Snarking at techbros 

@bgcarlisle
I wasn't aware that Linux kernel developers were doing unethical research on scholar.social , or defending those who did so. Maybe the victims of unethical research should sympathise with each other and work together against the problem?

I submitted my journal article earlier this week and I got approval from my committee to write my thesis and plan my oral examination! The end is in sight!

hello everyone, I'm stephanie (she/her)!

I'm a researcher at a big tech company, based in the UK. I did my phd in computational biology+medicine. I focus very much on ML for health, specifically critical care, physiological time series, "how to do ML well in health", etc.

Non-research activities include rollerskating/derby, gaming (computer/table-top/board), sewing, looking at birds.

I gave a talk yesterday as part of the Fragile Nucleosome Seminar Series. The talk was recorded and put online, so if anyone wants to learn about prostate cancer, the 3D genome, and structural variants, take a look!

youtube.com/watch?v=YsFFN2AY62

Like all my scientific work, feedback and questions are always appreciated

@mwt That's great! I'm glad you can find some inspiration for good coding style in the source code

Today on the #bioinformatics chat, Lindsay Pino discusses the difficulties of comparing proteomic (mass spec) measurements across different samples, potentially acquired in different labs, as well as a method she has developed recently for calibrating these measurements without the need for expensive reagents

bioinformatics.chat/proteomics

@mwt Unlike most source code *using* R, unfortunately

This was a really neat discussion of various computer processes and how they can get slowed down or take up lots of space.

gregoryszorc.com/blog/2021/04/

The most interesting one, for me, was about the slowness of zlib. In bioinformatics, I use gzipped files all the time, and I've always wondered about the silly FASTQ format (zipped or unzipped). I wonder how much faster and more compressed things would be if we used zstandard instead

@coldwave I think you can accomplish this with awk, if you know the line number.

1. Try using `less -N` to search for the line and figure out the line number. Say it's line 1235
2. Use `awk '{if (NR != 1235) print}' old-file.txt > new-file.txt

You can also try some inline vim solution, like this: unix.stackexchange.com/questio

But modifying a file in place is always risky. If your command fails, you'll probably lose all the data. The safest practice is still to write to a new file

research woes 

@drdrago Definitely this, probably ~60% of the time. for me.

Another 30%: someone needs to make a normalization method for this group of problems...but it ain't gonna be me!

The last 10%: I guess I have to make this method myself and tell everyone around me why it needs to be done so that they don't think I'm just doing nothing.

@drdrago Welcome! Always happy to meet other computational biologists

All too often I hear "how can we justify funds to maintain research software?"

But really, we should be asking "How can we justify _not_ funding it?"

My colleagues and I wrote a thing: nature.com/articles/s43588-021

Wow, I just had my first interaction with GitHub's dependabot.

It was able to
1. detect the requirements.txt file with Python packages
2. recognize the vulnerable version
3. test for compatibility with the other package requirements
4. open a new branch and PR that addresses the security issue
5. display all the relevant information in an easy to read format

That's amazing, to be honest. Just wow

@petrichor Right, I've seen this before. I forgot that there was some confusion over "Nix" being used for the package manager, the name of the markup language, and the Linux OS itself.

Good to know that you were able to use the package manager for a long time! That garbage collection feature you mentioned seems pretty useful, I think I should try this out at some point

@petrichor That's very cool, I've heard lots of good things about NixOS but am hesitant about making the switch. How long have you been using NixOS? Did you have any migration issues from another OS?

I got my hands on an old Illumina NextSeq flow cell and got to tear it apart.

jrhawley.ca/2021/03/13/flow-ce

There's a lot of cool design choices and stuff in here! As a computational biologist, I don't see this kind of stuff that often, but it was fun to see this side of sequencing machines.

The latest bioinformatics chat episode is up! We interviewed Molly Gasperini about the essential, yet sometimes underappreciated, problem of defining enhancer elements and subsequently identifying them. bioinformatics.chat/enhancers

A good comparison of csv and for parsing large tables of data.

able.bio/haixuanTao/data-manip

tl;dr Pandas is way easier to work with since working with tabular data in Rust is still immature. As expected, though, certain operations in Rust are WAY faster, showing its got potential for building efficient crates for processing data like this

This is a good description of how to work well with your manager

jvns.ca/blog/things-your-manag

This also works as good advice for effectively communicating with your academic supervisor!

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