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We hope to see many of you there! 👩‍💻
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📅 November 17-19, 2025 at Stanford University, California
🏛️ Format: 2 days of main conference + 1 day of satellite workshops across the Bay Area
ℹ️ More info: scverse.org/conference2025
🚀 Ready to join us?
Register: www.eventbrite.com/e/scverse-co...
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🎉 scverse conference 2025 Registration & Call for Abstracts NOW OPEN! 🎉
We're excited to announce that registration and the call for abstracts are officially open for the scverse Conference 2025!
Details in thread!
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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).

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...

Working on this project has been a great privilege, thanks to the many contributions from all team members, including members from the @scverse.bsky.social and BioCypher communities.

If you are interested in building out the biomedical MCP ecosystem, we invite you to share your work through BioContextAI and to connect via GitHub (github.com/biocontext-ai) or through the @scverse.bsky.social Zulip (scverse.zulipchat.com), were you can find us in the "[wg] biocontext-ai" channel.

🔗 Ecosystem

CORNETO is powering LIANA+ (liana-py.readthedocs.io), linking cell–cell communication events to intracellular signaling (@scverse.bsky.social). It’s also at the core of NetworkCommons (networkcommons.readthedocs.io), our community-driven platform for network methods.

Public view of scverse | Zulip team chat Browse the publicly accessible channels in scverse without logging in.

Zoom registration link: scverse.zulipchat.com#narrow/chann...

To get a preview, check out the latest docs and bring questions! anndata.readthedocs.io/en/latest/

We will have our next community meeting on Tuesday, 2025-07-08 at 18:00 CEST! Ilan will be speaking about the new upcoming anndata release.
(Zoom registration link and more information in thread!)

Zoom registration link: scverse.zulipchat.com#narrow/chann...

To get a preview check out the latest docs and bring questions! anndata.readthedocs.io/en/latest/

We will have our next community meeting on Tuesday, 2025-07-08 at 18:00 CEST! Ilan will be speaking about the new upcoming anndata release.
(Zoom registration link and more information in thread!)

🔧 decoupler 2.0.6 is out thanks to @paubadiam.bsky.social‬, now as a core @scverse.bsky.social package scverse.org

This release includes a streamlined API aligned with scverse standards, updated vignettes, and a new one on pseudotime enrichment analysis 👇
decoupler.readthedocs.io/en/latest/

Great open-source QC reporting tool from @robp.bsky.social Rob Patro’s group, member of our management committee!

Zoom registration link: scverse.zulipchat.com#narrow/chann...

For more information, check out the SCARlink github repo (github.com/snehamitra/S...) and publication (www.nature.com/articles/s41...)!

We will have our next community meeting on Tuesday, 2025-06-24 at 18:00 CEST! Sneha Mitra (@snehamitra.bsky.social) will speak about SCARlink.
(Zoom registration link and more information in thread!)

Zoom registration link: scverse.zulipchat.com#narrow/chann...

For more information, check out the SCARlink github repo (github.com/snehamitra/S...) and publication (www.nature.com/articles/s41...)!

We will have our next community meeting on Tuesday, 2025-06-24 at 18:00 CEST! Sneha Mitra (@snehamitra.bsky.social) will speak about SCARlink.
(Zoom registration link and more information in thread!)

🧠 Built on the @scverse.bsky.social ‬ecosystem 🐍, LazySlide makes advanced histopathology analysis accessible with minimal code. Segment tissue, classify cells, run vision-language queries or integrate with omics data - all these without training, and in an already familiar API. lazyslide.rtfd.io

So glad you found us. With scverse, we focus on bringing interoperable tools for all things single-cell and spatial to the Python community. Lots to learn from BioC. Curious to hear what the community thinks.

Zoom registration link: scverse.zulipchat.com#narrow/chann...

For more information, check out the LaminDB github repo: github.com/laminlabs/la... , blog post: blog.lamin.ai/arrayloader-... , and details about MappedCollection: docs.lamin.ai/lamindb.core... !

We will have our next community meeting on Tuesday, 2025-06-10 at 18:00 CEST! Sergei Rybakov will speak about MappedCollection.
(Zoom registration link and more information in thread!)

GitHub - COMBINE-lab/forseti Contribute to COMBINE-lab/forseti development by creating an account on GitHub.

Zoom registration link: scverse.zulipchat.com#narrow/chann...

For more information, check out the LaminDB github repo: github.com/laminlabs/la... , blog post: blog.lamin.ai/arrayloader-... , and details about MappedCollection: docs.lamin.ai/lamindb.core... !

We will have our next community meeting on Tuesday, 2025-06-10 at 18:00 CEST! @Sergei will speak about MappedCollection.
(Zoom registration link and more information in thread!)

GitHub - COMBINE-lab/forseti Contribute to COMBINE-lab/forseti development by creating an account on GitHub.

Zoom registration link: scverse.zulipchat.com#narrow/chann...

For more information, check out the Forseti GitHub: github.com/COMBINE-lab/..., publication: doi.org/10.1093/bioi..., and QCatch GitHub: github.com/COMBINE-lab/...

Tuesday, 2025-05-27 at 18:00 CEST, we will have our next community meeting!
Yuan Gao will speak about Forseti and introduce the Patro lab's upcoming tool, QCatch.
(Zoom registration link in thread!)

GitHub - COMBINE-lab/forseti Contribute to COMBINE-lab/forseti development by creating an account on GitHub.

Zoom registration link: scverse.zulipchat.com#narrow/chann...

For more information, check out the Forseti GitHub: github.com/COMBINE-lab/..., publication: doi.org/10.1093/bioi..., and QCatch GitHub: github.com/COMBINE-lab/...

Public view of scverse | Zulip team chat Browse the publicly accessible channels in scverse without logging in.

This Tuesday, 2025-05-27 at 18:00 CEST, we will have our next community meeting!
Yuan Gao will speak about Forseti and introduce the Patro lab's upcoming tool, QCatch.
(Zoom registration link in thread!)

scverse turns 3!
What started as a shared vision for interoperable single-cell analysis has become a vibrant, global community.
From AnnData to full multimodal pipelines, we’re building the future of everything single-cell and spatial omics, together.
Here’s to what’s next!

Public view of scverse | Zulip team chat Browse the publicly accessible channels in scverse without logging in.

Zoom link: scverse.zulipchat.com#narrow/chann...

This Tuesday, 2025-05-13 at 18:00 CEST, we will have our next community meeting!

Gregor Sturm will present on scirpy! Check out more information here: scirpy.scverse.org/en/latest/ , and register for the zoom link below: