@thatdnaguy@genomic.social
@thatdnaguy@genomic.social avatar

thatdnaguy

@thatdnaguy@genomic.social

Using human genetics and genomics with applied bioinformatics to understand human disease. Just enough stats and server to make me dangerous with data. Well-marbled.

Lifetime achievement: Making an SRO tell me I might want to remove a grant review budget comment that a specific institutional charge rate was mob level extortion.

#genetics #genomics #rarevariants #DNASeq #RNASeq #singlecell

#inflammation #hidradenitis #arthritis #systemicsclerosis #autophagy

#rstats #python #snakemake

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thatdnaguy, to random
@thatdnaguy@genomic.social avatar
  1. Publishing kills me sometimes. My placement makes no sense at my university. I have a PhD in human genetics and use genomics and bioinformatics methods mostly. My appointment is in the Division of Rheumatology in the School of Medicine.

A few months ago LLMs came up at a dinner. None of the MDs had a clue they could hallucinate, there was no guarantee of ground truth, or understood the potential for breaches of PHI and confidentiality. I ended up having to do a division seminar about it.

thatdnaguy, to linux
@thatdnaguy@genomic.social avatar

If you work on the command-line in Linux a lot, find + exec is your friend.

"I have many copies of MYFILE because my project got sloppy over time. Are they different?"

find . -type f -readable -name "MYFILE*" -exec md5sum {} ;

Also handy for if temporary files get out of control and rm chokes.

find . -type f -readable -name "*.temp" -exec rm {} ;

#Linux
#CommandLine
#Bioinformatics
#Genomics

thatdnaguy,
@thatdnaguy@genomic.social avatar

@visone that's true! I forget that option because a fair amount of the data is sensitive so I end up using shred --remove instead. :-)

thatdnaguy, to random
@thatdnaguy@genomic.social avatar

A zstd wrapper for R.

https://fosstodon.org/@coolbutuseless/111997465588916181

I put an issue ggplot some time ago suggesting that it might be worth adding zstd to read and write. This might work in the meantime for some uses.

thatdnaguy, to random
@thatdnaguy@genomic.social avatar

I'm just a guy. Sighing deeply on a Sunday. Because I see an email I haven't opened. That I believe is from someone who should have asked for my assistance on something a long time ago. And didn't. And has promised it's under control. And is about to make it my problem.

I'm sighing deeply. And searching for the strength to deal with this situation in a reasonable way without being too honest.

thatdnaguy, to random
@thatdnaguy@genomic.social avatar


Long shot, but I thought I would ask. Anyone have access to the times article about IBM's Tom Watson being decorated by Hitler for service to the reich?

Title: Thomas J. Watson Is Decorated by Hitler For Work in Bettering Economic Relations

I think it's July 2, 1937.

KestrelSWard, to academicchatter
@KestrelSWard@glammr.us avatar

Today I am discovering the wonderful world of Open Access APCs. I, a poor queer independent researcher, would like to publish my research open access because I believe it should be free to any who need it. The publication we were pointed to as being ideal for publishing our work....wants to charge over $3000USD. I thought I was misreading that at first, but no apparently not. @academicchatter

thatdnaguy,
@thatdnaguy@genomic.social avatar

@KestrelSWard @academicchatter gotta pad those meager profits somewhere

elduvelle, to twitter
@elduvelle@neuromatch.social avatar

So let me get this right..

1-Scientists go to Twitter, invest time and effort in it to build their profile, post cool content, help optimize it, attract readers to it etc.

2-Jack Dorsey (& others) sells Twitter to Elon Musk

3-Elon Musk destroys Twitter

4-Jack Dorsey creates a new platform, Bluesky

5-Scientists go to BlueSky, invest time and effort to build their profile … … …

…am I missing something? Why are they doing it again? 😳

Edits: sorry, acting up with my formatting again

thatdnaguy,
@thatdnaguy@genomic.social avatar

@elduvelle but surely they won't do the same thing again!!!

thatdnaguy, to bioinformatics
@thatdnaguy@genomic.social avatar

In January I get to give a division talk about artificial intelligence / machine learning.

I'm looking to gather as many instances of poor learning sets, bigotry, and other biases. It's going to be primarily clinical / clinical research people who are being sold that 'the algorithm' will save medicine because machines are unbiased. Shoot me your examples of why you shouldn't trust a confident algorithmic liar

skykiss, to cs
@skykiss@sfba.social avatar

deleted_by_author

    •
    thatdnaguy,
    @thatdnaguy@genomic.social avatar

    @skykiss good luck. Dell bakes quite a lot in. So does windows for that matter. Usually I just go through the installed programs/apps menu and start there looking for things I don't care about to remove. Then to startup options to disable all the things I don't need on startup.

    b0rk, (edited ) to random
    @b0rk@jvns.ca avatar

    a couple of years ago on twitter I asked why man pages don't have examples and had a surprisingly interesting discussion https://twitter.com/b0rk/status/1427308140916363269

    I learned that:

    • GNU tools intentionally left examples out of man pages, because the idea was that the examples were in the "info" pages instead (which I never heard of it in ~15 years of using Linux, apparently it’s am emacs thing)
    • BSD man pages do tend to have examples (for example man grep on Mac OS has some examples, on Linux it doesn't)
    thatdnaguy,
    @thatdnaguy@genomic.social avatar

    @b0rk that's interesting. I don't think I knew info pages even existed.

    thatdnaguy, to bioinformatics
    @thatdnaguy@genomic.social avatar

    Uni cluster runs using Docker images, so I have snakemake setup to specify the images appropriately dispatching jobs.

    But I'm switch back and forth between our Linux servers and the cluster. Aiming to run jobs on our servers using the same images to avoid version conflicts and unexpected behavior.

    Anyone using snakemake with dockerhub images on a standard Linux server? The docs aren't clear on compatibility and how to set it up so far.

    thatdnaguy,
    @thatdnaguy@genomic.social avatar

    @Elendol well I've got the images all public on docker hub. So accessing them isn't a problem. But what I'm looking to do is have our local server you singularity or whatever built-in tools that snake make can handle to run the actual rules inside specific docker containers

    thatdnaguy,
    @thatdnaguy@genomic.social avatar

    @Elendol not a problem. Automating image updates would be helpful too. :-)

    godlessmom, to Youtube
    @godlessmom@mas.to avatar

    Two types of content I consume when I want something relaxing and vanilla:

    1. Magnet fishing YouTube videos - omg this is so fun! 12/10 highly recommend

    2. ASMR antique restoration YouTube videos - soooooo satisfying.

    thatdnaguy,
    @thatdnaguy@genomic.social avatar

    @godlessmom I feel like pressure washing dirty things falls in that category as well

    thatdnaguy,
    @thatdnaguy@genomic.social avatar

    @godlessmom word. I lean toward cars, but rugs hide it so well

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