binomicalabs.org - Profile | ThreadSky | a Reddit-style client for Bluesky

🧫🦠

submitted 1 day ago • 0 comments

Our NSF HSI STEM grant w/ @drmtrujillo.bsky.social & Dr. Olga Calderon was terminated today. The goal was to help community college students transition to 4 yr schools and train them in wastewater epidemiology. We had an amazing 1st cohort and had a strong positive impact on their lives.

submitted 1 day ago • 10 comments

I'm fond of sharing and discovering preprints on this platform. Here's how I made a small extension (Firefox only) that simplifies posting preprints from @biorxivpreprint.bsky.social and @medrxivpreprint.bsky.social : thenode.biologists.com/painless-pre...

submitted 2 days ago • 1 comment

Sure, when a baby elephant does it, it's cute, but when I do it, all of a sudden I'm not welcome in Pizza Hut anymore.

submitted 3 days ago • 132 comments

Question for dorado correct/herro users out there. What's the final corrected fasta yield like on your end? I'm feeding in r10 fastq with 13 billion bases and getting back 2.4 m bases in return, not sure if this is expected 😅 Granted, I'm still trying to figure out a proper use case for this 💻🧬

submitted 3 days ago • 0 comments

Small update from AllTheBacteria (allthebacteria.org). Assemblies can be bulk downloaded from OSF as before, or you can now get individual assemblies from AWS. We now also have a LexicMap index on AWS, so you can align your favourite gene against 2.4million bacteria (next post for price estimates)

submitted 5 days ago • 1 comment

New genome graph visualization tool currently under heavy development. Looks promising!

submitted 3 days ago • 0 comments

So what are people using to visualize genome gfa these days? I've been using ctlab fork of BandageNG (github.com/ctlab/Bandag...) but it looks like older BandageNG is finally getting updated too (github.com/asl/BandageNG) Or are there better gfa graph visualization solutions out there now? 🖥️🧬

submitted 3 days ago • 2 comments

Hoot Hoot I Scream ice cream parlor, Los Angeles, CA, 1928

submitted 4 days ago • 6 comments

Finally cut my hair short after... 7~8 years? Time to sort out the mess for donation to locks of love. Haven't done this in a crazy while.

submitted 4 days ago • 0 comments

My lab's incubator bit the dust early on in the Haloarchaea sequencing project, so I've been using an aquarium + reptile heating pad & LED light panel hooked up to a PID. It's been working for 7 sequencing run worth of cultures so far. Just need to remember to sandwich the plates in plastic 🧫🦠

submitted 4 days ago • 1 comment

#microsky

submitted 4 days ago • 0 comments

I've sequenced more genomes in the last two weeks than a certain medical college sequencing core did in the last six months. Honestly quite a bit higher quality output as well. Let's not even go into the whole overhead & costs comparison. I'm not sure what this means - but it must mean something.

submitted 4 days ago • 0 comments

It looks like I need to manually untangle and thread my way through 100k bp worth of this 😬

submitted 5 days ago • 2 comments

Welp due to overwhelming demand (=one[1] nudge from the inimitable @jopabinia.bsky.social) I'm making an informational comic about dicyemids #invertefest 🦑🌊 I do not know how long it will take to finish, so please enjoy the heck out of this title page for now

submitted 5 days ago • 10 comments

Hmm. Thinking of going for vertical poster again - maybe not ideal for presentation, but it's far easier to find local commercial printers on the cheap!

submitted 5 days ago • 0 comments

Got the final go-ahead for poster presentation at BBM 2025! Extremely happy to finally share at least some of the Deinococcus research I've been mulling over for so long. May-June will be crazy couple of months.

submitted 5 days ago • 1 comment

Don’t destroy your seed corn, says a VC director. “The only thing more damaging than the recent attacks on our research universities is the silence from my colleagues in the venture capital world, especially from those who have the ear of the president.” www.nytimes.com/2025/04/28/o...

submitted 5 days ago • 4 comments

Question for #archaeasky 🦠🧫 folks: I'm looking at a specific contig in an Archaeal genome with repeat elements that remain difficult to resolve even with 100~1000x coverage and minimum 10k read length. Anyone else dealt with something similar? What could I even be looking at?

submitted 6 days ago • 3 comments

Unique investigation of some errors in long read assemblers. In particular these remarkably chimeric contigs are 😱, if rare.... Improving long read assemblers is definitely the space to be in when it comes to the future of metagenomics, as short reads won't be part of it 😉

submitted 9 days ago • 3 comments

For bioinformatics crowd 🧬🖥️ looking at different backup solutions. I know backblaze had been mentioned by some before, but they seem to have issues "Backblaze: A Loss-Making Data Storage Business Mired in Lawsuits, Sham Accounting, and Brazen Insider Dumping" www.morpheus-research.com/backblaze/

submitted 6 days ago • 1 comment

Perk of being friends with a bunch of cinephiles in #nyc - got to check out a 35mm screening of the Chinatown at the Metrograph today. This film hits somewhat differently the older I get. Darker and more dreadful, like when Noah Cross proclaims he doesn't even want money - he wants the future.

submitted 6 days ago • 0 comments

Testing out Autocycler for some tough genomes - which also means I get to test out new crop of assemblers as well. For certain types of repeat-rich Archaeal genomes, hifiasm seems to be a great choice. Certainly more than good enough complement to the standard Flye output! 🦠🧫🧬💻

submitted 8 days ago • 0 comments

Depressing, but not surprising. Playbook for current administration is to go after organizations that has known issues - but twist it so the outcome is naked obedience for the regime, not addressing of genuine problems. www.theverge.com/news/656720/...

submitted 8 days ago • 0 comments

Good! I've never understood "scientific consensus"; it is not how the scientific method works. "Convergent evidence" seems more appropriate. The independent formulation of natural selection by Darwin & Wallace is an example of convergent evidence www.science.org/doi/10.1126/... 🧪#philsci #ecoevo

submitted 9 days ago • 3 comments

My nightmare in #eDNA is to detect a rare or threatened species that turns out to be a false positive, so we set out to evaluate some of the commonly used taxonomic classifiers. The results are finally out: onlinelibrary.wiley.com/doi/full/10.... 1/3

submitted 11 days ago • 1 comment

#MicroSky #PhageSky

submitted 9 days ago • 0 comments

#DNAday

submitted 9 days ago • 0 comments

It's publication day of my first book: The Tree of Life. The tree of life is a time machine that can take us back 4 billion years to meet our most distant ancestor. It is the magic that lets us tell the origin stories, beginning with this ancient relative, of everything from mushrooms to man.

submitted 10 days ago • 31 comments

“New horizons for Julia”: My article about #Julialang and new directions for the language. I talk about new tooling for installation, compilation to small binaries, and more. Julia is simply the best and most fun language for #science and #engineering. lwn.net/Articles/100...

submitted 10 days ago • 0 comments

New genomic & genetic insights into Mendel’s pea genes, including previously uncharacterised alleles 159 years after Mendel published his work, this is a real delight (especially for a geneticist) 🧪 @nature.com www.nature.com/articles/s41...

submitted 10 days ago • 2 comments

Starting #RECOMBseq with @rayanchikhi.bsky.social 's keynote. Here stressing our responsibility as scientists to enable access to a common good: genomic data

submitted 10 days ago • 1 comment

📅 Genomic Technologies Open Science Day - June 9 FREE event featuring expert developers and users! Register: www.jax.org/scienceday25/ Happening in person at @washu.bsky.social and online in partnership with NHGRI and @jacksonlab.bsky.social 🧪🧬🖥️👩‍🔬 #STS Learn more at genometdcc.org#outreachevents

submitted 11 days ago • 0 comments