Happy to announce the release of IggyTop, a metadatabase for immune receptor–epitope interactions. It's integrated with scirpy v0.24 so you can readily use it to annotate your single-cell TCR datasets. iggytop.readthedocs.io/en/latest/

Here's our preprint from the 2025 ELIXIR BioHackathon in Berlin! 🎉 @slobentanzer.bsky.social @ifb-elixir-fr.bsky.social @elixir-europe.org @bioconductor.bsky.social

BioHackrXiv@biohackrxiv.fediscience.org.ap.brid.gy · 4mo ago

"Improving package annotation in metabolomics andproteomics via robust, ontology-driven LLM integration" https://doi.org/10.37044/osf.io/x5v6b_v1 "At BioHackathon Europe 2025, our team explored how Large Language Models (LLMs) can assist this process through […] [Original post on fediscience.org]

Looking for reviewers: OneCite, a universal citation & academic reference toolkit—multi-source lookup, metadata completion, de-duplication, and multi-style output. Proficient in open source willing to help? I'd be happy to onboard you. Here's the issue for the submission: github.com/pyOpenSci/so...

[SUBMISSION] OneCite — Universal citation & academic reference toolkit · Issue #267 · pyOpenSci/software-submission

Submitting Author: (@HzaCode) All current maintainers: (@HzaCode) Package Name: OneCite One-Line Description of Package: Universal citation & academic reference toolkit—multi-source lookup (DOI/PMI...

github.com

How do we know whether our AI solutions are up to our standards, for instance in clinical recommendations? We try to contribute to the answer by our recent study on *Benchmarking large language models for personalized, biomarker-based health intervention recommendations* rdcu.be/eMVeL

Benchmarking large language models for personalized, biomarker-based health intervention recommendations

npj Digital Medicine - Benchmarking large language models for personalized, biomarker-based health intervention recommendations

rdcu.be

Registration is now open for this year's German BioHackathon, where we have a project for transforming systems biology models into knowledge graphs. Would be great to see some of you there. :) www.denbi.de/de-nbi-event...

Interesting work by @slobentanzer.bsky.social and team, making BioCypher available through MCP! Check it out on biocontext.ai/registry/bio... or try it in BioContextAI Chat (biocontext.ai/chat, click "cogs" icon to add the remote MCP server).

BioContextAI@biocontext.ai · 11mo ago

🤖🧬 New biomedical MCP server added to the registry: BioCypher Knowledge Graph MCP Check it out at https://biocontext.ai/registry/biocypher/biocypher-mcp

Want to use BioCypher, but struggle with the complexity of the workflow and pipeline creation? We might just have a solution for you: an MCP server that you can connect to from your favourite co-programmer, to help you understand the framework and implementation details.

BioContextAI@biocontext.ai · 11mo ago

🤖🧬 New biomedical MCP server added to the registry: BioCypher Knowledge Graph MCP Check it out at https://biocontext.ai/registry/biocypher/biocypher-mcp

Check out our new collab on a decentralised way to deal with biomedical MCP servers for agentic tool use. Preprint out now, for more info, see the Malte's thread 👇

Malte Kuehl@maltekuehl.com · last yr.

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...

BioHackathon Europe 2025: In-person registration has closed, but there will be a waiting list. Remote participation is still open for registration. Check out the many interesting projects this year!

Bioconductor@bioconductor.bsky.social · last yr.

💻🧬 Join the Bioconductor project at BioHackathon Europe 2025 (Berlin, Nov 3–7)! In-person registration closes Tuesday, July 15 Project: github.com/elixir-europ... #BioHackathon #Bioinformatics #Bioconductor

💻🧬 Join the Bioconductor project at BioHackathon Europe 2025 (Berlin, Nov 3–7)! In-person registration closes Tuesday, July 15 Project: github.com/elixir-europ... #BioHackathon #Bioinformatics #Bioconductor

Projects

BioHackathon Europe projects

biohackathon-europe.org

EDITORS NEEDED WITH PHYSICS Background Could that be you? We are looking to onboard a new editor with Physics background to lead software reviews for pyOpenSci. Learn more and sign up below! Please share with your communities! bit.ly.com/pyoseditor #opensource #openscience #python

I'm attending #ISMBECCB2025 in Liverpool, United Kingdom from July 20-24. Talking on agentic systems and foundation models: how can we make them accessible via open-source solutions?

I'm participating the ISMB/ECCB 2025 conference, join me!

Register now

invt.io

I will be giving a talk in the foundation model session of HAICON25 on Jun 5, titled "Agentic systems are upon us": on how we deal with the myriad new opportunities that are opening up for us very rapidly through GenAI. Hope to see some of you there!

Helmholtz AI@helmholtzai.bsky.social · last yr.

📢 Registration & abstract submission for the Helmholtz AI Conference 2025: AI for Science (June 3-5, Karlsruhe, Germany) are NOW OPEN! Join us & shape the future of AI for science - register & submit an abstract below: 🔗 haicon.cc 👋 See you in Karlsruhe!

Congrats & Good luck to our @slobentanzer.bsky.social as he starts his group @diabresearch-dzd.bsky.social & @comphealthmunich.bsky.social - he is hiring 👇

Computational Health Center@comphealthmunich.bsky.social · last yr.

We‘re excited to welcome @slobentanzer.bsky.social, new PI at the intersection of @diabresearch-dzd.bsky.social and @comphealthmunich.bsky.social @www.helmholtz-munich.de! His group focuses on „Accessible Biomedical AI Research“ - and he‘s hiring! Open positions on slolab.ai and: bit.ly/slolab.

We're happy to welcome @slobentanzer.bsky.social, new PI at the intersection of @www.helmholtz-munich.de, @diabresearch-dzd.bsky.social + @comphealthmunich.bsky.social. We look forward to working together to advance #biomedical science by developing open source, user-friendly #AI software.

Computational Health Center@comphealthmunich.bsky.social · last yr.

We‘re excited to welcome @slobentanzer.bsky.social, new PI at the intersection of @diabresearch-dzd.bsky.social and @comphealthmunich.bsky.social @www.helmholtz-munich.de! His group focuses on „Accessible Biomedical AI Research“ - and he‘s hiring! Open positions on slolab.ai and: bit.ly/slolab.

Yesterday's webinar has been recorded and is available on demand (www.ebi.ac.uk/training/eve... and www.youtube.com/watch?v=jn-p...). The slides are also available on the EBI site. Many thanks to @ebi.embl.org for organising this series and inviting me! Please reach out to me for collab or jobs.

We‘re excited to welcome @slobentanzer.bsky.social, new PI at the intersection of @diabresearch-dzd.bsky.social and @comphealthmunich.bsky.social @www.helmholtz-munich.de! His group focuses on „Accessible Biomedical AI Research“ - and he‘s hiring! Open positions on slolab.ai and: bit.ly/slolab.

PhD Candidates and Postdocs in Accessible Biomedical AI (f/m/x)

jobs.helmholtz-muenchen.de

Yes, there's "accessible" in my group's title. Come at me, Trump! Just kidding, don't come at me, except if you're looking for a job in biomedical AI. Hiring at all levels, up to 100% of E13. If you're enthusiastic about science and open source, consider applying! Please help spread the word. :)

Computational Health Center@comphealthmunich.bsky.social · last yr.

We‘re excited to welcome @slobentanzer.bsky.social, new PI at the intersection of @diabresearch-dzd.bsky.social and @comphealthmunich.bsky.social @www.helmholtz-munich.de! His group focuses on „Accessible Biomedical AI Research“ - and he‘s hiring! Open positions on slolab.ai and: bit.ly/slolab.

I will be giving the last lecture in this series: LLM applications and where does the future lead. Looking forward, please register and tune in!

EMBL-EBI Training@training.ebi.embl.org · last yr.

Are you curious about how LLMs can be applied to bioinformatics? This series of four webinars covers fundamentals through to cutting-edge applications in knowledge extraction & summarisation. Registration is free but essential for each webinar: www.ebi.ac.uk/training/eve... #GeneSky 🖥️🧬🧪

Are you curious about how LLMs can be applied to bioinformatics? This series of four webinars covers fundamentals through to cutting-edge applications in knowledge extraction & summarisation. Registration is free but essential for each webinar: www.ebi.ac.uk/training/eve... #GeneSky 🖥️🧬🧪

Applying LLMs to biomedical research today can go one of two ways: we either use a closed-source web app, or we get coding ourselves. Many researchers lack training for the latter, so their only choice is the former. We want to change that. www.nature.com/articles/s41...

AI has the potential to transform the way we access and handle datasets. Meet BioChatter: an open large language model framework designed to support biomedical research 💻 An exciting project by @ebi.embl.org with contributions from @noahbruderer.bsky.social, out now in @naturebiotech.bsky.social 👏

BioChatter: making large language models accessible for biomedical research

A team led by researchers at EMBL's European Bioinformatics Institute (EMBL-EBI), in collaboration with a PhD candidate in the Christiaen group, developed an open-source large language model (LLM) fra...

tinyurl.com

Large language models (LLMs) are everywhere, but using commercially available LLMs isn't always possible in research. Introducing BioChatter, an open-source framework for developing LLMs for biomedical research, developed in line with open science principles. www.ebi.ac.uk/about/news/r...

rdcu.be/d68Ek

A platform for the biomedical application of large language models

Nature Biotechnology - A platform for the biomedical application of large language models

rdcu.be

Eric Topol@erictopol.bsky.social · 2y ago

BioChatter, a new open-source platform for large language of life models, "to bridge the gap between complex custom solutions and close-source commercial platforms" www.nature.com/articles/s41... @slobentanzer.bsky.social @juliosaezrod.bsky.social

BioChatter, a new open-source platform for large language of life models, "to bridge the gap between complex custom solutions and close-source commercial platforms" www.nature.com/articles/s41... @slobentanzer.bsky.social @juliosaezrod.bsky.social

Inessa Pawson won the 2024 NumFocus community leadership award. We're thrilled to celebrate her. She's been key in building the pyOpenSci community and other vital parts of the #python #opensource #community, fostering connection & promoting open source values 💖 Read more: https://buff.ly/3P4MnOY

We are delighted to announce The Health Privacy Challenge, an interactive opportunity for advancement at the intersection of computational biology and privacy research, brought to you as a part of CAMDA Conference at #ISMB/ECCB2025 🫐🍅 Register to participate: benchmarks.elsa-ai.eu?ch=4

I love Zulip; it works very well for organizing the different projects in the lab. Highly recommended! @zulip.bsky.social