There are two recent papers that use sourmash in creative ways - and it gladdens my heart! pubmed.ncbi.nlm.nih.gov/40812187/ by @silask.bsky.social et al looks cleverly at human gut subspecies. www.biorxiv.org/content/10.1... by @rayanchikhi.bsky.social et al counts billions of k-mers. Super neat!
We had a last minute cancellation for STAMPS -- a phenomenal course on microbiome data analysis. Woods Hole, MA, July 14-24 2025.
If you or *anyone* you know is interested to attend, please email Titus &/or me... and we'll do what we can!!!
Thx for sharing widely! 🤞❤️
Economic loss due to NIH budget cuts by congressional district, scienceimpacts.org/fy26
The #SCIMaP team announces a major update: an analysis of the economic impacts of the White House's NIH FY26 budget.
Bottom-line, we estimate $46B in total economic loss, 202K lost jobs, and impacts in communities nationwide.
Interactive map and shareable report:
scienceimpacts.org/fy26
a 🧵
the issue arose due to some NCBI changes and has been solved! :)
My HPC team at UC Davis is hiring! Looking for an experienced sysadmin to help build and maintain clusters (hardware and software). HPC experience great, but if you’re an experienced sysadmin and willing to learn, please apply!
careerspub.universityofcalifornia.edu/psc/ucdavis/...
Another super cool bioinformatics tool (this one using pyani and sourmash) - genomeRxiv, for exploring multiscale taxonomic relationships between genomes. From @borisvinatzer.bsky.social group, by Reza Mazloom, and also with Lenny Heath - all at VT.
For whatever reason, the US government have decided the US should no longer lead in science. Great economic opening for other countries, but really bad for America. This could be stopped by a handful of majority senators. That they aren't doing it tells you they want us to cede 70 years of building
As we start the new year, I would like to remind everyone that it is now almost 120 years since the US decided consumer protection - by which I mean regulation - mattered. Given the upcoming presidential inauguration, let's talk about how that happened - and why it's so important. (A thread)
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!
Regularly tempted to write in my NIH grants innovation section: "Funding software that already exists and works well would be highly innovative for the NIH."
(I bet half the panel would break down ROFL, but I'm also highly skeptical that I'd get a good score, or that the PO would be amused.)
40% of the mass of everything transported by a ship in 2023 was a fossil fuel.
That stat paired with this new study shines a pretty harsh spotlight on how obscenely bad-faith the right-wing concern trolling around offshore wind + whales is
www.seattletimes.com/seattle-news...
I've been putting off sending a professional email since July because I've dreaded the response.
I sent it today, and received a reply of "no worries that's fine" in about three minutes.
I will learn nothing from this.
🧬🔍There are 50 petabases of freely-available DNA sequencing data. We introducing Logan Search which allows you to search for any DNA sequence in minutes, bringing Earth’s largest genomic resource to your fingertips.
🏔️ logan-search.org 🏔️
#Genomics #Bioinformatics #OpenScience
This was an interesting take on software dev, and gave me a generalized perspective on some of the challenges we've faced with sourmash over time. www.baldurbjarnason.com/2022/theory-.... Thanks @luizirber.bsky.social for sharing!
View with grape vines in the foreground and rolling hills with trees in the background. Cloudy sky with the beginnings of yellow sunset.
These grapes were beautiful, inside and out.
Doing good science is 90% finding a science buddy to constantly talk to about the project.
🧪 🍎 📍 🌊 🦑 pathwaystoscience.org
Paid Summer 2025 Undergraduate Research Placements; financial support in graduate school; tips on applications and other resources; opportunities in ocean sciences and engineering
Very cool
It’s been a pleasure to co-mentor on this project, excited about the progress!
Just updated taxid-changelog. Now you can track each NCBI Taxonomy taxon's detailed changes in the past 10 years😮😱😃
This is the proudest work I've done in my past 10+ year academic career, cause it's useful and funny but no one else did this, haha.
github.com/shenwei356/t...
This is a very important idea, and worthwhile for those developing bioinformatics software to consider. One massive shortcoming, over which the scientists & devs have quite little control, however, is the huge dearth in funding software dev & maintenance. Software is its own product & requires $!
Align to AllTheBacteria with low RAM (1-2Gb) and quickly (seconds if just 1000s of hits, 15 mins for a gene present in all 2.4 million genomes) using @shenwei356.bsky.social Lexicmap. So you can basically BLAST AllTheBacteria locally - but need 3-4Tb disk for index
www.biorxiv.org/content/10.1...
A thread with some new starter packs in genomics and bioinformatics 🧵 1/13...
Hi, I’d love to be added! I write software for metagenomics analysis.
I made a starter pack for algorithmic genomics. It's certainly incomplete, but already has a ton of awesome peeps. Let me know if you know people I should add (with a focus on algorithms and data structures in genomics)
go.bsky.app/TRWCnZs
Would love to be added 👋
It's important to realize how long scientists have warned those in power. Climate change is not somebody's fault for not recycling beer cans. It's the result of a fraud against the public by corporations who have flooded the zone with bribes and misinformation.
Don't miss out on this free #metagenomics webinar next week!
PacBio HiFi sequencing on Revio can be used to generate single-contig, complete MAGs from the most difficult sample type to assemble - soil.
Results for wetland and grassland soil shown here, from my talk at LAMG.
bit.ly/3Tf9qJj