not perfectly sure on the questions. + +## 2023-10-30 + +HG545 class, mostly on DNA repair. Makes the case that a lot of DNA repair +reuses the same polymerases (e.g. δ) as replication (but not all, e.g. +single-base repair uses something else (I think β?)), and you can kind of think +of it as just another form of replication. + +Another important point: replication is not deterministic, because it doesn't +have to be. As long as the whole genome (well, chromosome) gets replicated, it +doesn't matter precisely where that replication started. This is very different +from e.g. transcription, because starting in a different place would transcribe +a different gene. + +Also important to define terms like lesion vs mutation: a lesion is detectable +DNA damage, which then get fixed into place (in the "use fixer on the photo +paper" sense, not the "repair" sense) by subsequent replication. + +I think I'm feeling a little better about the homework questions now after +talking through it a bit. Need to get some rough drafts sketched out for when +I meet with the study group tomorrow. + +## 2023-10-31 + +BS521. Chi-square test. + +BI500. Senior student discussion panel. Each gave us advice: + +* Find a mentor that works for you (specifically what *you* need, will be + different for everyone). +* Use these years as training, not 100% research. +* Take care of yourself, set boundaries. Marathon, not sprint. +* Take ownership of your time here, do things that'll help you grow. +* The novelty of a PhD will wear off, stick with it. +* Have hobbies. +* Keep a calendar. +* Talk with your peers a lot, don't keep everything to yourself. + +PIBS800. Career planning. + +Met with HG545 folks. This module was a bit better than the rest. + +Finished and submitted HG545 homework. + +Made BS521 note sheet for the exam Thursday. + diff -r e2e3eb42c430 -r 665b6ddcdfd5 README.markdown --- a/README.markdown Tue Nov 14 16:16:35 2023 -0500 +++ b/README.markdown Wed Nov 15 13:41:22 2023 -0500 @@ -5,608 +5,6 @@ [TOC] -# October 2023 - -## 2023-10-01 - -Put up a bunch of stuff for sale on the PIBS list. Need to declutter my -apartment now that I've mostly moved in. - -Did a few hours of work on Lab 1 for BS521. Too much unproductive screwing -around in R trying to figure out how to get decent fonts. Should be able to -finish it up tomorrow though. Random notes jotted down from the process follow. - -Side-by-side figures in LaTeX: - - \begin{figure}[h] - \begin{minipage}[t]{0.48\textwidth} - \includegraphics[width=\linewidth]{figures/bp-histogram} - \caption{Distribution of blood pressure among participants.} - \label{fig:bp-histogram} - \end{minipage} - \hfill - \begin{minipage}[t]{0.48\textwidth} - \includegraphics[width=\linewidth]{figures/bp-nqq} - \caption{Normal QQ plot of blood pressure values.} - \label{fig:bp-nqq} - \end{minipage} - \end{figure} - - -Reasonable quantile plot in R: - - qplot <- function(filename, data, label, main, ...) { - n = length(data) - plot(((1:n - 1)/(n - 1)), sort(data), - type = "l", - main = main, - xlab = "Quantile", - ylab = label, - ...) - } - -QQ plot with the damn line in R: - - nqqplot <- function(data, ...) { - qqnorm(data, ...) - qqline(data) - } - -Reading in a CSV with specific column types: - - data <- read_csv("EPID_521_lab_data.csv", col_types="iddfiffdffdd") - -Note that this seems to give you a "tibble", whatever the hell that is. Some -kind of tidyverse thing? It's very confusing that everywhere you look there's -a hairball of a mess of base R, tidyverse, and ggplot2 and everyone just assumes -you understand which is part of what. - -Reordering levels: - - data <- mutate(data, diet=factor(data$diet, levels=c("Poor", "Fair", "Good", "VeryGood", "Excellent"))) - - -Removing rows with `NA`s for e.g. the `cot` column: - - data <- data[complete.cases(data$cot),] - -Histograms with specific bin widths, rather than a number of bins: - - hist(data$age, breaks=seq(from=15, to=90, by=1), main="", xlab="Age") - -Multiple box plots in one image: - - boxplot(bmi~sex, data=data) - -Marking and/or filtering on a boolean condition: - - data$locot <- data$cot <= 0.011 - locot <- subset(data, cot <= 0.011) - hicot <- subset(data, cot > 0.011) - -## 2023-10-02 - -HG545 review this morning. Need to go back and review the first module again -tomorrow since it's been a while. - -Finish BS521 lab 1, finally. That was a lot more work than I expected. - -Met with a professor about possible rotation. Need to chat with my advisor to -see if there's special paperwork I'll need. - -## 2023-10-03 - -BS521. Confidence intervals. - -BI500. Research writing. - -Finally got around to splitting my Vimrc into minimal and extra files, so I can -sync the minimal one to servers and not hate myself when trying to edit. There's -some jank involved around the colorschemes and `set termguicolors` but I think -have have something that should work. - -PIBS800. Mentor/mentee relationships. - -## 2023-10-04 - -Advising meeting. Need to do a couple of things in EdM and register for 602, -but I'm currently blocked on both by other folks so I'm good for now. - -HG545 exam. - -## 2023-10-05 - -Finished the HG545 exam last night. That was… deeply unpleasant. - -BS521. Hypothesis testing. - -BS521 reading. - -Read the paper for HG545. I get the general idea, and it seems like a pretty -clear experiment. I wonder how much we'll stick to the paper vs going off topic -this time. - -Needed to convert some PDF graphs to PNG to put in a presentation, but `convert` -was whining about some security crap: - - ><((°> convert n50.pdf n50.png - convert-im6.q16: attempt to perform an operation not allowed by the security policy `PDF' @ error/constitute.c/IsCoderAuthorized/421. - -Turns out there was a bug in ghostscript, which was fixed, but convert still -doesn't trust it so won't convert stuff. Great. Have to edit -`/etc/ImageMagick-6/policy.xml` and comment out these lines to make it behave: - - - - - - - - - -Skimmed through the slides for HG545 tomorrow. It's nice to be able to get -a preview of things again. - -## 2023-10-06 - -HG545, class was about splicing. I feel much better about this module thanks to -being able to prepare a bit with the preview last night. - -## 2023-10-07 - -Installed — might come in handy here and -there. - -## 2023-10-08 - -Reread the paper for HG545. It's… a little clearer now? Though honestly it -wasn't too bad before compared to the other papers. Just a lot of acronyms. -Got a list of things to ask. - -## 2023-10-09 - -HG545 this morning, about co/post-transcriptional modification. The downside of -having slides is that people put a ton of things on them and you can't take -notes fast enough. Need to go back over the slides and write down things once -I get home so I don't forget them. - -## 2023-10-10 - -BS521, hypothesis testing, p values, t distribution. - -BI500, code quality tips. Checked with Prof. Sartor and submitting a LaTeX PDF -for the references homework is fine. - -Pinged a few students in a lab I'm interested in to see if they're willing to -chat about their experience. Just need to nail down my third rotation and then -I'll be all set. - -Ordered a used copy of the Grammar of Graphics book. I've read enough in the -ebook copy from the library that I know I want the entire thing, even though -it's quite expensive. - -Read chapter 4 of the book while the straggler genomes finish in the last batch, -about variables and basic transformations on them. The book uses the ridiculous -terms "homoscedasticity" and "heteroscedasticity" to mean "homogeneous variance" -and "heterogeneous variance", which I *think* is the same idea as Cleveland's -"monotone spread" (or possibly a more general version of it). - -I really wish the book wouldn't omit the axis-drawing code from the diagrams -— it makes it unclear where each piece of the output is coming from. I think -I *mostly* understand it, but would prefer if it were all explicit (even if it -would make things a bit longer). - -Read chapter 5 too, on algebras. This was much, much more confusing and would -have been much clearer with more explicit examples. Need to read this at least -one more time to get it, I'm sure. - -Going back to take some notes for HG545 while they're still (vaguely) fresh in -my mind. First: notes from the class on splicing. - -The "R-loop" terminology is confusing. It's inspired by the name "D-loop", -which notes how DNA will unzip to show a loop when it's being duplicated (and -there's a complementary strand bound to one side). "R-loop" *also* refers to -the loop *in the DNA* when it's bound *to RNA* (e.g. when it's being -transcribed). Again: the actual loop in an "R-loop" is a loop of DNA. - -An RNA molecule has 3 relevant sites when considering splicing: - -``` - 5' exon | intron | 3' exon - ======AG|GUAAGU============================YNYURAY====Y₁₁NCAG|G============== - ↑ - 5' Splice Site Branch Site 3' Splice Site -``` - -Note that in this case the branch site is specifically an adenine. That's -important (reason comes later). - -One important aspect of RNA that allows it to be spliced (contrasted with DNA) -is the hydroxyl group on the 2' carbon in RNA, which is not present in DNA -(that's why it's *deoxy*ribose). That hydroxyl group is what attacks the -phosphate bond at the 5' splice site and cleaves it apart (after being brought -close to it by the spliceosome). That leaves a hydroxyl group exposed hanging -off of the 5' exon, and in the next step *that* group is brought close to the 3' -splice site and attacks it. Once that bond is broken the intron (as -a lariat-shaped thing) floats away, and the exons are spliced together. - -The chemistry of the breaks is called "transesterification": two -phosphodi*ester* bonds are broken (at intron/exon and exon/intron boundaries), -and two more are created (one in the lariat, and the splice between exons). - -(Of course like everything in biology, in reality it's all a giant mess and there -are multiple kinds of splicing, including self-splicing.) - -The spliceosome is a giant thing made of a bunch of different proteins and also -5 RNAs that mediates splicing. The RNAs are important because those are what -recognize the splice and branch sites through complementary pairing, e.g. at the -5' splice site we have: - - ____________ - / U1 \ U1 component of spliceosome - \ / - \__CAUUCA__/ - ┆┆┆┆┆┆ - ==GUAAGU== RNA - -In a similar way, the U2 component binds to the branch site, but the binding -sequence specifically skips the adenine at the site, which "extrudes" it from -the RNA a little bit: - - extruded adenine - ↓ - A - ======U A C U A C======= RNA - ┆ ┆ ┆ ┆ ┆ ┆ - .——C A U U C A——. - / \ - / U2 \ U2 component of spliceosome - \___________________/ - -Alternate splicing is also a big deal, because it allows the creation of many -different mRNAs from the same gene by bringing together different exon/intron -boundaries to be spliced instead of always splicing the closest one. - -Of course there's other complications too, like splicing enhancers and silencers -that can recruit/block the splicing machinery. - -Skimmed over tomorrow's HG545 slides so I don't have to go in blind again. Seems -pretty reasonable, though the end seems pretty rushed and I *think* it's -relevant to one of the questions in the homework. Need to pay attention at the -end. - -PIBS800, how to read a research paper. I feel like I've had three versions of -this presentation by different people at different times at this point. - -Started BS521 homework 5. A bit more confusing than the previous homeworks, and -it's been a week or so since I touched LaTeX so I once again have to fight it -every step of the way. - -## 2023-10-11 - -HG545 this morning, about translation. - -VA onboarding after that. Took a couple of hours, but I now finally have -a badge. - -Been reading the GoG book during some spare free minutes here and there. -Skimming over a lot of the formalism, I still feel like this could be much -improved by showing some full examples with everything laid out. - -Sketched out some answers to HG545 questions. - -Finished BS521 homework 5, turned it in. - -Cleaned up HG545 answers. Need to do one final pass tomorrow. - -## 2023-10-12 - -BS521, started talking about two-distribution t tests. - -Finally got around to swapping my search engine on my phone to Kagi. The -degoogling continues. - -I really need to figure out a decent way to do proper pivot tables in Postgres. -From reading the docs it looks *surprisingly* janky for what I'd expect from -Postgres. - -Read up on index operator classes, which was preventing Postgres from using an -index when searching for a prefix of a string, e.g. `SELECT name FROM foo WHERE -name LIKE 'pref%';`. Fixed by telling Postgres this index will be used with -text patterns by e.g. `CREATE INDEX i__foo__name ON foo(name -text_pattern_ops);`. - -## 2023-10-13 - -HG545 discussion. - -## 2023-10-14 - -Fall break. - -## 2023-10-15 - -Did the BIOINF-500 homework on reference management/citation. Figured out how -to get Latex set up to do references. Lots of jank, but I think I've got it -working now. JabRef produces a `.bib` file as its database. Then in the Latex -document, add a preamble: - - - \usepackage[ - backend=biber, - style=nature, - sorting=ynt - ]{biblatex} - \addbibresource{sjl.bib} - -Cite things with `\cite{foo}` and `\cite{bar,baz}`. Then `\printbibliography` -to put the references section into the paper there. - -This is complicated by the fact that you have to run `biber` between runs of -`pdflatex`, so I kludged together a `mklatex` script that does something -horrifying like `pdflatex; biber; pdflatex; pdflatex` to actually make the damn -document. Gross. - -I really need to get my latex stuff into a set of files, rather than -copy/pasting everything into every single document. - -## 2023-10-18 - -Back from fall break. Time to get back into the swing of classes. - -HG545 this morning, starting the section about transposable elements. The -professor put up slides, videos, and a narrative document in advance which is -really great — I was able to prepare and not be completely lost. - -Read over animal ethics stuff for tomorrow. Need to consider if I want to -really do a rotation with animal subjects. I'm a little less sure now. - -## 2023-10-19 - -BS521 this morning. The second half of the class has a different lecturer, -starting today. Talked about paired t-tests (which are essentially just doing -a one-sample t-test on the difference of the paired values) and ANOVA for -many-sample t-testing. - -First PIBS503 discussion section. This is (I think) the only one that's in -person, and it's in the middle of goddamn nowhere on the North Campus. -I managed to find my way there, but dear god are these buildings confusing. - -BISTRO at 4. Topic: HMMSTR, using HMMs for tandem repeat copy number detection -from ONT reads. - -Need to remember to ask Alan if he has any suggestions on reading material -I should look at over the weekend before I start with him on Monday. - -## 2023-10-20 - -HG545. More on transposable elements, this time about LTR retrotransposons. - -Met with Bob about rotation paperwork. - -Last day of my first rotation! I think it went well. Looking forward to trying -out more things in the next few rotations, but this one was great! - -## 2023-10-21 - -Finished reading the HG545 paper, finally. It was long, but a lot more clear -than the other papers thanks to the supplementary material actually *explaining* -things. So even though it was a little tedious to get through with so many -abbreviations, I think I preferred it overall to the other papers so far. - -Finally got around to hooking up a keyboard shortcut for `switch-yubikeys` -since I find myself actually using it a lot again, now that I'm not working from -home full time. - -Sent my lab notebook to the PI, which is my last official act of the rotation. - -Swapped out a fresh VM for my next rotation. Keeping the old one around for -a few weeks in case I end up needing anything from it. Glad I've got everything -scripted up around this — much easier to do it this time. - -Started BS Lab 2. Not going to do the extra credit this time, I just don't have -the spare time at the moment. Too much going on all at once. - -Installed Weechat+wee-slack and irssi on my laptop. Going to give irssi a try -for a while as an IRC client, which would let me reserve Weechat (which I don't -really like all that much) for Slack. Irssi config was a little janky, but -I think I got something dogfoodable for now. - -Installed the Python lib for the next rotation on the VM in a venv. - -## 2023-10-22 - -Finish BS lab 2. Didn't go the extra mile on this one either, still trying to -catch up from break. I'm getting there though. - -Figured out some travel/break logistics for between semesters. - -Finished BS homework 7. I should be all caught up on stuff for that class -(aside from reading, which goes quick) for a while now. Next big thing for it -is the exam on 11/02. - -Got a couple of LaTeX snippets to remember after all the biostat stuff. First, -often worth making shortcuts for frequently used stuff in a given assignment: - - \def\h0{\textbf{H}_0} - \def\hA{\textbf{H}_A} - \def\tstar#1{t^\star_\textit{#1}} - -Adding spacing between equation lines with `\jot`: - - \begin{equation*} - \setlength{\jot}{10pt} - \begin{split} - T & = \frac{\bar{X} - \mu_D}{s/\sqrt{n}} \\ - & = \frac{-0.545 - 0}{8.887/\sqrt{200}} \\ - & = \frac{-0.545}{0.6284058} \\ - T & \approx -0.867 \\ - \end{split} - \end{equation*} - -Started HG545 homework, just sketching out notes. Burned out before getting too -far, will have to actually get a rough draft done tomorrow (then cleaned up on -Tuesday). - -## 2023-10-23 - -HG545, about the L1 transposition assaying and Alu. - -First day of the new lab rotation! Set up `black` on the laptop since I'll be -doing Python. Ended up installing it into a venv and symlinking to the binary, -which seems to have worked okay. - -Need to figure out how to get Irssi to autoload scripts properly and set up -e.g. `/toggle awl_viewer` on startup so I don't have to do it by hand every -time. - -Got a first draft of HW5 90% done. Will finish tomorrow. - -Did some reading for BS521. Still have a little left for Thursday. - -## 2023-10-24 - -BS521 today. Got another intuitive explanation of ANOVA (which was nice) and -talked about categorical CIs/hypothesis testing. - -BI500. Presentations by faculty who are looking to recruit students: - -1. Statistical/online bioinformatics. -2. Cell lineage trees via imaging + ML. If only there was a way to kludge - something into mitosis that would tag descendant genomes ala service request - ID tagging (or even just e.g. a plasmid that would mutate quickly as - a clock). -3. Head/neck cancer and ALS research via multiomics and large cohort studies. -4. How molecular/biological clocks work. -5. How cell cell signaling controls cell fate in human pluripotent stem cells. -6. Exercise, multiomics, and wearables, cell communications and differential - expression with ML. -7. Wearable and multiomics data to identify biomarkers for early - detection/prevention of disease. - -Should also look into the additional ones who couldn't be fit into timeslots to -present. - -Lunch at Maizie's. - -PIBS 800 about grants, e.g. - -which can be done as a pre-candidate *and* candidate. I think I should get Cat -to explain this to me in idiot terms so I can figure out all the stuff I'm -missing. - -Met with study group for HG545 homework. I feel like I understand everything -very well, but trying to fit a coherent explanation into the line limits of the -homework is absolutely miserable. - -Finished HG545 homework. Walking unsteadily as I emerge from the prose-gutting -facility covered in texual viscera and stinking of article blood, my filleting -backspace key dull in its socket. - -## 2023-10-25 - -HG545 discussion this morning. Chatted about a bunch of stuff, nothing too -groundbreaking. - -Spent the rest of the day in the lab. - -Put together my new table at home. Looks nice. - -Reviewed the files for the next two 503 discussions this week. Nothing -really surprising here. - -Did the BS521 reading for tomorrow. - -## 2023-10-26 - -BS521 class this morning. - -I've got the 503 discussion thing at 2, need to figure out a good place to take -that Zoom call. Maybe the study rooms at the top of THSL? Need to figure out -how to reserve those at some point. - -PIBS 503 discussion class zoom meeting. - -Started reading the next HG545 paper and glanced over the slides. I wish we had -lectures recorded like the last module. - -## 2023-10-27 - -HG545 lecture. New module starts today, on replication. - -There's more than just one DNA Polymerase. Three main ones are called α, δ, and -ε. Roughly, α starts, then hands off to δ. On the lagging strand, that's all -it has time for before it falls off and the process starts again for the next -Okazaki fragment. But on the leading strand, δ has time to hand off to ε, which -is much more stable and can continue along the strand. - -Proofreading and mismatch repair are both very important. The initial -polymerization process has an error rate somewhere around 10⁻⁶. Mismatch repair -happens *in-line* with the replication process: DNA Pol doesn't like continuing -from a mismatch based, so most of the time it will pause for a bit and the -proofreading machinery that's also in the replication complex will chomp off the -bad base, then DNA Pol will continue. Mismatch repair happens separately: one -protein recognizes the mismatch and recruits another protein that excises the -match *and a big chunk of the downstream strand*, and that whole chunk gets -resynthesized. - -Another PIBS 503 class discussion zoom meeting. 3 down, 4 to go. - -## 2023-10-28 - -Started digging into the HG545 paper. I hate that we only have 2 classes for -this one, it feels far too rushed. - -## 2023-10-29 - -Finished the second readthrough of the paper. I feel a little better now, but -am still not perfectly sure on the questions. - -## 2023-10-30 - -HG545 class, mostly on DNA repair. Makes the case that a lot of DNA repair -reuses the same polymerases (e.g. δ) as replication (but not all, e.g. -single-base repair uses something else (I think β?)), and you can kind of think -of it as just another form of replication. - -Another important point: replication is not deterministic, because it doesn't -have to be. As long as the whole genome (well, chromosome) gets replicated, it -doesn't matter precisely where that replication started. This is very different -from e.g. transcription, because starting in a different place would transcribe -a different gene. - -Also important to define terms like lesion vs mutation: a lesion is detectable -DNA damage, which then get fixed into place (in the "use fixer on the photo -paper" sense, not the "repair" sense) by subsequent replication. - -I think I'm feeling a little better about the homework questions now after -talking through it a bit. Need to get some rough drafts sketched out for when -I meet with the study group tomorrow. - -## 2023-10-31 - -BS521. Chi-square test. - -BI500. Senior student discussion panel. Each gave us advice: - -* Find a mentor that works for you (specifically what *you* need, will be - different for everyone). -* Use these years as training, not 100% research. -* Take care of yourself, set boundaries. Marathon, not sprint. -* Take ownership of your time here, do things that'll help you grow. -* The novelty of a PhD will wear off, stick with it. -* Have hobbies. -* Keep a calendar. -* Talk with your peers a lot, don't keep everything to yourself. - -PIBS800. Career planning. - -Met with HG545 folks. This module was a bit better than the rest. - -Finished and submitted HG545 homework. - -Made BS521 note sheet for the exam Thursday. - # November 2023 ## 2023-11-01 @@ -928,3 +326,25 @@ their grad students later this week. PIBS800. + +Finished the 3D printing course on the library site so I can potentially use the +3D printers there now. Still need to learn how to make stuff in e.g. TinkerCAD +first I think. + +Read the review papers for HG545 tomorrow to prime my brain. I'm still +expecting it to be a lot to take in. + +Started the TinkerCAD tutorials. Seems simple enough so far. + +## 2023-11-15 + +HG545, start of the Epigenetics module. + +Registered for classes. Mostly went smoothly except for two: + +* Needed to swap out the BS521 lab for a lab session on Mondays. Given that + I haven't been really using the lab sessions much at all, this is fine. +* Need instructor permission for BIOINF-545, and also apparently it's Tuesday + and *Friday*? Strange set of days. So much for my free Fridays. Oh well, at + least Thursdays will be less wild I guess. +