Tim Fallon, PhD

@[email protected]
338 Followers
412 Following
703 Posts

biologist, biochemist, genomics enthusiast, bioinformatician, roboticist, natural products disciple. MIT PhD. Current postdoc in the Moore lab @ SIO/UCSD https://photocyte.github.io

#biology #biochemistry #bioluminescence #evolution #genomics #bioinformatics #cheminformatics #semanticweb #wikidata #biosynthesis #algae

Twitter: @photocyte

🌍 WEBSITEhttps://photocyte.github.io
🎓 ORCIDhttps://orcid.org/0000-0002-3048-7679
PRONOUNShe/him/his
Tim Fallon, PhDOct 27, 2024
Yumechi | ゆめち   Oct 27, 2024
Refining my #nextflow #cuda #GPU process for #bioinformatics , does anyone have some pointers on how to:

- Assign individual GPU IDs to docker run? The process only uses one GPU but the server may have multiple GPUs, how does each sample know which GPU ID to use?
- Is there an established way to detect CUDA versions and choose the right image? I wrote a pipeline to build and tag for every possible version but not sure how to make it happen on nextflow. https://hub.docker.com/r/l1drm/dreg/

I partially solved (2) by a hack:

https://github.com/Functional-Genomics-Lab/dREG-nf/blob/main/modules/local/dreg/main.nf

https://github.com/Functional-Genomics-Lab/dREG-nf/blob/main/bin/cuda_version.sh
Show threadTim Fallon, PhDOct 14, 2024

@jonny See also: the 194 GB "Reference_Proteomes_2024_05.tar.gz"
from

https://ftp.ebi.ac.uk/pub/databases/uniprot/current_release/knowledgebase/reference_proteomes/

Index of /pub/databases/uniprot/current_release/knowledgebase/reference_proteomes

Tim Fallon, PhDOct 14, 2024

Hey @jonny I'm running into very typical pain point of having to download huge files in bioinformatics (almost 1 TB Kraken2 index). Although they are available "instantly" on public clouds, distributed downloading globally and distributed sharing internally would be really neat (or at least, a simple solution to point people towards versus just centralizing it all on a shared filesystem).

What's your recommended tool for doing this? Good ole bittorrent?

File example:
https://github.com/BenLangmead/aws-indexes?tab=readme-ov-file

GitHub - BenLangmead/aws-indexes: Catalog of genomic indexes freely available from public clouds

Catalog of genomic indexes freely available from public clouds - BenLangmead/aws-indexes

GitHub
Tim Fallon, PhDAug 8, 2024
It came from the deep(ish) ocean... and then transitioned to a euryhaline lifestyle causing widespread fish-killing blooms in brackish water throughout Texas and Europe... It's Prymnesium parvum and their #PKZILLA s! Out today in @ScienceMagazine https://www.science.org/doi/10.1126/science.ado3290
Show threadTim Fallon, PhDMay 31, 2024

@jonny Speak of the devil, this PDF just showed up in my inbox!

The "contract doesn't allow strikes" point (see last section) is concerning to me. What's the counterpoint? Perhaps presumably whatever downsides (i.e. the UC & UAW going into breach of contract litigation & the contract ultimately is dissolved) is ultimately a moot point for UCSD because UCLA and UCSC (and other campuses?) are already striking?

https://drive.google.com/file/d/1T38Q9r8tS3GC6tR8qCba9I8-4JFijXxK/view?usp=share_link

4/2

edit: link to PDF, not parent folder.

2nd UAW Communication.pdf

Google Docs
Show threadTim Fallon, PhDMay 31, 2024

When I googled for the "look for the helpers" quote, this article came up. I look forward to reading it, it seems pretty against my philsophy from the title "Mr. Rogers's "Look for the Helpers” Is Bad for Adults" but it wouldn't be the #1 hit on Google if it didn't say something useful and journalism needs to have a catchy title to "sell" right? 4/4

https://www.theatlantic.com/technology/archive/2018/10/look-for-the-helpers-mr-rogers-is-bad-for-adults/574210/

The Fetishization of Mr. Rogers’s ‘Look for the Helpers’

Turning the reassuring line for children into a meme for adults should make everyone uncomfortable.

The Atlantic
Show threadTim Fallon, PhDMay 31, 2024
I keep rewatching this TED talk in 1 of 3. It's so dang inspiring. My takeaway, maybe a bit weird, is how incredibly powerful humor and fun are. Sonia Vallabh and Eric Minikel embody the helpers ala Fred Roger's "look for the helpers", to find the strength to help too. 3/3
Show threadTim Fallon, PhDMay 31, 2024

If you aren't familiar with CJD or prion diseases, this is a useful intro:

https://en.wikipedia.org/wiki/Creutzfeldt–Jakob_disease

2/2

Creutzfeldt–Jakob disease - Wikipedia

Show threadTim Fallon, PhDMay 31, 2024
@jonny P.s. If I don't respond quickly please don't read into it, I am trying to check le Twit and Mastodon on a only a few time a week basis, so might not get to it for some days 3/2
Show threadTim Fallon, PhDMay 31, 2024

@jonny one solution is just to avoid the line since I know the campus well and know where the line likely to be, but carrying my e-bike up/down some alternative route to avoid the line feels shameful right...

I want to be able to look my collegues in the eye, but I don't really know what the strike is about, or, if my difficulties rise to the level that warrant crossing the picket...

DMs fine too! Just wanted to be sure you saw this... We haved posted back and forth but not DMed before...2/2