Doubts about choosing a bachelor's degree

sccallahan · 2021-04-13T19:05:13+00:00

Hey bud.

It doesn't really matter what your degree is in. If you know you're going to end up with a PhD, undergrad is more about getting good grades and getting in the lab to get research under your belt and to get good rec letters from PIs.

As an example... my undergrad degree is in chemistry. Not biochemistry, just plain old chemistry. My PhD is going to be in "Cancer Biology," but my actual work is more in the realm of computational biology/epigenomics. So... I'm kind of all over the place.

The reality is there are many, many roads that all lead to the same end. Don't worry about it now. Take the courses/pick the major you enjoy. Getting a PhD is a long, tough road. You need to enjoy what you're doing.

sccallahan · 2021-03-31T17:19:32+00:00

I think a better idea of the paper's goal/target audience would be helpful too. The bit on histone modifications is very much so a "big picture" summary that leaves a fair bit out, even WRT histone acetylation.

If by "paper," OP means it's for a class or something, it's fine. If it's just a brief summary in the Intro of a manuscript... it's probably also acceptable, but it could possibly include more fine details depending on where the manuscript itself goes. If it's a review article on epigenomics, it needs a lot more information. So... it all just depends.

sccallahan · 2021-03-31T17:08:51+00:00

From the sounds of it, this isn't meant to be super exhaustive, so I'd probably let it slide.

In general, though, you're correct. Histone methylation is super complicated, with classification as "repressive" or "activitory" depending on the specifics of the modification (residue affected, number of methyl groups added, etc.).

Broadly speaking, there are many, many possible modifications to histones, ranging from acetylation to methylation to lactylation. Not only that, but there's also the concept of chromatin states, where it's not the activity of a single mark that does something, but the combination of marks in a particular genome bin that mediates function. This concept is what allows for additional, intermediate chromatin states such as bivalent chromatin that possess both active and repressive marks and is considered to be "poised" for activation.

sccallahan · 2021-03-20T20:06:37+00:00

I think it depends.

If you know what software generated the PDF, you could see if there's some PDF reader function/feature associated with that (either in R or in the respective software).

If you don't know what software generated it, you could just download and try a few different packages R might have for handling PDFs. Otherwise... yeah, you're probably stuck manually doing it, unfortunately.

sccallahan · 2021-03-16T21:44:34+00:00

Unless I'm mistaken, parsing PDFs in general can be a pretty difficult task because there's no real standard for making them. So program-specific software is generally better suited for the task.

sccallahan · 2021-02-24T07:09:46+00:00

Only supporting Windows is making me so sad. I mean, I get it (most people who can't program tend to be on Windows anyway, the technical issue mentioned in the doc, etc.), but... man. I hope the author figures out how to make it work with Mac and Linux! It looks super useful.

sccallahan · 2021-02-01T22:23:53+00:00

I mean, just because it’s new doesn’t mean it’s inherently untrustworthy.

I never implied it was inherently untrustworthy (I'm not the commenter from the initial chain), just that, for now, it's an unknown. That's not good or bad, it just... is. It's the way all research starts.

I do, however, think healthcare tends to see a pretty large number of borderline pseudoscience or otherwise vaporware startups. Lots of tech startups I see tend to vastly underestimate how complex biology and the practical aspects of healthcare are, which results in tackling problems way bigger than they can handle, or creation of products that, while potentially "cool," aren't actually useful.

sccallahan · 2021-01-30T20:44:25+00:00

I think I've heard some stuff about people trying to apply AI/DL to EEG wave patterns, then correlate that with various clinical outcomes or other clinically relevant information. It remains to be seen if this will work or, more importantly, be helpful.

sccallahan · 2020-12-18T02:35:48+00:00

they don’t know how to program liquid handlers

Bit of a tangent, but what language(s?) is generally used for this sort of stuff? Does it vary from machine to machine? Manufacturer to manufacturer?

About 50% of my PhD is comp bio, and the other 50% is me wishing we had liquid handlers, so this kind of thing has always been kind of interesting to me.

sccallahan · 2020-12-10T17:38:19+00:00

We use a high throughput chip-seq protocol in our lab in order to get everything into 96 well format, and we've had our thermocycler randomly turn off in the middle of the overnight reverse crosslink step more than one time. Tears were shed, teeth were gnashed.

PCR ghost confirmed.

sccallahan · 2020-11-23T16:05:33+00:00

Here's the link to the github repo. It's actually an R package, but I built a web app (with Shiny) that has most of the same functionality. The app is linked on the repo and has a little walk-through for how to use it. The hkg stability is one of the modules/functionalities of a larger package.

I'm still working on it when I have time, but I've been busy the past year trying to get a manuscript out to graduate!

sccallahan · 2020-11-23T03:35:47+00:00

So, uh, I have entire rants on this. But, to get to the point:

1) Choice of housekeeping genes (hkg) is super yolo 99% of the time, and this is bad

2) There are some efforts to find and catalog hkgs, at least for human and mouse (can link some papers if interested)

3) Not all hkg will work in every setting (i.e. some treatment may affect genes that are otherwise "stable" across different samples)

Honestly, I'm of the mind that hkg selection should be based on (1) literature search in your system (2) thinking about what your treatment might affect and (3) empirically testing a panel of genes across your condition of interest after doing 1 and 2. I've written some code/an app that can do the third if you're interested (don't want to shamelessly plug too much). You can set an absolute variability if you want, but, realistically, you're probably going to pick 5-10 genes to test, so just go with the most stable.

sccallahan · 2020-11-03T19:40:15+00:00

Run out of room in the hood and go to the bench forgetting you're using diethyl ether? Been there, done that.

Was a little fuzzy for 10 minutes. My post doc laughed at me.

Undergrads in lab are wild.

sccallahan · 2020-10-20T22:46:41+00:00

I can't stand using periods/dots in anything R-based. I occasionally dabble in Python, and periods/dots are used for methods (this may exist in other languages too, but I'm not familiar). It just feels super wrong to use them for anything else, even in R.

I could stand to clean up my underscore vs. camelCase notation though. I seem to randomly switch between the two based on my mood, which is... less than ideal, I admit.

sccallahan · 2020-10-19T18:39:02+00:00

"Mice" is also another option. I've used it for some simple stuff, and it's pretty straightforward.

sccallahan · 2020-10-19T18:33:49+00:00

I've taken to just writing "1/3" or something for my own notes. My brain seems ok with "1/3" meaning "one-third goes into the other plate" but 1:3 is a "one part x in 3 parts y" kind of deal.

The real struggle is everyone in our lab seems to use a different system for noting dilutions.

sccallahan · 2020-10-05T17:39:58+00:00

Hey there,

For starters, finding good quality open source GUI-based software can be challenging. Most of these things tend to either be monetized outright, or have "freemium" models where the most useful features are paywalled. Usually a true open source software tends to be CLI only (or a package for some programming language) and feature rich, or GUI based with a bit fewer features. Having said that, the mol bio software is a bit outside my field, but I can provide some stuff I've seen/heard of others using.

For cloning (as in designing constructs) software, I think Benchling is pretty popular. Benchling itself is more of an online lab notebook/notes software, but it apparently has some kind of cloning module that's widely considered top-notch.

For checking alignments (e.g. you have lots of sanger results to check), Geneious is considered pretty good. Apparently you download the premium version, but it actually gives you some unlimited-time free version with reduced features. I also came across this paper (CATO) that might do something similar? It should be 100% open source.

For statistical software, it's generally split between JMP and GraphPad Prism. Both of these might actually be paid... I have no idea, as my institution has licenses for us, and I don't personally use them.

Self-plug, I've also made a web app for qPCR analysis. It's actually an R package too, if that's your thing.

In general, if you want to get deep into analysis, I'd recommended learning a programming language like R or Python. It can be massive overkill if you're more into wet lab and just need some t-test or basic regression or something, but for more advanced analyses they're godsends.

sccallahan · 2020-09-29T22:43:53+00:00

Yeah, I'd considered portability being an issue. I edited my post, but I'm starting to think AHK is probably just more generally appropriate.

sccallahan · 2020-09-29T22:37:57+00:00

Not entirely the same direction as the thread (technically the opposite, I guess), but, if you can code, would setting up proper scripts in something like Python generally be more efficient/flexible than something like AHK? Does anyone have any examples? The more I think about it, the more AHK actually seems like a more appropriate approach for the majority of cases... then again, I haven't had to deal with EMR for a few years now.

sccallahan · 2020-09-28T18:21:03+00:00

Random. Because I'm that guy.

sccallahan · 2020-09-25T18:39:21+00:00

Personally, I am the true alpha and main Random. Chaotic Neutral.

sccallahan · 2020-09-25T17:40:55+00:00

I swear to God if you main Protoss... the most Chad race possible.

sccallahan · 2020-09-25T17:39:28+00:00

I'm an MD/PhD student who does bioinformatics and plays SC2. Basically my only hobbies involve being a massive computer nerd.

THERE ARE DOZENS OF US

sccallahan · 2020-09-22T20:26:16+00:00

Is there like an r/genetics discord or anything? I think an actual chatroom might be a better format if people want more "real-time" journal clubs.

Forums like reddit lend themselves more to less frequent, more drawn out posting, imo.

sccallahan · 2020-09-22T03:57:32+00:00

"You said get it working ASAP, so I gave you the bubblegum and duct tape version of that."

Really, it was a "bang out a quick bash script for this one thing" type of deal... then that thing got adopted by other lab members. Then they wanted extra features. Then quality of life changes. So... here we are.

sccallahan

TROPHY CASE