Lukas Heumos

Meet the keynote speakers for the 2025 scverse conference!

Erika Alden DeBenedictis, Co-founder of The Align Foundation 🧵

@erika-alden.bsky.social
@alignbio.bsky.social
@pioneerlabs.bsky.social

#scverse #scverse2025 #StructuralBiology #Biotech #Stanford

"Usability besides performance is also key."

Cannot stress this enough. There's a ton of methods out there that might not even be the best but are used because a substantial amount of time was invested into making it fast, accessible, and documented. Such methods are benchmarked in real use cases

🌟 Thank You to Our Platinum Sponsor: 10x Genomics! 🌟

We're delighted to recognize 10x Genomics as a Platinum Sponsor of scverse conference 2025! 🏆

@10xgenomics.bsky.social
#scverse2025 #ComputationalBiology #SingleCell #SpatialOmics #10xGenomics #Bioinformatics #Biotechnology

Hi bioinformatics, genomics and CS friends! Please help me spread the word. I'm hiring a postdoc! Come work on cutting edge method development in algorithmic genomics with me and my group at @umdscience.bsky.social! 🖥️🧬

I see where you're coming from but what is your opinion on scientific-python.org/specs/spec-0... then? I find it valuable that the pydata ecosystem moves together.

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

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!

It is pretty heart warming to see people start their really good pull request with "this is my first open source contribution. I hope that this is good.". Everyone starts somewhere and we're always happy to guide at @scverse.bsky.social .

Our benchmark + guidelines for atlas-level differential gene expression of single cells is online:

academic.oup.com/bib/article/...

Bottom line: Use pseudobulk + DESeq2 in simple and pseudobulk + DREAM in more complex settings.

Collab w/ @leonhafner.bsky.social @itisalist.bsky.social

I hate reference limits of journals so much. I'm sitting here trying to find a few more references to remove despite me knowing that I'll either remove context & evidence for scientific conclusions or not mention tools that very much deserve to be mentioned and cited.

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!