Remote

Tim Fallon, PhD

@photocyte@genomic.social

mastodon 4.7.3

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@genomic.social

337 Followers

411 Following

8 Posts

Joined November 25, 2022

🌍 WEBSITE:

https://photocyte.github.io

🎓 ORCID:

https://orcid.org/0000-0002-3048-7679

PRONOUNS:

he/him/his

Tim Fallon, PhD @photocyte@genomic.social

· 26mo ago

@failedLyndonLaRouchite@mas.to @cmdcolin@genomic.social @ScienceMagazine@press.coop

Doesn't happen every day! All credit to the algae for having simultaneously novel and interpretable giant enzymes. Based on this preprint, titin takes ~6 hours to translate, and spontaneous frameshift (and translational aborition) probability during this lengthy translation gets almost expected.

So P. parvum definitely work hard to make their PKZILLAs!

https://www.biorxiv.org/content/10.1101/2024.04.08.588516v1

biorxiv.org

Tim Fallon, PhD @photocyte@genomic.social

· 26mo ago

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@press.coop https://www.science.org/doi/10.1126/science.ado3290

science.org

Tim Fallon, PhD @photocyte@genomic.social

· 24mo ago

Replying to

@jonny@neuromatch.social 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/

ftp.ebi.ac.uk

Tim Fallon, PhD @photocyte@genomic.social

· 23mo ago

Replying to

@jonny@neuromatch.social Still working on this suprisingly! (our server's storage has been acting up, so many retries on downloads) Do you know any existing example of an automated pipeline to download, do some ETL type things, build a derived database, and then publish it to bittorrent & a simple website? This is a common pattern in bioinformatics. There are a lot of moving parts there, and while I could come up with it, would be helpful if someone already navigated...

Tim Fallon, PhD @photocyte@genomic.social

· 43mo ago

Replying to

@oritpeleg Have you contacted Larry Buschman? He might be in Colorado but either way would be a good person to relay this through. I've also forwarded it to my Colorado firefly network ;)

Tim Fallon, PhD @photocyte@genomic.social

· 26mo ago

Replying to

@cmdcolin@genomic.social @ScienceMagazine@press.coop Your help played a part! Really appreciate it, I can't remember exactly where I used it, perhaps the modules on the genomic coordinates in Fig S6 , S7. It's called somewhere in the Zenodo items though... https://genomic.social/@cmdcolin/112100755859796058

genomic.social

Tim Fallon, PhD @photocyte@genomic.social

· 24mo ago

Replying to

@jonny@neuromatch.social Thanks! Okay, I gave Linux CLI bittorrent clients a quick google, and picked Transmission as that seems still developed vs rtorrent , and claimed a CLI client, but in looking into it in more depth the CLI clients seem deprecated? What do you use? Looking for something that would allow Linux CLI for finding & downloading or publishing a given file via low-friction (trackerless / DHT? / Zeroconf / mDNS ) approaches.