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

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

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...

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.

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

🧬🖥️ I am strongly of the opinion that bioinformatics needs to move away entirely from text-based and "loosely" structured file formats for essentially any type of data. File formats should be binary-first, and designed for *correct* and *efficient* machine parsing 1/3

Preprint alert 🚨 Do you use chatbots in your work or even build MCP servers and agentic systems yourself? Or would you like to find a way to use biomedical tools using natural language? Then check out biocontext.ai, now out on bioRxiv: www.biorxiv.org/content/10.1...

Annotated matrices are much more valuable! AnnData can easily be read into R/Bioc as well unlocking more stats tools.

amtrak’s marketing team gets it

Metadata & Standards Developer – FAIR Bioimaging We seek a developer to advance metadata standards for imaging data (e.g. OME-Zarr, NGFF) 📌 Schema design (JSON-LD, RDF, SHACL), FAIR principles, open dev 🤝 Work with RO-Crate, ELIXIR, RDA & global partners 🌍 Remote | TVöD 13–14 | Deadline: 30.06

📣 Mark your calendars! The 2025 edition of the scverse conference will take place on 17-19 November at Stanford University (US) scverse.org/conference20... Call for abstracts and registrations coming soon!

Based on present trends I expect the Pope-assassination Signal chat to be leaked middle of next week.

You may be fearing your 401k is no longer enough for you to retire. But with all the cuts to NIH and Medicare you also won't live as long. So the policies are integrated.

Pleased to announce I am substantially better at making economic/financial predictions than Wall Street.

Hello world! 👋 🔥 The Scientific Python community is building tools to power our ecosystem and support contributors and maintainers! 🚀 Discover our projects and learn how you can get involved by following us on GitHub: 🔗 github.com/scientific-python

1/ As a data platform company, we get a unique view of how other companies use data. In light of the recent cuts at @noaa.gov, our CEO, @rabernat.bsky.social, reached out to our customers to get their perspective on the value of NOAA’s data and services.

Our paper benchmarking feature selection for scRNA-seq integration and reference usage is out now www.nature.com/articles/s41...! Keep reading for more about how we did the study and what we found out 🧵 👇 1/16

A pre-trained SCVI model of our Tahoe-100M cell atlas is now available as a HubModel! It can be used for gene expression visualization, differential expression, or cell clustering. Available at Hugging Face with instructions on how to load it (see thread)

Random but this claim about absolute size of GDP is not true. I was trying to work out if there was some economic rationale for preferring Russia as a trade partner/ally to the UK. I wish Google had not added a feature that randomly lies to you when you search for information. Cooler if they didn't.

It's @scipyconf.bsky.social submission time again! This year I am running the Bioinf/Comp Bio/Neuroscience track, covering how Python is advancing science and problem-solving in those fields. Let me know if y'all have questions, and looking forward to the submissions!

🎉 Scanpy 1.11.0 is out! 🎉 just after reaching 2000 stars on GitHub! - sc.pp.sample replaces subsample with many new features - Sparse Dask support pca - session-info2 package for more reproducible notebooks See the release notes:

Trump & Musk are making massive cuts to the National Institutes of Health. I know there is a lot going on right now, but this is one of worst things they have done so far, will affect cancer research and trials, the search for cures, innovation and competitiveness, our universities. Your lives.

Recently, we held the first #scverse SpatialData 3-day hackathon in Basel (Switzerland), where we brought together 20 developers from the Python, R, and web communities to work on interoperability, performance, and ergonomics for spatial omics data. Here is what we worked on!

🚀 We're hiring! Join the German BioImaging Team as a Software Developer! 💻 Build scalable #bioimaging solutions 🌍 Collaborate globally 🎯 Contribute to open science through #OMEZarr @openmicroscopy.org Remote, full-time. Apply by 31 Jan 2025: bit.ly/3Zrd4SR

✍️ New Bioconductor blog post on the SpatialData hackathon and workshop, organized by https://buff.ly/4j1UidT with Bioconductor participation. Check it out: https://buff.ly/4fM1qrH Thanks @arturmansl.bsky.social‬ ! #Bioconductor #SpatialData #scverse #Bioinformatics #OpenScience #RStats

It’s been a real fun (& productive) event, as well as a great demo of how R/Bioc and Python/scverse communities can come together to pursuit mutually beneficial (vs. redundant/diverging) efforts. — Thanks @scverse.bsky.social & all of the SpatialData team for having us!

We just released zarr-python 3.0! It ships with support for sharding, performance improvements, better extensibility and a fully modernized code base. Check out the docs for details: zarr.readthedocs.io/en/stable/ I want to thank everybody who helped with this big lift! It was a pleasure. @zarr.dev

Maybe this has some gems for people studying chromatin arxiv.org/abs/2501.00536

Pileup support is shaping up to be both performant and beautiful thanks to the Rust powered Oxbow package: github.com/abdenlab/oxb... Big shout out to @nvictus.bsky.social and @manzt.sh for implementing key features like buffering and file-like pointer support!

To bring to light data science topics that usually don’t make it into publications I started a blog on this topic: hrovatin.github.io By interviewing different researchers, I plan to find out what is going on in the community.

🧪 E11 Bio is excited to share a major step towards brain mapping at 100x lower cost, making whole-brain connectomics at human & mouse scale feasible (🧠→🔬→💻). Critical for curing brain disorders, building human-like AI systems, and even simulating human brains. Read more: e11.bio/news/roadmap

Formulaic is the go-to way to specify design formulas in Python, e.g. ~treatment + timepoint. To compare sth, one needs to specify a contrast, e.g "on treatment vs baseline". To make this easier, we developed "formulaic-contrasts": formulaic-contrasts.readthedocs.io/en/latest/

Coding in Python and looking to perform bulk RNA sequencing analysis? With pytximport recently published in Bioinformatics and version 0.11.0 out today with many improvements, it’s time for my first Bluetorial! A thread 🧵 (1/12)