Austin Richardson
@agdr.org
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📥 347
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Metagenomics, Software Engineering
pinned post!
NCBI's Taxonomy changes over time. We built Taxonomy Time Machine to track these changes: 🕰️ app:
taxonomy.onecodex.com
📄 pre-print:
www.biorxiv.org/content/10.1...
about 1 year ago
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Torsten Seemann
11 days ago
💾 Prokka 1.15.6 is released! This is the last major release of Prokka. But don't be sad, because
@oschwengers.bsky.social
already has an excellent replacement called Bakta you can migrate to.
#bioinformatics
#microbiology
#genomics
github.com/tseemann/pro...
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Release Heading into the sunset · tseemann/prokka
The future This is probably the last release of Prokka. I won't be making any code changes except bug fixes. I will update the databases occasionally. I strongly recommend you use Bakta by @oschwen...
https://github.com/tseemann/prokka/releases/tag/v1.15.6
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Antonio Camargo
about 2 months ago
🚨New preprint out! We present a foundational genomic resource of human gut microbiome viruses. It delivers high-quality, deeply curated data spanning taxonomy, predicted hosts, structures, and functions, providing a reference for gut virome research. (1/8)
www.biorxiv.org/content/10.1...
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Michael Baym
2 months ago
When you buy a cutting board from bioinformaticians
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Two-Word Horror
9 months ago
gut fauna
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qntm
2 months ago
Tech snow day
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🧬Jacob L Steenwyk
3 months ago
Apple's approach to protein structure is great for accessibility - & potentially biological realism - reasons. Eg, prediction could be achieved w/ smaller compute & the generative nature of prediction allows for multiple conformations A summary here:
genomely.substack.com/p/simplefold...
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SimpleFold and the Future of Protein Folding
A Generative Shift in Protein Folding
https://genomely.substack.com/p/simplefold-and-the-future-of-protein
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Paul Medvedev
3 months ago
If you're wondering why we're hosting the pre-print via dropbox, its because arXiv (and bioRxiv) did not accept it (because it is a review). Its a bit disconcerting, because a review is precisely the type of paper that would benefit a lot from pre-publication dissemination and feedback.
add a skeleton here at some point
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Closed my eyes for a sec and summoned another earthquake
3 months ago
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they should invent a type of volatile memory that gets heavier the more data it contains
3 months ago
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Bede Constantinides
4 months ago
Blogged about how zstd --long fills the gap between fast and slow-but-high-ratio genome compression methods
log.bede.im/2025/09/12/z...
add a skeleton here at some point
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NCBI BLAST can now output a proper CSV with headers 👏🎉:
www.ncbi.nlm.nih.gov/books/NBK131...
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BLAST+ Release Notes
Note: If building BLAST+ from source code, the Zlib, Zstandard and Bzip2 libraries will be needed.
https://www.ncbi.nlm.nih.gov/books/NBK131777/
4 months ago
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you can just pour milk over trail mix and eat it like cereal
4 months ago
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Ragnar {Groot Koerkamp}
5 months ago
Little writeup on the speed of fasta parsers, at last. Basically: both needletail and paraseq are process input linearly, and thus have a limit around 4 GB/s. By giving each thread its own slice of the input file, we're limited by RAM bandwidth instead :)
curiouscoding.nl/posts/fasta-...
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Dr. Stephanie
5 months ago
I do not enjoy that we now live in a world where seeing this banner at the top of PubMed makes me nervous.
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Alex Crits-Christoph
5 months ago
TIL the EBV genome is *included in the hg38 assembly* so that EBV reads are not erroneously mapped elsewhere to the human genome. That's certainly .... an interesting solution ... 🤯 But it enabled this extremely cool work:
add a skeleton here at some point
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Philipp Bayer
5 months ago
This is a bad take
stevensalzberg.substack.com/p/i-know-gen...
Saying that DNA data is like your browsing data and can can therefore be leaked is a false equivalence. Thing A is on fire so it's fine for thing B to be on fire, too-style argumentation.
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I know genomes. Don't delete your DNA
Too many people are panicking about 23andMe.
https://stevensalzberg.substack.com/p/i-know-genomes-dont-delete-your-dna
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Q: what do viruses and potatoes have in common? A: both are "acellular root"
6 months ago
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Andrew Rambaut
6 months ago
Handy to keep up with the ICTV's changes to virus taxonomy and species names:
taxonomy.onecodex.com/taxon/694009...
vs:
taxonomy.onecodex.com/taxon/694009...
or
taxonomy.onecodex.com/taxon/11676/...
vs
taxonomy.onecodex.com/taxon/11676/...
add a skeleton here at some point
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Jonathan Jacobs
6 months ago
Are you attending
#ASMicrobe
this is week? Stop by my talk on Friday morning (10AM) and say hello! 👋 if you can’t make it and want to meet up - just drop me a DM! I love this meeting and connecting with so many friends and colleagues over the years has made it really a special meeting.
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🌳 Taxonomy Time Machine now supports batch lookups! Quickly resolve lists of names/TaxIDs to their current NCBI taxonomy →
taxonomy.onecodex.com/bulk-resolver
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6 months ago
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🚀 Pushed some updates to
taxonomy.onecodex.com
- Example queries to help you get started - Summary section for easier interpretation - Perf. improvements
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Taxonomy Time Machine
Explore and compare the history of the NCBI Taxonomy Database. Instantly browse, search, and reconstruct taxonomic lineages at any point in time. Open source, web-based, and API-accessible.
https://taxonomy.onecodex.com
7 months ago
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Jonathan Jacobs
9 months ago
🧵 The ATCC Genome Portal hit 5,500 authenticated microbial genomes (>2,600 species)! 🎉🥳 We've sequenced, assembled, annotated 4,538 bacteria, 479 viruses, 479 fungi, and 4 protists! All NGS in-house @ ATCC under ISO, and >90% on BOTH
@nanoporetech.com
and
#Illumina
😎
www.atcc.org/applications...
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Discover the ATCC Genome Portal | ATCCCart
https://www.atcc.org/applications/reference-quality-data/discover-the-atcc-genome-portal
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Something happened to my $PATH and now nothing works Trisolarans: “the Sophons have succeeded in disrupting science”
9 months ago
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Bad day for VCF files
9 months ago
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Kai Blin
10 months ago
It's clearly a DNS issue, but overall, the NCBI is the least reliable I've ever experienced in my career. And I'm in this long enough to remember the Entrez API giving you only part of the file every 50-100th time.
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using github copilot to fail at github workflows aka boiling the ocean
11 months ago
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I call it the London Smaug (Tension Tamer + espresso latte)
11 months ago
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Martin Steinegger 🇺🇦
11 months ago
Join us at SNU and gain access to leading-edge hardware:
m.youtube.com/watch?v=ztth...
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Mac OS9 for Bioinformatics in SNU
YouTube video by 갈로아 Galois
https://m.youtube.com/watch?v=zttheqGB9T8
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How many arginines are in mStrawberry?
11 months ago
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Bluesky, RedNote, Green...?
12 months ago
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Flo Débarre
12 months ago
Five years ago (Saturday 11 Jan 2020), first public announcement and availability of a sequence of the new coronavirus. It was posted by
@eddieholmes.bsky.social
at 01:05 UTC on Virological, and announced on Twitter at 01:08 UTC. ▫️1/
web.archive.org/web/20200118...
archive.is/z880d
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Andrew Page
12 months ago
I'm putting together a Microbial Bioinformatics starter pack to help get everyone connected in our community. Let me know if there are any bluesky users to be added and share so that twitter refugees can tune back in to the fantastic world microbes
go.bsky.app/3ezLo7e
add a skeleton here at some point
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Titus Brown
12 months ago
Hi all, here's my passion project for December - a Web site for ~realtime DNA sample screening/composition analysis. Let me know what you think!
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Announcing: the chill-filter Web site - DNA sample composition at a glance!
what's in my sample, dude?
http://ivory.idyll.org/blog/2024-announcing-chill-filter.html
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Niema Moshiri
about 1 year ago
Got something interesting cooking up... 👀
@robert.bio
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Wei Shen 沈 伟
about 1 year ago
The story behind Sylph, from
@jimshaw.bsky.social
. It's quite inspiring to read.
jim-shaw-bluenote.github.io/blog/2024/de...
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Developing sylph - a look into bioinformatics tool development | Jim Shaw
Jim Shaw's academic website.
https://jim-shaw-bluenote.github.io/blog/2024/developing-sylph/
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Molly White
about 1 year ago
As the writer of an email newsletter, I perhaps ironically also much prefer RSS. For what it’s worth, an increasing number of RSS readers have functionality to receive email newsletters and plonk them into your feeds, and there are services like
kill-the-newsletter.com
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Kill the Newsletter!
Convert email newsletters into Atom feeds
https://kill-the-newsletter.com/
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Zamin Iqbal
about 1 year ago
Ha, a taxonomy time machine. I bet it has fun with with virus names over coming months
add a skeleton here at some point
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NCBI's Taxonomy changes over time. We built Taxonomy Time Machine to track these changes: 🕰️ app:
taxonomy.onecodex.com
📄 pre-print:
www.biorxiv.org/content/10.1...
about 1 year ago
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Austin Richardson
Yunha Hwang
about 1 year ago
Hello 🦋
#protein
/
#microbio
/
#BioML
community! We are excited to release Gaia🌎, a context-aware protein search tool, extending protein search and discovery capabilities beyond sequence and structure, to include *genomic context*. Search your favorite protein sequences with on
gaia.tatta.bio
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There is a genus of fungi named Drosophila.
www.ncbi.nlm.nih.gov/Taxonomy/Bro...
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Taxonomy browser (Drosophila)
THE NCBI Taxonomy database allows browsing of the taxonomy tree, which contains a classification of organisms.
https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=2081351&lvl=3&lin=f&keep=1&srchmode=1&unlock
about 1 year ago
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TIL whales can get the flu. I mean it makes sense I just never thought about whale flu before:
www.ncbi.nlm.nih.gov/Taxonomy/Bro...
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Taxonomy browser (Influenza A virus (A/whale/Maine/328B/1984(H13N2)))
THE NCBI Taxonomy database allows browsing of the taxonomy tree, which contains a classification of organisms.
https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=1457348
about 1 year ago
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over 1 year ago
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Which one of you nerds did this?
over 1 year ago
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