Isaac Virshup
@ivirshup.bsky.social
Software engineer at CZI, https://scverse.org steering council, check out my https://github.com/ivirshup
Reposted by Isaac Virshup
This is what hacking *actually* looks like. #OME_NGFF_Hackathon
November 12, 2025 at 5:00 PM
This is what hacking *actually* looks like. #OME_NGFF_Hackathon
Reposted by Isaac Virshup
no amount of state propaganda will ever convince me this man is my enemy
November 9, 2025 at 3:05 PM
no amount of state propaganda will ever convince me this man is my enemy
Reposted by Isaac Virshup
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 6:28 PM
BioContextAI is a community hub for agentic biomedical systems - @puellesv.bsky.social @biocontext.ai go.nature.com/3JmqKux
Reposted by Isaac Virshup
The Data Science team at EMBL is hiring for two open positions! First, for a Scientific Community Manager, focusing on community aspects and training on data science. embl.wd103.myworkdayjobs.com/en-US/EMBL/j...
Scientific Community Manager
EMBL is Europe’s flagship research laboratory for the life sciences – an intergovernmental organisation with more than 110 independent research groups and teams performing scientific research in disci...
embl.wd103.myworkdayjobs.com
October 8, 2025 at 7:08 AM
The Data Science team at EMBL is hiring for two open positions! First, for a Scientific Community Manager, focusing on community aspects and training on data science. embl.wd103.myworkdayjobs.com/en-US/EMBL/j...
Reposted by Isaac Virshup
Join us as we explore emerging trends in agentic AI applications across bioinformatics workflows.
✨ Featured Panelists:
Kexin Huang - Stanford University
Vega Shah, PhD - NVIDIA
Loic Royer - Chan Zuckerberg Biohub Network
Jonah Cool - Anthropic
✨ Featured Panelists:
Kexin Huang - Stanford University
Vega Shah, PhD - NVIDIA
Loic Royer - Chan Zuckerberg Biohub Network
Jonah Cool - Anthropic
October 3, 2025 at 3:43 PM
Join us as we explore emerging trends in agentic AI applications across bioinformatics workflows.
✨ Featured Panelists:
Kexin Huang - Stanford University
Vega Shah, PhD - NVIDIA
Loic Royer - Chan Zuckerberg Biohub Network
Jonah Cool - Anthropic
✨ Featured Panelists:
Kexin Huang - Stanford University
Vega Shah, PhD - NVIDIA
Loic Royer - Chan Zuckerberg Biohub Network
Jonah Cool - Anthropic
Reposted by Isaac Virshup
🚀 NEW PANEL ANNOUNCEMENT: Agentic Workflows in Bioinformatics at scverse 2025! 🚀
We're thrilled to introduce an exciting panel discussion at the upcoming scverse Conference 2025!
More information in 🧵
#scverse2025 #Bioinformatics #AgenticAI #Conference
We're thrilled to introduce an exciting panel discussion at the upcoming scverse Conference 2025!
More information in 🧵
#scverse2025 #Bioinformatics #AgenticAI #Conference
October 3, 2025 at 3:43 PM
🚀 NEW PANEL ANNOUNCEMENT: Agentic Workflows in Bioinformatics at scverse 2025! 🚀
We're thrilled to introduce an exciting panel discussion at the upcoming scverse Conference 2025!
More information in 🧵
#scverse2025 #Bioinformatics #AgenticAI #Conference
We're thrilled to introduce an exciting panel discussion at the upcoming scverse Conference 2025!
More information in 🧵
#scverse2025 #Bioinformatics #AgenticAI #Conference
Reposted by Isaac Virshup
E11 Bio is excited to unveil PRISM technology for mapping brain wiring with simple light microscopes. Today, brain mapping in humans and other mammals is bottlenecked by accurate neuron tracing. PRISM uses molecular ID codes and AI to help neurons trace themselves.
Read more: e11.bio/blog/prism
Read more: e11.bio/blog/prism
October 1, 2025 at 2:16 PM
E11 Bio is excited to unveil PRISM technology for mapping brain wiring with simple light microscopes. Today, brain mapping in humans and other mammals is bottlenecked by accurate neuron tracing. PRISM uses molecular ID codes and AI to help neurons trace themselves.
Read more: e11.bio/blog/prism
Read more: e11.bio/blog/prism
Reposted by Isaac Virshup
Luca Marconato at the European Bioconductor Conference 2025 in Barcelona, on advancing spatial biology analysis across programming languages — R, Python, JS.
Important infrastructure for data ingest, representation, visualization, analysis for emerging spatial omics techniques
Important infrastructure for data ingest, representation, visualization, analysis for emerging spatial omics techniques
September 18, 2025 at 9:29 AM
Luca Marconato at the European Bioconductor Conference 2025 in Barcelona, on advancing spatial biology analysis across programming languages — R, Python, JS.
Important infrastructure for data ingest, representation, visualization, analysis for emerging spatial omics techniques
Important infrastructure for data ingest, representation, visualization, analysis for emerging spatial omics techniques
Reposted by Isaac Virshup
korean reporting is nightmarish on the conditions Korean workers were contained in
September 14, 2025 at 6:06 PM
korean reporting is nightmarish on the conditions Korean workers were contained in
Reposted by Isaac Virshup
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
Submissions and travel grant applications close in 3 days. Find out more and apply at scverse.org/conference2025
@scverse.bsky.social
September 12, 2025 at 8:11 PM
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
Submissions and travel grant applications close in 3 days. Find out more and apply at scverse.org/conference2025
@scverse.bsky.social
Reposted by Isaac Virshup
Here's a GIANT one: C3 photosynthesis using RUBISCO is inefficient, but scientists have designed and run a new and more efficient photosynthetic pathway in Arabidopsis:
https://arstechnica.com/science/2025/09/new-pathway-engineered-into-plants-lets-them-suck-up-more-co₂/
https://arstechnica.com/science/2025/09/new-pathway-engineered-into-plants-lets-them-suck-up-more-co₂/
September 13, 2025 at 4:50 PM
Here's a GIANT one: C3 photosynthesis using RUBISCO is inefficient, but scientists have designed and run a new and more efficient photosynthetic pathway in Arabidopsis:
https://arstechnica.com/science/2025/09/new-pathway-engineered-into-plants-lets-them-suck-up-more-co₂/
https://arstechnica.com/science/2025/09/new-pathway-engineered-into-plants-lets-them-suck-up-more-co₂/
Reposted by Isaac Virshup
Anndata now supports @zarr.dev v3, great for both performance and interoperability. Check out our guide for more info, especially sharding: anndata.readthedocs.io/en/stable/tu.... Don’t worry though, we remain fully v2 backwards compatible - upgrade fearlessly!
August 11, 2025 at 4:51 PM
Anndata now supports @zarr.dev v3, great for both performance and interoperability. Check out our guide for more info, especially sharding: anndata.readthedocs.io/en/stable/tu.... Don’t worry though, we remain fully v2 backwards compatible - upgrade fearlessly!
Reposted by Isaac Virshup
🔬 CZI Workshop at scverse 2025 🔬
Multimodal And Spatial Single Cell Data: From Data APIs to AI-driven Biological Discovery
🧵
@chanzuckerberg.bsky.social
#scverse2025 #SingleCell #SpatialOmics #CELLxGENE #VirtualCells #AIBiology
Multimodal And Spatial Single Cell Data: From Data APIs to AI-driven Biological Discovery
🧵
@chanzuckerberg.bsky.social
#scverse2025 #SingleCell #SpatialOmics #CELLxGENE #VirtualCells #AIBiology
September 4, 2025 at 3:03 PM
🔬 CZI Workshop at scverse 2025 🔬
Multimodal And Spatial Single Cell Data: From Data APIs to AI-driven Biological Discovery
🧵
@chanzuckerberg.bsky.social
#scverse2025 #SingleCell #SpatialOmics #CELLxGENE #VirtualCells #AIBiology
Multimodal And Spatial Single Cell Data: From Data APIs to AI-driven Biological Discovery
🧵
@chanzuckerberg.bsky.social
#scverse2025 #SingleCell #SpatialOmics #CELLxGENE #VirtualCells #AIBiology
Reposted by Isaac Virshup
It's taken more than 2 years but we can officially announce anndataR!
There's still a lot of features to add but we hope a robust, "official", R-native H5AD reader/writer will unlock the defacto single-cell storage format for R users by avoiding issues with current solutions like zellkonverter.
There's still a lot of features to add but we hope a robust, "official", R-native H5AD reader/writer will unlock the defacto single-cell storage format for R users by avoiding issues with current solutions like zellkonverter.
We're excited to share that our preprint on anndataR, a new package bringing Python's AnnData to R, is now available on bioRxiv 🎉
🔗 Read the paper: www.biorxiv.org/content/10.1...
💻 Check the package in action: anndatar.data-intuitive.com
🔗 Read the paper: www.biorxiv.org/content/10.1...
💻 Check the package in action: anndatar.data-intuitive.com
August 26, 2025 at 5:36 AM
It's taken more than 2 years but we can officially announce anndataR!
There's still a lot of features to add but we hope a robust, "official", R-native H5AD reader/writer will unlock the defacto single-cell storage format for R users by avoiding issues with current solutions like zellkonverter.
There's still a lot of features to add but we hope a robust, "official", R-native H5AD reader/writer will unlock the defacto single-cell storage format for R users by avoiding issues with current solutions like zellkonverter.
Reposted by Isaac Virshup
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!
🎉 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
August 26, 2025 at 6:50 PM
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!
Reposted by Isaac Virshup
Want to contribute to the scverse omics ecosystem? Join the NVIDIA and scverse Hackathon: Accelerate Omics Workflows! Collaborate with NVIDIA experts, GPU-accelerated tools, and the scverse community. Apply by Aug 27, 2025. #Omics #DataScience #Hackathon #GPU
LINK: buff.ly/OCUdlks
LINK: buff.ly/OCUdlks
NVIDIA Accelerate Omics Hackathon
Take Omics tools to the next level with GPU acceleration.
buff.ly
August 14, 2025 at 3:06 PM
Want to contribute to the scverse omics ecosystem? Join the NVIDIA and scverse Hackathon: Accelerate Omics Workflows! Collaborate with NVIDIA experts, GPU-accelerated tools, and the scverse community. Apply by Aug 27, 2025. #Omics #DataScience #Hackathon #GPU
LINK: buff.ly/OCUdlks
LINK: buff.ly/OCUdlks
Reposted by Isaac Virshup
🧬🖥️ I am strongly of the opinion that bioinformatics needs to move away entirely from text-based and "loosely" structured file formats for essentially any type of data. File formats should be binary-first, and designed for *correct* and *efficient* machine parsing 1/3
August 5, 2025 at 4:39 PM
🧬🖥️ I am strongly of the opinion that bioinformatics needs to move away entirely from text-based and "loosely" structured file formats for essentially any type of data. File formats should be binary-first, and designed for *correct* and *efficient* machine parsing 1/3
Reposted by Isaac Virshup
🎉 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
August 2, 2025 at 3:00 PM
🎉 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
Reposted by Isaac Virshup
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...
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...
July 29, 2025 at 12:41 PM
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...
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...
Reposted by Isaac Virshup
Annotated matrices are much more valuable!
AnnData can easily be read into R/Bioc as well unlocking more stats tools.
AnnData can easily be read into R/Bioc as well unlocking more stats tools.
July 25, 2025 at 7:33 AM
Annotated matrices are much more valuable!
AnnData can easily be read into R/Bioc as well unlocking more stats tools.
AnnData can easily be read into R/Bioc as well unlocking more stats tools.
Reposted by Isaac Virshup
amtrak’s marketing team gets it
June 21, 2025 at 12:21 PM
amtrak’s marketing team gets it
Reposted by Isaac Virshup
Metadata & Standards Developer – FAIR Bioimaging
We seek a developer to advance metadata standards for imaging data (e.g. OME-Zarr, NGFF)
📌 Schema design (JSON-LD, RDF, SHACL), FAIR principles, open dev
🤝 Work with RO-Crate, ELIXIR, RDA & global partners
🌍 Remote | TVöD 13–14 | Deadline: 30.06
We seek a developer to advance metadata standards for imaging data (e.g. OME-Zarr, NGFF)
📌 Schema design (JSON-LD, RDF, SHACL), FAIR principles, open dev
🤝 Work with RO-Crate, ELIXIR, RDA & global partners
🌍 Remote | TVöD 13–14 | Deadline: 30.06
June 3, 2025 at 5:47 AM
Metadata & Standards Developer – FAIR Bioimaging
We seek a developer to advance metadata standards for imaging data (e.g. OME-Zarr, NGFF)
📌 Schema design (JSON-LD, RDF, SHACL), FAIR principles, open dev
🤝 Work with RO-Crate, ELIXIR, RDA & global partners
🌍 Remote | TVöD 13–14 | Deadline: 30.06
We seek a developer to advance metadata standards for imaging data (e.g. OME-Zarr, NGFF)
📌 Schema design (JSON-LD, RDF, SHACL), FAIR principles, open dev
🤝 Work with RO-Crate, ELIXIR, RDA & global partners
🌍 Remote | TVöD 13–14 | Deadline: 30.06
Reposted by Isaac Virshup
📣 Mark your calendars! The 2025 edition of the scverse conference will take place on 17-19 November at Stanford University (US) scverse.org/conference20...
Call for abstracts and registrations coming soon!
Call for abstracts and registrations coming soon!
scverse conference 2025
Follow us on our channels to learn more details in the coming weeks
scverse.org
May 12, 2025 at 10:47 PM
📣 Mark your calendars! The 2025 edition of the scverse conference will take place on 17-19 November at Stanford University (US) scverse.org/conference20...
Call for abstracts and registrations coming soon!
Call for abstracts and registrations coming soon!
Reposted by Isaac Virshup
Based on present trends I expect the Pope-assassination Signal chat to be leaked middle of next week.
April 21, 2025 at 10:36 AM
Based on present trends I expect the Pope-assassination Signal chat to be leaked middle of next week.
Reposted by Isaac Virshup
You may be fearing your 401k is no longer enough for you to retire. But with all the cuts to NIH and Medicare you also won't live as long. So the policies are integrated.
April 7, 2025 at 1:20 AM
You may be fearing your 401k is no longer enough for you to retire. But with all the cuts to NIH and Medicare you also won't live as long. So the policies are integrated.