iiinova — where your digital self keeps evolving

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Loïc A. Royer 💻🔬🧪 @loicaroyer.bsky.social · 23/09/2026

What if any dataset, any size, any number of dimensions, opened in a browser tab from a link? 🔬🧪💻 Luxar is out today: write it in Python, share it as a link, explore it in any browser. Open source. 🧵 @biohub.org Preprint: doi.org/10.5281/zen... Code: github.com/royerlab/luxar

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Nezar Abdennur @nvictus.bsky.social · 16/07/2026

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

abdenlab.org

Declare, Don't Parse: Toward composable genomic analysis - Slidev

SciPy 2026 — Nezar Abdennur and Conrad Bzura

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Biohub @biohub.org · 27/05/2026

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

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Utz Ermel @uermel.bsky.social · 20/04/2026

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

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Phil Ewels @ewels.bsky.social · 02/04/2026

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/

seqeralabs.github.io

Welcome to RustQC

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

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bioRxiv Plant Bio @biorxiv-plants.bsky.social · 27/03/2026

A tool to shoot genes with massive air from a compressor (TSGMAC) www.biorxiv.org/content/10.64898/20…

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Juan Nunez-Iglesias @jni.codes · 16/03/2026

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.

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Image Cooperative @image.coop · 16/03/2026

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

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Johannes Soltwedel @jo-soltwedel.bsky.social · 12/02/2026

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

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scverse @scverse.bsky.social · 12/12/2025

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...

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Aaron Quinlan (he/him) @aaronquinlan.bsky.social · 02/12/2025

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

quinlanlab.org

Intro to Bedder – The Quinlan Lab

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Luca Marconato @lucamarconato.bsky.social · 27/11/2025

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.

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Pau Badia i Mompel @paubadiam.bsky.social · 21/11/2025

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 😄

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scverse @scverse.bsky.social · 20/11/2025

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.

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Johannes Soltwedel @jo-soltwedel.bsky.social · 12/11/2025

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

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ceej @ceej.online · 09/11/2025

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

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Erick Ratamero @erickratamero.com · 08/10/2025

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...

embl.wd103.myworkdayjobs.com

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...

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scverse @scverse.bsky.social · 03/10/2025

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

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scverse @scverse.bsky.social · 03/10/2025

🚀 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

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Andrew Payne @andrewcpayne.bsky.social · 01/10/2025

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

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Wolfgang Huber @wkhuber.bsky.social · 18/09/2025

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

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Sharon 🪳🌹 @sharonk.bsky.social · 14/09/2025

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

Their waists and hands were tied together, forcing them to bend down and lick water to drink. The unscreened bathrooms contained only a single sheet to cover their lower bodies. Sunlight barely penetrated through a fist-sized hole, and they were only allowed access to the small yard for two hours. Detained by US immigration authorities for eight days, the workers and their families expressed shock, describing human rights violations and absurdities they could not have imagined as ordinary Koreans living in 2025.

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Luca Marconato @lucamarconato.bsky.social · 12/09/2025

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

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Charlie Stross @cstross.bsky.social · 13/09/2025

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: arstechnica.com/science/2025/09/new…

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scverse @scverse.bsky.social · 11/08/2025

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!

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scverse @scverse.bsky.social · 04/09/2025

🔬 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

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Luke Zappia @lazappi.bsky.social · 26/08/2025

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.

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Anshul Kundaje @anshulkundaje.bsky.social · 26/08/2025

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!

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scverse @scverse.bsky.social · 14/08/2025

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

buff.ly

NVIDIA Accelerate Omics Hackathon

Take Omics tools to the next level with GPU acceleration.

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Rob Patro @robp.bsky.social · 05/08/2025

🧬🖥️ 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

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Malte Kuehl @maltekuehl.com · 29/07/2025

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...

Diagram showing MCP-enabled research architecture. Part A illustrates the flow between MCP servers (including BioContextAI Knowledgebase MCP and Community-developed MCP servers), Agentic systems connected via Model Context Protocol, and researchers asking research questions. MCP servers connect to knowledgebases and specialized software. Part B details the BioContextAI project components, divided into Registry (Schema.org ontology, Web interface, Open source licensing, MCP-enabled chatbot, Continuous integration) and Community (Documentation, Community forums, MCP server reviews, Shareable collections, Interoperability with tools like BioChatter).

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Michael Love @mikelove.bsky.social · 25/07/2025

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

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pork, cheese, broccoli rabe @garlicbuffalo.gobirds.biz · 21/06/2025

amtrak’s marketing team gets it

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German BioImaging @gerbi-gmb.de · 03/06/2025

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

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scverse @scverse.bsky.social · 12/05/2025

📣 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!

scverse.org

scverse conference 2025

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Spook-ass, Christ oh boo! boo! @loukas.bsky.social · 21/04/2025

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

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Josh Marshall @joshtpm.bsky.social · 07/04/2025

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.

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WRONG or METAPHYSICAL IN NATURE @jsthrill.modphi.com · 05/04/2025

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

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scientific-python.org @scientific-python.org · 04/04/2025

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

github.com

Scientific Python

Community developed, community owned. Scientific Python has 43 repositories available. Follow their code on GitHub.

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Earthmover @earthmover.io · 18/03/2025

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.

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Luke Zappia @lazappi.bsky.social · 18/03/2025

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

nature.com

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Valentine Svensson @nxn.se · 06/03/2025

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)

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lastpositivist.bsky.social @lastpositivist.bsky.social · 04/03/2025

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.

a search for "GDP of UK vs Russia" and I get "AI Overview

Can the UK economy outperform Russia? | The Spectator
Russia has a larger GDP than the United Kingdom, and is expected to continue to grow faster in the coming years. "

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Jacob Schreiber @jmschreiber91.bsky.social · 10/01/2025

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!

cfp.scipy.org

SciPy 2025

Schedule, talks and talk submissions for SciPy 2025

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scverse @scverse.bsky.social · 14/02/2025

🎉 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:

buff.ly

Release notes

Version 1.11: 1.11.0 2025-02-14: Release candidates: rc2 2025-01-24, rc1 2024-12-20. Features: rc1 sample() supports both upsampling and downsampling of observations and variables. subsample() is n...

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Sen. Adam Schiff @schiff.senate.gov · 08/02/2025

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.

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scverse @scverse.bsky.social · 20/01/2025

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!

outside picture showing the 20 participants of the SpatialData basel hackathon.

some participants while working at their laptops.

some other participants while working at their laptops.

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