scverse
@scverse.bsky.social
Foundational tools for omics data (mostly in python).
Pinned
scverse
@scverse.bsky.social
· Aug 2
🎉 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!
🧵 1/3
We're excited to announce that registration and the call for abstracts are officially open for the scverse Conference 2025!
Details in thread!
🧵 1/3
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...
Deadline January 10, 2026!
More details here: jobs.helmholtz-muenchen.de/jobposting/d...
December 12, 2025 at 7:43 PM
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...
Deadline January 10, 2026!
More details here: jobs.helmholtz-muenchen.de/jobposting/d...
We will have our final community meeting of 2026 on Tuesday, 2025-12-09 at 11:00 CST/ 9:00 PST!
Mikaela Koutrouli (@MKoutrouli) will wrap up a great year of meetings by giving an update on the state of scverse!
Zoom registration link for the meeting: lnkd.in/dZpbKKsY
Mikaela Koutrouli (@MKoutrouli) will wrap up a great year of meetings by giving an update on the state of scverse!
Zoom registration link for the meeting: lnkd.in/dZpbKKsY
December 8, 2025 at 3:17 PM
We will have our final community meeting of 2026 on Tuesday, 2025-12-09 at 11:00 CST/ 9:00 PST!
Mikaela Koutrouli (@MKoutrouli) will wrap up a great year of meetings by giving an update on the state of scverse!
Zoom registration link for the meeting: lnkd.in/dZpbKKsY
Mikaela Koutrouli (@MKoutrouli) will wrap up a great year of meetings by giving an update on the state of scverse!
Zoom registration link for the meeting: lnkd.in/dZpbKKsY
We will have our final community meeting of 2026 on Tuesday, 2025-12-09 at 11:00 CST/ 9:00 PST!
Mikaela Koutrouli (@mkoutrouli.bsky.social) will wrap up a great year of meetings by giving an update on the state of scverse!
Zoom registration link for the meeting: lnkd.in/dZpbKKsY
Mikaela Koutrouli (@mkoutrouli.bsky.social) will wrap up a great year of meetings by giving an update on the state of scverse!
Zoom registration link for the meeting: lnkd.in/dZpbKKsY
December 3, 2025 at 3:47 PM
We will have our final community meeting of 2026 on Tuesday, 2025-12-09 at 11:00 CST/ 9:00 PST!
Mikaela Koutrouli (@mkoutrouli.bsky.social) will wrap up a great year of meetings by giving an update on the state of scverse!
Zoom registration link for the meeting: lnkd.in/dZpbKKsY
Mikaela Koutrouli (@mkoutrouli.bsky.social) will wrap up a great year of meetings by giving an update on the state of scverse!
Zoom registration link for the meeting: lnkd.in/dZpbKKsY
We wrapped up an inspiring week with a visit to NVIDIA headquarters right after the scverse conference. Huge thanks to the NVIDIA Healthcare team and @severin7.bsky.social for hosting us and for the great discussions on scaling single-cell analysis and accelerating open science ⚡️
November 26, 2025 at 4:53 PM
We wrapped up an inspiring week with a visit to NVIDIA headquarters right after the scverse conference. Huge thanks to the NVIDIA Healthcare team and @severin7.bsky.social for hosting us and for the great discussions on scaling single-cell analysis and accelerating open science ⚡️
We will have our next community meeting on Tuesday, 2025-11-25 at 11:00 CST!
Malte Kuehl (@maltekuehl.com) will be presenting on BioContextAI!
More information and Zoom registration link in 🧵
Malte Kuehl (@maltekuehl.com) will be presenting on BioContextAI!
More information and Zoom registration link in 🧵
November 24, 2025 at 4:39 PM
We will have our next community meeting on Tuesday, 2025-11-25 at 11:00 CST!
Malte Kuehl (@maltekuehl.com) will be presenting on BioContextAI!
More information and Zoom registration link in 🧵
Malte Kuehl (@maltekuehl.com) will be presenting on BioContextAI!
More information and Zoom registration link in 🧵
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.
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.
November 20, 2025 at 12:34 AM
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.
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.
We will have our next community meeting on Tuesday, 2025-11-25 at 11:00 CST!
Malte Kuehl (@maltekuehl.com) will be presenting on BioContextAI!
More information and Zoom registration link in 🧵
Malte Kuehl (@maltekuehl.com) will be presenting on BioContextAI!
More information and Zoom registration link in 🧵
November 19, 2025 at 2:56 PM
We will have our next community meeting on Tuesday, 2025-11-25 at 11:00 CST!
Malte Kuehl (@maltekuehl.com) will be presenting on BioContextAI!
More information and Zoom registration link in 🧵
Malte Kuehl (@maltekuehl.com) will be presenting on BioContextAI!
More information and Zoom registration link in 🧵
We are proud to announce that we're partnering with @biocontext.ai (biocontext.ai), a new open-source initiative for building agentic systems in biomedical research. Learn more in our announcement: scverse.org/blog/2025-11...
November 11, 2025 at 7:41 PM
We are proud to announce that we're partnering with @biocontext.ai (biocontext.ai), a new open-source initiative for building agentic systems in biomedical research. Learn more in our announcement: scverse.org/blog/2025-11...
We just released scanpy 1.12rc1 (scanpy.readthedocs.io/en/latest/re...)
Highlights:
- Dask support in `sc.get.aggregate` for pseudobatching + `highly_variable_genes(flavor='seurat_v3')`
- More functions allow specifying `layers` and `obsm`
- Turn off quirky behavior (new defaults for scanpy 2.0)
Highlights:
- Dask support in `sc.get.aggregate` for pseudobatching + `highly_variable_genes(flavor='seurat_v3')`
- More functions allow specifying `layers` and `obsm`
- Turn off quirky behavior (new defaults for scanpy 2.0)
Release notes
Version 1.12: 1.12.0rc1 2025-11-10: Breaking changes: Adopt the Scientific Python deprecation schedule: remove Python ≤3.11 support and officially add Python 3.13 and 3.14 support, require anndata≥...
scanpy.readthedocs.io
November 11, 2025 at 10:55 AM
We just released scanpy 1.12rc1 (scanpy.readthedocs.io/en/latest/re...)
Highlights:
- Dask support in `sc.get.aggregate` for pseudobatching + `highly_variable_genes(flavor='seurat_v3')`
- More functions allow specifying `layers` and `obsm`
- Turn off quirky behavior (new defaults for scanpy 2.0)
Highlights:
- Dask support in `sc.get.aggregate` for pseudobatching + `highly_variable_genes(flavor='seurat_v3')`
- More functions allow specifying `layers` and `obsm`
- Turn off quirky behavior (new defaults for scanpy 2.0)
We will have our next community meeting on Tuesday, 2025-11-11 at 11:00 CST!
Eric Armingol will be presenting on scCellFie!
More information and Zoom registration link in 🧵
Eric Armingol will be presenting on scCellFie!
More information and Zoom registration link in 🧵
November 10, 2025 at 3:16 PM
We will have our next community meeting on Tuesday, 2025-11-11 at 11:00 CST!
Eric Armingol will be presenting on scCellFie!
More information and Zoom registration link in 🧵
Eric Armingol will be presenting on scCellFie!
More information and Zoom registration link in 🧵
Reposted by scverse
Excited to see a home for MCP servers in bioinformatics emerge! The community needs a central hub for developing MCP servers for key bioinfo tools. At @scverse.bsky.social we're contributing to this effort - can't wait to share what we're building
BioContextAI is a community hub for agentic biomedical systems - @puellesv.bsky.social @biocontext.ai go.nature.com/3JmqKux
BioContextAI is a community hub for agentic biomedical systems - Nature Biotechnology
Nature Biotechnology - BioContextAI is a community hub for agentic biomedical systems
go.nature.com
November 6, 2025 at 7:28 PM
Excited to see a home for MCP servers in bioinformatics emerge! The community needs a central hub for developing MCP servers for key bioinfo tools. At @scverse.bsky.social we're contributing to this effort - can't wait to share what we're building
Meet the keynote speakers for the 2025 scverse conference!
Elham Azizi, Associate Professor of Cancer Data Research and Biomedical Engineering at Columbia University
🧵
@elhamazizi.bsky.social
@columbiauniversity.bsky.social
#scverse #scverse2025 #machinelearning #genomics #cancerimmunology
Elham Azizi, Associate Professor of Cancer Data Research and Biomedical Engineering at Columbia University
🧵
@elhamazizi.bsky.social
@columbiauniversity.bsky.social
#scverse #scverse2025 #machinelearning #genomics #cancerimmunology
November 6, 2025 at 3:59 PM
Meet the keynote speakers for the 2025 scverse conference!
Elham Azizi, Associate Professor of Cancer Data Research and Biomedical Engineering at Columbia University
🧵
@elhamazizi.bsky.social
@columbiauniversity.bsky.social
#scverse #scverse2025 #machinelearning #genomics #cancerimmunology
Elham Azizi, Associate Professor of Cancer Data Research and Biomedical Engineering at Columbia University
🧵
@elhamazizi.bsky.social
@columbiauniversity.bsky.social
#scverse #scverse2025 #machinelearning #genomics #cancerimmunology
We're pleased to announce that we are now offering online attendance via Zoom.
Remote attendance is available for 30 USD, and you can secure your spot by registering at www.eventbrite.com/e/scverse-co....
We hope to see you online at the conference!
Remote attendance is available for 30 USD, and you can secure your spot by registering at www.eventbrite.com/e/scverse-co....
We hope to see you online at the conference!
Scverse Conference 2025
From the foundational open-source software in the life sciences — to its large community coming together
www.eventbrite.com
November 6, 2025 at 4:14 AM
We're pleased to announce that we are now offering online attendance via Zoom.
Remote attendance is available for 30 USD, and you can secure your spot by registering at www.eventbrite.com/e/scverse-co....
We hope to see you online at the conference!
Remote attendance is available for 30 USD, and you can secure your spot by registering at www.eventbrite.com/e/scverse-co....
We hope to see you online at the conference!
We will have our next community meeting on Tuesday, 2025-11-11 at 11:00 CST!
Eric Armingol will be presenting on scCellFie!
More information and Zoom registration link in 🧵
Eric Armingol will be presenting on scCellFie!
More information and Zoom registration link in 🧵
November 5, 2025 at 4:39 PM
We will have our next community meeting on Tuesday, 2025-11-11 at 11:00 CST!
Eric Armingol will be presenting on scCellFie!
More information and Zoom registration link in 🧵
Eric Armingol will be presenting on scCellFie!
More information and Zoom registration link in 🧵
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
Erika Alden DeBenedictis, Co-founder of The Align Foundation 🧵
@erika-alden.bsky.social
@alignbio.bsky.social
@pioneerlabs.bsky.social
#scverse #scverse2025 #StructuralBiology #Biotech #Stanford
November 4, 2025 at 4:38 PM
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
Erika Alden DeBenedictis, Co-founder of The Align Foundation 🧵
@erika-alden.bsky.social
@alignbio.bsky.social
@pioneerlabs.bsky.social
#scverse #scverse2025 #StructuralBiology #Biotech #Stanford
Meet the keynote speakers for the 2025 scverse conference!
John Marioni, Head of Computation at Genentech Research and Early Development and former head of EBI
🧵
#scverse #scverse2025 #AI #DrugDevelopment #MachineLearning #ComputationalBiology #Biotech #Pharma #Genentech
John Marioni, Head of Computation at Genentech Research and Early Development and former head of EBI
🧵
#scverse #scverse2025 #AI #DrugDevelopment #MachineLearning #ComputationalBiology #Biotech #Pharma #Genentech
October 30, 2025 at 3:18 PM
Meet the keynote speakers for the 2025 scverse conference!
John Marioni, Head of Computation at Genentech Research and Early Development and former head of EBI
🧵
#scverse #scverse2025 #AI #DrugDevelopment #MachineLearning #ComputationalBiology #Biotech #Pharma #Genentech
John Marioni, Head of Computation at Genentech Research and Early Development and former head of EBI
🧵
#scverse #scverse2025 #AI #DrugDevelopment #MachineLearning #ComputationalBiology #Biotech #Pharma #Genentech
Meet the keynote speakers for the 2025 scverse conference!
Panos Roussos, Professor at Icahn School of Medicine at Mount Sinai 🧵
@panosroussos.bsky.social
#scverse #scverse2025 #SingleCell #SpatialTranscriptomics #Conference #Keynote
Panos Roussos, Professor at Icahn School of Medicine at Mount Sinai 🧵
@panosroussos.bsky.social
#scverse #scverse2025 #SingleCell #SpatialTranscriptomics #Conference #Keynote
October 28, 2025 at 4:00 PM
Meet the keynote speakers for the 2025 scverse conference!
Panos Roussos, Professor at Icahn School of Medicine at Mount Sinai 🧵
@panosroussos.bsky.social
#scverse #scverse2025 #SingleCell #SpatialTranscriptomics #Conference #Keynote
Panos Roussos, Professor at Icahn School of Medicine at Mount Sinai 🧵
@panosroussos.bsky.social
#scverse #scverse2025 #SingleCell #SpatialTranscriptomics #Conference #Keynote
We will have our next community meeting on Tuesday, 2025-10-28 at 18:00 CEST!
@kexinhuang.bsky.social will be presenting on Biomni: Building a Virtual Biomedical Scientist.
(Zoom registration link and more information in thread!)
🧵
@kexinhuang.bsky.social will be presenting on Biomni: Building a Virtual Biomedical Scientist.
(Zoom registration link and more information in thread!)
🧵
October 27, 2025 at 3:57 PM
We will have our next community meeting on Tuesday, 2025-10-28 at 18:00 CEST!
@kexinhuang.bsky.social will be presenting on Biomni: Building a Virtual Biomedical Scientist.
(Zoom registration link and more information in thread!)
🧵
@kexinhuang.bsky.social will be presenting on Biomni: Building a Virtual Biomedical Scientist.
(Zoom registration link and more information in thread!)
🧵
We will have our next community meeting on Tuesday, 2025-10-28 at 18:00 CEST! @kexinhuang.bsky.social will be presenting on Biomni: Building a Virtual Biomedical Scientist.
(Zoom registration link and more information in thread!)
🧵
(Zoom registration link and more information in thread!)
🧵
October 24, 2025 at 3:55 PM
We will have our next community meeting on Tuesday, 2025-10-28 at 18:00 CEST! @kexinhuang.bsky.social will be presenting on Biomni: Building a Virtual Biomedical Scientist.
(Zoom registration link and more information in thread!)
🧵
(Zoom registration link and more information in thread!)
🧵
🌟 Thank You to Our Diamond Sponsor: Somite! 🌟
We're thrilled to recognize Somite as a Diamond Sponsor of scverse conference 2025! 💎
#scverse2025 #ComputationalBiology #SingleCell #FoundationModels #CellTherapy #RegenerativeMedicine #AIinBiology
We're thrilled to recognize Somite as a Diamond Sponsor of scverse conference 2025! 💎
#scverse2025 #ComputationalBiology #SingleCell #FoundationModels #CellTherapy #RegenerativeMedicine #AIinBiology
October 23, 2025 at 4:13 PM
🌟 Thank You to Our Diamond Sponsor: Somite! 🌟
We're thrilled to recognize Somite as a Diamond Sponsor of scverse conference 2025! 💎
#scverse2025 #ComputationalBiology #SingleCell #FoundationModels #CellTherapy #RegenerativeMedicine #AIinBiology
We're thrilled to recognize Somite as a Diamond Sponsor of scverse conference 2025! 💎
#scverse2025 #ComputationalBiology #SingleCell #FoundationModels #CellTherapy #RegenerativeMedicine #AIinBiology
🌟 Thank You to Our Gold Sponsor: Genentech! 🌟
We're delighted to recognize Genentech as a Gold Sponsor of scverse conference 2025! 🏆
#scverse2025 #ComputationalBiology #SingleCell #DrugDiscovery #Genentech #SpatialOmics #Bioinformatics #Biotechnology
We're delighted to recognize Genentech as a Gold Sponsor of scverse conference 2025! 🏆
#scverse2025 #ComputationalBiology #SingleCell #DrugDiscovery #Genentech #SpatialOmics #Bioinformatics #Biotechnology
October 21, 2025 at 4:54 PM
🌟 Thank You to Our Gold Sponsor: Genentech! 🌟
We're delighted to recognize Genentech as a Gold Sponsor of scverse conference 2025! 🏆
#scverse2025 #ComputationalBiology #SingleCell #DrugDiscovery #Genentech #SpatialOmics #Bioinformatics #Biotechnology
We're delighted to recognize Genentech as a Gold Sponsor of scverse conference 2025! 🏆
#scverse2025 #ComputationalBiology #SingleCell #DrugDiscovery #Genentech #SpatialOmics #Bioinformatics #Biotechnology
🌟 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
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
October 16, 2025 at 3:11 PM
🌟 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
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
🧬 Tahoe Workshop at scverse conference 2025 🧬
Disease Biology and Therapeutics in the Age of Frontier Datasets
@tahoetherapeutics.bsky.social
#scverse2025 #ComputationalBiology #DrugDiscovery #TahoeTherapeutics #SingleCell #PerturbationBiology
Disease Biology and Therapeutics in the Age of Frontier Datasets
@tahoetherapeutics.bsky.social
#scverse2025 #ComputationalBiology #DrugDiscovery #TahoeTherapeutics #SingleCell #PerturbationBiology
October 15, 2025 at 2:28 PM
🧬 Tahoe Workshop at scverse conference 2025 🧬
Disease Biology and Therapeutics in the Age of Frontier Datasets
@tahoetherapeutics.bsky.social
#scverse2025 #ComputationalBiology #DrugDiscovery #TahoeTherapeutics #SingleCell #PerturbationBiology
Disease Biology and Therapeutics in the Age of Frontier Datasets
@tahoetherapeutics.bsky.social
#scverse2025 #ComputationalBiology #DrugDiscovery #TahoeTherapeutics #SingleCell #PerturbationBiology
🌟 Thank You to Our Silver Sponsor: Proteintech! 🌟
We're excited to recognize Proteintech as a Silver Sponsor of scverse conference 2025! 🥈
@proteintech.bsky.social
#scverse2025 #Proteintech #ComputationalBiology #SingleCell #Antibodies #ProteomicsTools #SpatialOmics #Bioinformatics
We're excited to recognize Proteintech as a Silver Sponsor of scverse conference 2025! 🥈
@proteintech.bsky.social
#scverse2025 #Proteintech #ComputationalBiology #SingleCell #Antibodies #ProteomicsTools #SpatialOmics #Bioinformatics
October 14, 2025 at 2:30 PM
🌟 Thank You to Our Silver Sponsor: Proteintech! 🌟
We're excited to recognize Proteintech as a Silver Sponsor of scverse conference 2025! 🥈
@proteintech.bsky.social
#scverse2025 #Proteintech #ComputationalBiology #SingleCell #Antibodies #ProteomicsTools #SpatialOmics #Bioinformatics
We're excited to recognize Proteintech as a Silver Sponsor of scverse conference 2025! 🥈
@proteintech.bsky.social
#scverse2025 #Proteintech #ComputationalBiology #SingleCell #Antibodies #ProteomicsTools #SpatialOmics #Bioinformatics
We will have our next community meeting on Tuesday, 2025-10-14 at 18:00 CEST! Yimin Zheng will be presenting on LazySlide, a Python framework for whole slide image (WSI) analysis.
(Zoom registration link and more information in thread!)
🧵
(Zoom registration link and more information in thread!)
🧵
October 13, 2025 at 3:54 PM
We will have our next community meeting on Tuesday, 2025-10-14 at 18:00 CEST! Yimin Zheng will be presenting on LazySlide, a Python framework for whole slide image (WSI) analysis.
(Zoom registration link and more information in thread!)
🧵
(Zoom registration link and more information in thread!)
🧵