I pushed a package to bioconda 2 weeks ago and it's still waiting for review. Anyone here a maintainer that could help get it unstuck? github.com/bioconda/bio... (We have a paper in review that mentions an option for bioconda install - would like to make that aspirational sentence reality!)

Add vatools by chrisamiller · Pull Request #67110 · bioconda/bioconda-recipes

Adds a new recipe for vatools (https://github.com/griffithlab/vatools), a package designed to ease manipulation of genomic data stored in VCF format

github.com

I don’t even follow basketball and I am not from and have never lived in NYC but this thread is genuinely lovely.

I'll be happily wearing my @flomask.bsky.social on each and every flight for the rest of my life. It is crazy how few people wear masks on flights these days.

Kelly@broadwaybabyto.bsky.social · 3mo ago

A KLM flight attendant who was in close proximity to one of the deceased is now in the hospital with symptoms. All passengers from the Hantavirus cruise should be quarantined and carefully screened. Instead, they’ve been allowed to take commercial flights home. We’ve learned absolutely nothing.

i'm not a hardcore anti-AI guy, but i cannot think of a single benefit of genAI that could possibly outweigh the harm it is doing to our social fabric, shared reality, and most basic abilities to parse information and learn.

Katie Mack@astrokatie.com · 3mo ago

Just FYI there’s an account on here called @redditspaceviewes.bsky.social (with over 200k followers) that is posting a bunch of AI slop (including a “Saturn polar hexagon” with 8 sides) and claiming it’s NASA imagery. If you see anything posted by them, it’s likely fake.

Blog post on "The AI Rewrite Dilemma": lh3.github.io/2026/04/17/t...

I have mixed feelings about re-writing existing tools (fragmentation, maintenance burden, etc) but a ton of thought has gone into the `rewrites` manifest. Worth discussing.

Phil Ewels@ewels.bsky.social · 4mo ago

I'm both excited and a little terrified. It feels like a wave of AI-assisted tool rewrites is coming to bioinformatics whether we like it or not. We figured that the best we can do is to try to get ahead of it, so we wrote down some principles for doing it responsibly: rewrites.bio

Such a cool project from @nilshomer.com.

Fulcrum Genomics@fulcrumgenomics.com · 5mo ago

HGVS parsing sounds straightforward until you run it at scale across real clinical variants. We just released ferro-hgvs, a Rust-based parser/normalizer that processes millions of variants per second & handles many tricky edge cases other tools struggle with. 🔗 hgvs.acgt.bio Details in blog post👇

I'm constantly trying (/failing) to get this point across. If you're a trained expert in a field, then it may be worthwhile to question the scientific consensus of your peers. If you're not, the scientific consensus is absolutely the best you can do and it's arbitrary foolishness to disregard it.

Are there any R users working for the Australian federal dept of health? I’d love to hear from you! New gig, new people to meet :)

I think it's best for everyone to understand that the unified class project of billionaires right now is to do to white collar workers what globalization and neoliberalism did to blue collar workers.

I've been in SF for four days and on each day I've had multiple conversations where people (self included) express deep feelings, fear, wonder and worry about their skills being replaced or (this is less named explicitly but an assumed driver I think) no longer valued by others. Big threats to feel

was banging my head against a bug (VEP classifying my in-exon variants as 'downstream') that Claude Sonnet 4.5 fixed in about 5 minutes. I can understand the scepticism on LLMs being jammed into every corner of life, but there's merit in these tools

Reminder for everyone operating at situationally-diminished capacity.

Getting older is like being out on the ocean in the Ship of Theseus but then at some point the guys just decided against replacing the decayed parts.

The comments on this are all about how sweet it is and I feel insane. Using AI to make fake memories of your grandma with dementia and telling her they happened and then filming her reaction

Pipeline release! nf-core/oncoanalyser v2.3.0 - 2.3.0 - Spotted Nightjar! Please see the changelog: https://github.com/nf-core/oncoanalyser/releases/tag/2.3.0

Release 2.3.0 - Spotted Nightjar · nf-core/oncoanalyser

What's Changed Post release bump by @scwatts in #246 Improve samplesheet validation by @scwatts in #247 Important! Template update for nf-core/tools v3.5.1 by @scwatts @nf-core-bot in #266 Apply H...

github.com

I recently discovered Conventional Comments (conventionalcomments.org) for providing a pseudo-standard set of labels for feedback and just tried it for an article review and it was really helpful to specify issues vs. thoughts vs. suggestions, etc. Hopefully it's helpful for the authors too!

Join the Clinical Genomics Laboratory Community (CGLC) meeting on 24 November. This session will explore how artificial intelligence and large language models (LLMs) are transforming variant interpretation. Register for the meeting: us02web.zoom.us/meeting/regi...

Welcome! You are invited to join a meeting: Clinical Genomics Laboratory Meeting. After registering, you will receive a confirmation email about joining the meeting.

The topic for this meeting will be AI and LLMs in Variant Classification

us02web.zoom.us

You have to wonder if White House staffers are simply showing him AI videos at this point and he thinks it's reality.

Aaron Rupar@atrupar.com · 10mo ago

Trump: "The people of Chicago are walking around with MAGA hats. You have women, beautiful Black women, walking around with MAGA hats. 'Please let the president in and we don't care how he does it ... bring in the Marines.'"

Reminder: a large (2.5M+) sibling control study found "no evidence of increased risk of autism, ADHD, or intellectual disability associated with acetaminophen use". Precisely the kind of data that requires serious consideration before declaring mission accomplished. jamanetwork.com/journals/jam...

Acetaminophen Use During Pregnancy and Children’s Risk of Autism, ADHD, and Intellectual Disability

This nationwide cohort study with sibling control analysis examines the association of acetaminophen use during pregnancy with children’s risk of autism, ADHD, and intellectual disability.

jamanetwork.com

Heads up: ignore samtools dot org, similarly minimap2 dot com and likely others. It's owned by a known phishing site and while the binaries they offer look valid currently (but note they may be serving us different binaries to others), that could change. Ie: it's not us (Samtools team)! Be warned

Breaking Google up was one of the last best hopes for preventing the free press from getting squeezed into oblivion and harvested into AI slop, and for saving the open web. The ruling that effectively lets Google continue operating as a monopoly isn't just disappointing, it's a disaster.

One of the last, best hopes for saving the open web and a free press is dead

The Google ruling is a disaster. Let the AI slop flow and the writers, journalists and creators get squeezed.

bloodinthemachine.com

At scale, the way that we store (and process) data matters! Many may think that the way we keep data, the file formats we adopt, and the way that we compress data are unimportant details, but they are, in fact, critical considerations to allow science to move forward at scale!

naturepoker@binomicalabs.org · 11mo ago

I can't believe the biggest bottleneck in my lab right now is scrounging to afford more storage for processing data, not sequencing costs, technique or analysis difficulty.

I do not know when or how this became a KPop Demon Hunters stan account, yet here we are www.billboard.com/lists/huntr-...

Led by HUNTR/X’s ‘Golden’ at No. 1, ‘KPop Demon Hunters’ Becomes First Soundtrack With Four Simultaneous Hot 100 Top 10s

Led by HUNTR/X’s “Golden” at No. 1, “KPop Demon Hunters” becomes the first soundtrack ever with four simultaneous Billboard Hot 100 top 10s.

billboard.com

In case you missed it, this is fucked www.nytimes.com/2025/08/21/u...

He's gonna buy up the only remaining left leaning outlets, give them the WaPo treatment which means more people are gonna end up launching substacks and I'm gonna walk into the sea

Karl Bode@karlbode.com · last yr.

Bezos rumored to be buying Condé Nast, which would include Vogue, Teen Vogue, The New Yorker, GQ, Vanity Fair, Wired, Architectural Digest, and Ars Technica. Wired and Teen Vogue have done some of the best reporting in the Trump era. Ars Technica one of a handful of good remaining tech pubs.

happy birthday to bill watterson who gave me the gift of encapsulating my entire ethical approach in one comic panel.

It’s a good thing Congress isn’t alive to see this

I still can't get past the idea that people in America are now supposed to accept that this is a valid form of law enforcement and just assume it's fine when random dudes in groups with face-coverings, no ID, no warrant, & no uniform grab people off the street and force them into unmarked vehicles

Jeff Lazarus@jlazarus.bsky.social · last yr.

Not an original point but worth saying again - there is not a single element in this picture that identifies any of these folks as law enforcement agents. No badges, no uniforms, no vests. Out of context it just looks like a bunch of random guys are kidnapping a mayoral candidate.