Really enjoyed presenting our genomics talk "Declare, don't parse" at #SciPy2026 with Conrad Bzura! tl; dr Problem #1: Genomics is coupled to file formats, not data Problem #2: Most genomic operations aren't even "genomic" Solution: Be composable! Slides here: abdenlab.org/scipy26

Proteins are the machinery of life. Billions of their sequences have been cataloged—but the biology behind most is still unknown. Today we're releasing ESMFold2, ESMC and ESM Atlas to help change that. Open source, open to every scientist. biohub.ai/esm/protein

Excited to share our paper about copick, a dataset API and toolkit for collaborative annotation and analysis of #cryoET data! Whether you're picking particles or curating segmentations, copick reduces friction and brings #OME-Zarr to cryoET without breaking pipelines. 🧵👇 doi.org/10.1002/pro.70578

Super excited to be launching two things today: #RustQC 🦀🧬 and rewrites.bio 🚀 I used AI to rewrite 15 RNA-seq QC tools into a single Rust binary (I've never written any Rust). It ended up being over 60x faster. Here's the story 🧵 seqeralabs.github.io/RustQC/

Welcome to RustQC

Fast quality control tools for sequencing data, written in Rust.

seqeralabs.github.io

A tool to shoot genes with massive air from a compressor (TSGMAC) https://www.biorxiv.org/content/10.64898/2026.03.24.713841v1

So… um… I (and Draga Doncila Pop and Eric Perlman and @joshmoore.bsky.social and @kevinyamauchi.bsky.social) started a thing! We are excited and terrified in equal measures, and look forward to working with you all in our amazing scientific imaging community! ❤️‍🔥 Read the linked post for the lowdown.

Image Cooperative@image.coop · 5mo ago

Hello, world! We are starting a worker cooperative to build, maintain, teach, and support open source scientific imaging software. image.coop/blog/posts/2...

Hello, world! We are starting a worker cooperative to build, maintain, teach, and support open source scientific imaging software. image.coop/blog/posts/2...

I'll never get tired of lazily browsing elastix-coregistered #WSI data in @napari.org using the upcoming @openmicroscopy.org ome-zarr @zarr.dev format version that allows to specify and read transformations directly from the image data itself. Data source: rodare.hzdr.de/record/3131

We’re looking for a Community Manager to help shape and support the growing scverse ecosystem. Deadline January 10, 2026! More details here: jobs.helmholtz-muenchen.de/jobposting/d...

We are thrilled to announce the first official release (v0.1.8) of #𝗯𝗲𝗱𝗱𝗲𝗿, the successor to one of our flagship tool, #𝗯𝗲𝗱𝘁𝗼𝗼𝗹𝘀! Based on ideas we conceived of long ago (!), this was achieved thanks to the dedication of Brent Pedersen. 1/n

It was fantastic to reunite with the teammates in the Bay for the 2nd #scverse conference. It’s been an incredible three years together, and I’m beyond excited about what we’ll build next.

scverse conference 2025 done ✅ Really engaging week at Stanford with scPerturb-seq work, agentic models in biology, and strong interest in scaling software to millions of cells. Organizing alongside the rest of the @scverse.bsky.social team was a blast! Hope attendees found it productive 😄

Full house for our Bi[o]hub workshop on Day 3! Communities aren’t just built, they are co-created. Together, we’re shaping an open, connected world of all-things-single-cell research, where sharing tools and ideas drives discovery.

This is what hacking *actually* looks like. #OME_NGFF_Hackathon

no amount of state propaganda will ever convince me this man is my enemy

@unioncity.bsky.social · 10mo ago

I for one will welcome our Chinese overlords #Beerjacket #China #Tsingtao

BioContextAI is a community hub for agentic biomedical systems - @puellesv.bsky.social @biocontext.ai go.nature.com/3JmqKux

BioContextAI is a community hub for agentic biomedical systems - Nature Biotechnology

Nature Biotechnology - BioContextAI is a community hub for agentic biomedical systems

go.nature.com

The Data Science team at EMBL is hiring for two open positions! First, for a Scientific Community Manager, focusing on community aspects and training on data science. embl.wd103.myworkdayjobs.com/en-US/EMBL/j...

Scientific Community Manager

EMBL is Europe’s flagship research laboratory for the life sciences – an intergovernmental organisation with more than 110 independent research groups and teams performing scientific research in disci...

embl.wd103.myworkdayjobs.com

Join us as we explore emerging trends in agentic AI applications across bioinformatics workflows. ✨ Featured Panelists: Kexin Huang - Stanford University Vega Shah, PhD - NVIDIA Loic Royer - Chan Zuckerberg Biohub Network Jonah Cool - Anthropic

🚀 NEW PANEL ANNOUNCEMENT: Agentic Workflows in Bioinformatics at scverse 2025! 🚀 We're thrilled to introduce an exciting panel discussion at the upcoming scverse Conference 2025! More information in 🧵 #scverse2025 #Bioinformatics #AgenticAI #Conference

E11 Bio is excited to unveil PRISM technology for mapping brain wiring with simple light microscopes. Today, brain mapping in humans and other mammals is bottlenecked by accurate neuron tracing. PRISM uses molecular ID codes and AI to help neurons trace themselves. Read more: e11.bio/blog/prism

Luca Marconato at the European Bioconductor Conference 2025 in Barcelona, on advancing spatial biology analysis across programming languages — R, Python, JS. Important infrastructure for data ingest, representation, visualization, analysis for emerging spatial omics techniques

korean reporting is nightmarish on the conditions Korean workers were contained in

My favorite part of last-year #scverse conference was to finally meet in-person many developers that I only knew from their GitHub username! Submissions and travel grant applications close in 3 days. Find out more and apply at scverse.org/conference2025 @scverse.bsky.social

Here's a GIANT one: C3 photosynthesis using RUBISCO is inefficient, but scientists have designed and run a new and more efficient photosynthetic pathway in Arabidopsis: https://arstechnica.com/science/2025/09/new-pathway-engineered-into-plants-lets-them-suck-up-more-co₂/

Anndata now supports @zarr.dev v3, great for both performance and interoperability. Check out our guide for more info, especially sharding: anndata.readthedocs.io/en/stable/tu.... Don’t worry though, we remain fully v2 backwards compatible - upgrade fearlessly!

🔬 CZI Workshop at scverse 2025 🔬 Multimodal And Spatial Single Cell Data: From Data APIs to AI-driven Biological Discovery 🧵 @chanzuckerberg.bsky.social #scverse2025 #SingleCell #SpatialOmics #CELLxGENE #VirtualCells #AIBiology

It's taken more than 2 years but we can officially announce anndataR! There's still a lot of features to add but we hope a robust, "official", R-native H5AD reader/writer will unlock the defacto single-cell storage format for R users by avoiding issues with current solutions like zellkonverter.

Louise Deconinck@louisedck.bsky.social · 12mo ago

We're excited to share that our preprint on anndataR, a new package bringing Python's AnnData to R, is now available on bioRxiv 🎉 🔗 Read the paper: www.biorxiv.org/content/10.1... 💻 Check the package in action: anndatar.data-intuitive.com

scVerse conference is at Stanford this year! Encourage folks (especially Bay Area/West coast folks) to sign up and attend. Cool workshops/talks and other events + great community of developers for one of the most widely used open source software for single cell data analysis!

Want to contribute to the scverse omics ecosystem? Join the NVIDIA and scverse Hackathon: Accelerate Omics Workflows! Collaborate with NVIDIA experts, GPU-accelerated tools, and the scverse community. Apply by Aug 27, 2025. #Omics #DataScience #Hackathon #GPU LINK: buff.ly/OCUdlks

NVIDIA Accelerate Omics Hackathon

Take Omics tools to the next level with GPU acceleration.

buff.ly