Now that we have mainstream AI... How many of you are enforcing the three laws of robotics?? BE HONEST.
🎙️ new episode of #microbinfie just dropped! In it, @happykhan.mstdn.science.ap.brid.gy , @andrewjpage.bsky.social , and I talk with Boston Women in Bioinformatics. on.soundcloud.com/RafSdL7grmyB...
154 - Boston women in bioinformatics
Nabil, Andrew, and Lee talk with Liyang Diao and Valisha Shah from the nonprofit organization, Boston Women in Bioinformatics, a community that supports bioinformaticians in the Greater Boston area. W
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We should probably acknowledge CDC now has a new Director. Welcome 👋 Your boss may be NotAScientist RFK Jr., but your mission is public health. When politics ignores evidence, CDC should choose science. Every. Single. Time.
Erica Schwartz confirmed as CDC director, filling nearly yearlong vacancy
Now confirmed, Erica Schwartz is the third CDC nominee since Trump took office for his second term.
statnews.com
The New York Times wouldn't let me write about the Age of Diarrhea so I had to do it myself.
Welcome to the Age of Diarrhea
The future is not knowing what ails you
stringinamaze.net
Peter@notalawyer.bsky.social · 2y agowelcome to the Age of Diarrhea
I wrote a post about how this all came together. About 20 iterations, switching between Claude conversational mode for structure and the GitHub agent for targeted fixes once I could see things rendering. Found that split worked surprisingly well. lskatz.github.io/personal/202...
Yearbook template
My wife volunteers on the school yearbook committee. Her job is to solicit pictures, organize them, and help with the yearbook layout. She and the other volunteers work in a proprietary web tool. Watc...
lskatz.github.io
Lee Katz@lskatz.github.io · 4mo agoMy wife volunteers on the school yearbook committee, working in a proprietary web tool. Watching her, I got curious: what if a yearbook was just a Git repo? So I built one as a Jekyll template. lskatz.github.io/yearbook-tem...
We're back baby! Talking about Seebot. You're not sure what it is either?? @andrewjpage.bsky.social and @lskatz.github.io grill @happykhan.mstdn.science.ap.brid.gy on the #microbinfie podcast, and HE SPILLED THE BEANS. m.soundcloud.com/microbinfie/...
153 - Seebot
Play 153 - Seebot by Micro Binfie Podcast on desktop and mobile. Play over 320 million tracks for free on SoundCloud.
m.soundcloud.com
the food safety stuff is another reminder that a large, huge, gigantic part of being a republican is going “lmao why are we spending money to prevent horrifying disasters from happening if they never happen 🤪”
Absolutely iconic that the parasite outbreak is one where ivermectin is not effective.
Help, I've crestfallen and can't get back up
Elmo Surrounded by Intense Fire
ALT: Elmo Surrounded by Intense Fire
static.klipy.com
Early versions were known as the Kapsak Spectac. Congratulations team!!
Jess Chen@drjesschen.bsky.social · 3mo agoHurray!! Big congrats to Arzoo and Mo from my team for developing this pipeline and getting it out there! Thanks to Justin, Peyton, @curtiskapsak.bsky.social and @lskatz.github.io their support of this work!
BREAKING: New proposed OMB regulation, applying to all federal grants, requiring grant reviews by senior political appointees and re-emphasizes that "peer review remains advisory and does not replace agency discretion". #standupforscience public-inspection.federalregister.gov/2026-10817.pdf
public-inspection.federalregister.gov
🦑 Kalamari v5.9 adds new outbreak‑relevant viral genomes to the curated set. This includes topical organisms related to ongoing outbreaks: measles, hantavirus, and ebola. 🔗 github.com/lskatz/Kalam...
Release v5.9 now with ebola, hentavirus, and measles (oh my!) · lskatz/Kalamari
What's Changed Fix build-sketch CI failure due to slash in github.ref_name for PRs by @Copilot in #72 Add Bundibugyo ebolavirus reference genome to Kalamari chromosome catalog by @Copilot in #80 F...
github.com
💉 Did you know, if you live in or are traveling to a measles outbreak area, your baby can receive the measles vaccine as early as 6 months❓ Babies under 12 mo are at highest risk for severe disease from measles. Early vaccination provides critical protection during outbreaks.
Measles Prevention and Control Implementation
Please use this page to implement practices in your office to prevent and control measles spread. You’ll find details about measles vaccination recommendations, a sample, customizable measles policy, and tips to help implement it in your office.
aap.org
Annapotater update! I found a very minor thing to change. So there is a new minor version today.
Lee Katz@lskatz.github.io · 4mo agoI finally put it onto Bioconda last night. Give it a go. github.com/lskatz/annap...
It has been many years since I created Annapotater out of the frustration that there was no simple SNP annotation tool at the time. The mainstream tool required Java and if you wanted to have a custom genome, then it was also a pain.
How well do ARG detection pipelines agree when applied to the same data? Spoiler: not very well. In our new preprint, we ran 10 pipelines on 270M microbial unigenes from GMGCv1. The same data can support conflicting biological conclusions! 🧵 www.biorxiv.org/content/10.6...
The elusive resistome: a global comparison reveals large discrepancies among detection pipelines
Identifying antibiotic resistance genes (ARGs) from metagenomic data is critical for studying antimicrobial resistance across microbial communities and pathogens. However, there is no standardized methodology for ARG annotation. Here, we compare ten commonly used ARG detection pipelines by analysing over 270 million prokaryotic genes from the Global Microbial Gene Catalogue across 13 distinct habitats. We observed up to a 45-fold difference in the number of reported ARGs, with a mean Jaccard index of only 16% between pipelines. Pipeline selection profoundly impacted downstream biological interpretations, with drastic changes to estimates of ARG relative abundance and richness, to the characterization of pan- and core-resistomes, and to the class-level composition of the inferred resistome. ARG detection pipelines make different, defensible trade-offs, and no single approach should be treated as authoritative. Therefore, users should justify and communicate choices carefully, as our analyses show that, taken uncritically, the same data can support conflicting biological and ecological interpretations. ### Competing Interest Statement The authors have declared no competing interest. National Health and Medical Research Council of Australia (NHMRC), 2031902 Australian Research Council (ARC), FT230100724 International Development Research Centre (IDRC), 109304-001 Deutsche Forschungsgemeinschaft (DFG), FO1279/6-1 Bundesministerium für Bildung und Forschung (BMBF), F01KI1909A, 01KI2404B Swedish Research Council (VR), 2024-06123, 2019-00299, 2023-01721 Knut and Alice Wallenberg Foundation, KAW 2020.0239 Swedish Foundation for Strategic Research, FFL21-0174
biorxiv.org
Here is the scientific thread bsky.app/profile/did:...
@bigdatabiology.bsky.social · 4mo agoHow well do ARG detection pipelines agree when applied to the same data? Spoiler: not very well. In our new preprint, we ran 10 pipelines on 270M microbial unigenes from GMGCv1. The same data can support conflicting biological conclusions! 🧵 www.biorxiv.org/content/10.6...
I added a new file to my mirrors site. Anything else I should add? I don't think it can be large files. lskatz.github.io/mirror/
Mirrors
This is an attempt to make a mirror for some commonly used bioinformatics datasets.
lskatz.github.io
1/ 🚀 Pathoplexus now supports the Andes variant of Hantavirus (ANDV). ANDV is the variant identified in the recent MV Hondius cases, & the Hantavirus variant previously identified as having occasional human-to-human transmission. pathoplexus.org/andv #hantavirus #hondius
Hantavirus is unlikely to spiral into a pandemic. But the real story is this: WHO is on the cruise ship. It's issuing clear guidance. It's coordinating across countries. CDC has been largely silent—no guidance to doctors, no public update.
Howdy! Happy to announce that Bactopia v4 is finally out! 🥳 This release supports the latest from @seqera.io Nextflow v26 (strict syntax, static types, and records! oh my!) It also open's the doors to start doing some fun things with Bactopia. To learn more, check out: bactopia.io/blog/bactopi...
Bactopia v4 Updates and Improvements | Bactopia
Learn about the new features and improvements in Bactopia version 4.
bactopia.io
I wrote a post about how this all came together. About 20 iterations, switching between Claude conversational mode for structure and the GitHub agent for targeted fixes once I could see things rendering. Found that split worked surprisingly well. lskatz.github.io/personal/202...
Yearbook template
My wife volunteers on the school yearbook committee. Her job is to solicit pictures, organize them, and help with the yearbook layout. She and the other volunteers work in a proprietary web tool. Watc...
lskatz.github.io
Lee Katz@lskatz.github.io · 4mo agoMy wife volunteers on the school yearbook committee, working in a proprietary web tool. Watching her, I got curious: what if a yearbook was just a Git repo? So I built one as a Jekyll template. lskatz.github.io/yearbook-tem...
My wife volunteers on the school yearbook committee, working in a proprietary web tool. Watching her, I got curious: what if a yearbook was just a Git repo? So I built one as a Jekyll template. lskatz.github.io/yearbook-tem...
"If you want to rewrite my tools with AI, please feel free to do so." I love how much this comes from a FOSS standpoint.
HHeng Li@lh3lh3.bsky.social · 5mo ago
Blog post on "The AI Rewrite Dilemma": lh3.github.io/2026/04/17/t...
I don't understand rewrites.bio at all. Most bioinformatics software is distributed with a license. The license specifies exactly what is and is not permitted to do with the software. Yet now one is supposed to ignore the license and adhere to requirements specified by someone on a website??
rewrites.bio - A manifesto for bioinformatics
Principles for responsible AI-assisted rewriting of bioinformatics tools.
rewrites.bio
Phil Ewels@ewels.bsky.social · 5mo agorewrites.bio is all pretty common sense stuff: credit original authors, emulate output exactly, maintain what you ship, don't spam open-source maintainers with AI-generated bug reports. I wrote a second blog post covering this part of the story here: seqera.io/blog/rewrite...
www.pnas.org/doi/10.1073/... If you ever need lto be convinced by how bad the "Contributed by" track is at @pnas.org ... Only author: David Lipman, handling editor: David Lipman. Only integrity-free person not embarrassed by such a paper: David Lipman. Even uses "I did" in the abstract. Shameful.
Genomic epidemiology of Salmonella and Campylobacter in poultry production: Quantifying the contribution of primary breeders | PNAS
The US broiler production system processes over 9.3 billion chickens annually through a highly integrated pyramid structure where two primary breed...
pnas.org
Host read removal sounds simple. It's not. 🧫 Ep. 151 of #microbinfie: we talk with @bede.im about Deacon — why alignment-based approaches fall short, the sensitivity/specificity tradeoff, and what it takes to remove host reads at scale. Part 1 of 2. #metagenomics on.soundcloud.com/gEm7QyaTauvd...
151 - Deacon part 1
In this Software Deep Dive episode, we talk with Dr. Bede Constantinides (University of Birmingham) about Deacon, a tool for removing host DNA reads from metagenomic datasets. We discuss why host read
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