Lukas Heumos

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...

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!)

Happy to have this finally out! Check out the updated vignettes and if something is broken please open a GitHub issue and I'll have a look 😉👇

GitHub - quadbio/cell-annotator: Automatically annotate cell types, consistently across samples. Automatically annotate cell types, consistently across samples. - quadbio/cell-annotator

Happy to share CellAnnotator, a lightweight Python package to query OpenAI models for initial cell type annotations: github.com/quadbio/cell...

Inspired by ideas in www.nature.com/articles/s41... and github.com/VPetukhov/GP..., implemented as an scVerse ecosystem package with docs and tutorials.

GitHub - theislab/multimil: Multimodal weakly supervised learning to identify disease-specific changes in single-cell atlases Multimodal weakly supervised learning to identify disease-specific changes in single-cell atlases - theislab/multimil

Tomorrow at 2025-04-15 18:00 CEST, we’ll have our next community meeting!

Anastasia Litinetskaya will present “Multimodal integration and identification of disease-specific changes in single-cell atlases”. Check out the GitHub repo here: github.com/theislab/mul...

We are back 🔥

Best practices for single-cell analysis across modalities - Nature Reviews Genetics Practitioners in the field of single-cell omics are now faced with diverse options for analytical tools to process and integrate data from various molecular modalities. In an Expert Recommendation art...

Best practices for single-cell analysis across modalities go.nature.com/4gJkk3c #ExpertRecommendation by @lukasheumos.bsky.social et al. (from the @fabiantheis.bsky.social lab) - now nearing 250k accesses!
Free to read here: rdcu.be/eabUB

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...

🎉 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:

We have additional available spots. Please consider joining! It will be a blast.

I keep being astonished at how terrible @microsoft.com Teams works on Firefox and I certainly don't blame Mozilla for it.

GitHub - nextflow-io/doom: A Nextflow pipeline to play Doom A Nextflow pipeline to play Doom. Contribute to nextflow-io/doom development by creating an account on GitHub.

Ahhh finally I can use @nextflow.io to run doom! github.com/nextflow-io/...

Scverse x Owkin Hackathon in Paris We're pleased to announce the next Scverse Hackathon will take place in the Owkin offices in Paris from 17/03/2025 9am to 19/03/2025 1:30pm. This hackathon is a joint initiative between the scverse c...

I am Stoked about our upcoming @scverse.bsky.social
and @owkin.bsky.social hackathon, focused on spatial omics data analysis.
📅 March 17-19, 2025
📍 Owkin office, Paris

Apply now: docs.google.com/forms/d/e/1F...

Why is there still no proper "thank you" emoji on @github.com ? I am grateful for other peoples time and feel like a thumbs up is kind of like a drive by reaction and a heart isn't always perfectly appropriate

I actually think that it' awesome that even fundamental packages like numpy, pandas, scipy, and others still develop rapidly and aren't afraid of making big API changes but it's quite time consuming to keep up when one maintains many packages. I can't imagine what e.g. the numba devs go through

Awesome, congratulations! It was a pleasure to attend Yimin's talk at the @scverse.bsky.social 2024 conference and it's really nice to see that it was encouraging for Yimin.

I was just looking at our @scverse.bsky.social zulip chat statistics and am super happy about our steady and healthy growth. The two bursts are our official launch in May 2022 and the inaugural scverse conference in September of 2024. Please join us! scverse.zulipchat.com

Reminder!Today at 18:00 CET will be the last community meeting of the year! @lukasheumos.bsky.social will talk about about pertpy, a Python-based modular framework for the analysis of large-scale perturbation single-cell experiments. Zoom link can be found here: scverse.zulipchat.com#narrow/chann...

GitHub - scverse/pertpy: Perturbation Analysis in the scverse ecosystem. Perturbation Analysis in the scverse ecosystem. Contribute to scverse/pertpy development by creating an account on GitHub.

Next Tuesday at 2024-12-10 18:00 CET, we will hold the last community meeting of the year!

@lukasheumos.bsky.social will talk about pertpy, a Python-based modular framework for the analysis of large-scale perturbation single-cell experiments. The GitHub repo: github.com/scverse/pertpy

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Reminder! Today at 18:00 CET will be another community meeting! Malte Lücken will talk about about Open Problems in Single-Cell Analysis. Zoom link can be found here:

We were thinking of keeping that starter pack only for scverse core team and board members. There's already other pure single-cell lists and we don't want to compete with them. We don't need several lists that have the same purpose. Thank you very much for your interest though!

I completely agree with you but also want to emphasize that quite many papers featured here are resource papers such as atlases that are imperative for future models.

It's all hype and people will realize soon enough that it's still all about high quality curated data. Without them - no models.

Open Problems in Single-Cell Analysis – Open Problems in Single Cell Analysis Computational biology is undergoing a revolution. Recent advances in microfluidic technology enable high-throughput and high-dimensional of individual cells at unprecedented scale. But there’s a…

Next Tuesday at 2024-11-26 18:00 CET will be another community meeting!

Malte Lücken will talk about about Open Problems in Single-Cell Analysis, a community-driven state-of-the-art benchmarking platform to facilitate development of single-cell methods. https://buff.ly/3CAGxSt

Explore the scverse Starter Pack!

Stay informed about the latest scverse events, software updates, and community news. Everything you need to know about foundational tools for single-cell omics analysis in one place.
go.bsky.app/UvFMa8d

An integrated transcriptomic cell atlas of human neural organoids - Nature A human neural organoid cell atlas integrating 36 single-cell transcriptomic datasets shows cell types and states and estimates transcriptomic similarity between primary and organoid counterparts, sho...

Super excited to share our Human Neural Organoid Atlas, now out in Nature! Led by @zhisonghe.bsky.social @josch1.bsky.social, and myself, this resource was created from 36 scRNA-seq datasets—totalling over 1.7 million cells! 🔬✨
 www.nature.com/articles/s41...


Find out how it can serve you ⏬

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Thanks - really nice w these starter packs, did that. Meanwhile @scverse.bsky.social has also created one - really like that. bsky.app/starter-pack...

I am stoked to see our EHR framework ehrapy (github.com/theislab/ehr...) being the cover of the most recent Nature Medicine issue. We consider ehrapy a MVP for a much grander ecosystem for EHR analysis like we have for single-cell data (@scverse). Read more: www.nature.com/articles/s41...