scverse
@scverse.bsky.social
Foundational tools for omics data (mostly in python).
Pinned
scverse
@scverse.bsky.social
Β· Aug 2
π scverse conference 2025 Registration & Call for Abstracts NOW OPEN! π
We're excited to announce that registration and the call for abstracts are officially open for the scverse Conference 2025!
Details in thread!
𧡠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!
𧡠1/3
BioContextAI: Biomedical Model Context Protocol servers for composable agentic systems.
For more information, check out their website: biocontext.ai and publication: nature.com/articles/s41...
Zoom registration link for the meeting: lnkd.in/dZpbKKsY
For more information, check out their website: biocontext.ai and publication: nature.com/articles/s41...
Zoom registration link for the meeting: lnkd.in/dZpbKKsY
November 24, 2025 at 4:39 PM
BioContextAI: Biomedical Model Context Protocol servers for composable agentic systems.
For more information, check out their website: biocontext.ai and publication: nature.com/articles/s41...
Zoom registration link for the meeting: lnkd.in/dZpbKKsY
For more information, check out their website: biocontext.ai and publication: nature.com/articles/s41...
Zoom registration link for the meeting: lnkd.in/dZpbKKsY
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 π§΅
Malte Kuehl (@maltekuehl.com) will be presenting on BioContextAI!
More information and Zoom registration link in π§΅
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 π§΅
Malte Kuehl (@maltekuehl.com) will be presenting on BioContextAI!
More information and Zoom registration link in π§΅
Full house for our Bi[o]hub workshop on Day 3!
Communities arenβt just built, they are co-created.
Together, weβre shaping an open, connected world of all-things-single-cell research, where sharing tools and ideas drives discovery.
Communities arenβt just built, they are co-created.
Together, weβre 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 arenβt just built, they are co-created.
Together, weβre shaping an open, connected world of all-things-single-cell research, where sharing tools and ideas drives discovery.
Communities arenβt just built, they are co-created.
Together, weβre shaping an open, connected world of all-things-single-cell research, where sharing tools and ideas drives discovery.
BioContextAI: Biomedical Model Context Protocol servers for composable agentic systems.
For more information, check out their website: biocontext.ai and publication: nature.com/articles/s41...
Zoom registration link for the meeting: lnkd.in/dZpbKKsY
For more information, check out their website: biocontext.ai and publication: nature.com/articles/s41...
Zoom registration link for the meeting: lnkd.in/dZpbKKsY
November 19, 2025 at 2:56 PM
BioContextAI: Biomedical Model Context Protocol servers for composable agentic systems.
For more information, check out their website: biocontext.ai and publication: nature.com/articles/s41...
Zoom registration link for the meeting: lnkd.in/dZpbKKsY
For more information, check out their website: biocontext.ai and publication: nature.com/articles/s41...
Zoom registration link for the meeting: lnkd.in/dZpbKKsY
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 π§΅
Malte Kuehl (@maltekuehl.com) will be presenting on BioContextAI!
More information and Zoom registration link in π§΅
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 π§΅
Malte Kuehl (@maltekuehl.com) will be presenting on BioContextAI!
More information and Zoom registration link in π§΅
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 β€3.11 support and officially add Python 3.13 and 3.14 support, require anndataβ₯...
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)
For more information, check out their documentation: sccellfie.readthedocs.io Meeting Zoom registration link: lnkd.in/dZpbKKsY
November 10, 2025 at 3:16 PM
For more information, check out their documentation: sccellfie.readthedocs.io Meeting Zoom registration link: lnkd.in/dZpbKKsY
scCellFie is a computational framework that infers metabolic activities from both single-cell and spatial transcriptomic data, enabling large-scale, interpretable analyses across cell atlases.
November 10, 2025 at 3:16 PM
scCellFie is a computational framework that infers metabolic activities from both single-cell and spatial transcriptomic data, enabling large-scale, interpretable analyses across cell atlases.
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 π§΅
Eric Armingol will be presenting on scCellFie!
More information and Zoom registration link in π§΅
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 π§΅
Eric Armingol will be presenting on scCellFie!
More information and Zoom registration link in π§΅
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
π
November 17-19, 2025 at Stanford University, California
ποΈ Format: 2 days of main conference + 1 day of satellite workshops across the Bay Area
βΉοΈ More info: scverse.org/conference2025
Register: buff.ly/18KAUfpSubmit
Abstract: buff.ly/5nboSpt
ποΈ Format: 2 days of main conference + 1 day of satellite workshops across the Bay Area
βΉοΈ More info: scverse.org/conference2025
Register: buff.ly/18KAUfpSubmit
Abstract: buff.ly/5nboSpt
November 6, 2025 at 3:59 PM
π
November 17-19, 2025 at Stanford University, California
ποΈ Format: 2 days of main conference + 1 day of satellite workshops across the Bay Area
βΉοΈ More info: scverse.org/conference2025
Register: buff.ly/18KAUfpSubmit
Abstract: buff.ly/5nboSpt
ποΈ Format: 2 days of main conference + 1 day of satellite workshops across the Bay Area
βΉοΈ More info: scverse.org/conference2025
Register: buff.ly/18KAUfpSubmit
Abstract: buff.ly/5nboSpt
Elham Azizi, Associate Professor of Cancer Data Research and Biomedical Engineering at Columbia University will be talking about her work using machine learning to decode the tumour microenvironment!
November 6, 2025 at 3:59 PM
Elham Azizi, Associate Professor of Cancer Data Research and Biomedical Engineering at Columbia University will be talking about her work using machine learning to decode the tumour microenvironment!
Meet the keynote speakers for the 2025 scverse conference!
Elham Azizi, Associate Professor of Cancer Data Research and Biomedical Engineering at Columbia University
π§΅
@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
π§΅
@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
π§΅
@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
π§΅
@elhamazizi.bsky.social
@columbiauniversity.bsky.social
#scverse #scverse2025 #machinelearning #genomics #cancerimmunology
Please note that remote attendance is available for the first two days of the conference (November 17th and 18th) only and does not include access to the workshops on the third day (November 19th), which are exclusively for in-person participants.
November 6, 2025 at 4:14 AM
Please note that remote attendance is available for the first two days of the conference (November 17th and 18th) only and does not include access to the workshops on the third day (November 19th), which are exclusively for in-person participants.
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 β 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!
For more information, check out their documentation: sccellfie.readthedocs.io
Meeting Zoom registration link: lnkd.in/dZpbKKsY
Meeting Zoom registration link: lnkd.in/dZpbKKsY
November 5, 2025 at 4:39 PM
For more information, check out their documentation: sccellfie.readthedocs.io
Meeting Zoom registration link: lnkd.in/dZpbKKsY
Meeting Zoom registration link: lnkd.in/dZpbKKsY
scCellFie is a computational framework that infers metabolic activities from both single-cell and spatial transcriptomic data, enabling large-scale, interpretable analyses across cell atlases.
November 5, 2025 at 4:39 PM
scCellFie is a computational framework that infers metabolic activities from both single-cell and spatial transcriptomic data, enabling large-scale, interpretable analyses across cell atlases.
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 π§΅
Eric Armingol will be presenting on scCellFie!
More information and Zoom registration link in π§΅
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 π§΅
Eric Armingol will be presenting on scCellFie!
More information and Zoom registration link in π§΅
π
November 17-19, 2025 at Stanford University, California
ποΈ Format: 2 days of main conference + 1 day of satellite workshops across the Bay Area
βΉοΈ More info: lnkd.in/dPc6sMHf
Register: lnkd.in/dTRydMwj
ποΈ Format: 2 days of main conference + 1 day of satellite workshops across the Bay Area
βΉοΈ More info: lnkd.in/dPc6sMHf
Register: lnkd.in/dTRydMwj
November 4, 2025 at 4:38 PM
π
November 17-19, 2025 at Stanford University, California
ποΈ Format: 2 days of main conference + 1 day of satellite workshops across the Bay Area
βΉοΈ More info: lnkd.in/dPc6sMHf
Register: lnkd.in/dTRydMwj
ποΈ Format: 2 days of main conference + 1 day of satellite workshops across the Bay Area
βΉοΈ More info: lnkd.in/dPc6sMHf
Register: lnkd.in/dTRydMwj
Erika Alden DeBenedictis, Co-founder of The Align Foundation & CEO of Pioneer Labs, will be joining us to talk about how Align Foundation's data platform advances structural biology!
November 4, 2025 at 4:38 PM
Erika Alden DeBenedictis, Co-founder of The Align Foundation & CEO of Pioneer Labs, will be joining us to talk about how Align Foundation's data platform advances structural biology!
Meet the keynote speakers for the 2025 scverse conference!
Erika Alden DeBenedictis, Co-founder of The Align Foundation π§΅
@erika-alden.bsky.social
@alignbio.bsky.social
@pioneerlabs.bsky.social
#scverse #scverse2025 #StructuralBiology #Biotech #Stanford
Erika Alden DeBenedictis, Co-founder of The Align Foundation π§΅
@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 π§΅
@erika-alden.bsky.social
@alignbio.bsky.social
@pioneerlabs.bsky.social
#scverse #scverse2025 #StructuralBiology #Biotech #Stanford
Erika Alden DeBenedictis, Co-founder of The Align Foundation π§΅
@erika-alden.bsky.social
@alignbio.bsky.social
@pioneerlabs.bsky.social
#scverse #scverse2025 #StructuralBiology #Biotech #Stanford
π
November 17-19, 2025 at Stanford University, California
ποΈ Format: 2 days of main conference + 1 day of satellite workshops across the Bay Area
βΉοΈ More info: scverse.org/conference2025
Register: buff.ly/18KAUfp
ποΈ Format: 2 days of main conference + 1 day of satellite workshops across the Bay Area
βΉοΈ More info: scverse.org/conference2025
Register: buff.ly/18KAUfp
scverse Conference 2025
scverse.org
October 30, 2025 at 3:18 PM
π
November 17-19, 2025 at Stanford University, California
ποΈ Format: 2 days of main conference + 1 day of satellite workshops across the Bay Area
βΉοΈ More info: scverse.org/conference2025
Register: buff.ly/18KAUfp
ποΈ Format: 2 days of main conference + 1 day of satellite workshops across the Bay Area
βΉοΈ More info: scverse.org/conference2025
Register: buff.ly/18KAUfp
John Marioni, Head of Computation at Genentech Research and Early Development and former head of EBI will be joining us to talk about his work interfacing AI and Drug Development!
October 30, 2025 at 3:18 PM
John Marioni, Head of Computation at Genentech Research and Early Development and former head of EBI will be joining us to talk about his work interfacing AI and Drug Development!
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
π§΅
#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
π§΅
#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
π§΅
#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
π§΅
#scverse #scverse2025 #AI #DrugDevelopment #MachineLearning #ComputationalBiology #Biotech #Pharma #Genentech