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Sebastian Lobentanzer @slobentanzer.bsky.social · Sep 2

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...

4th BioHackathon Germany

The 'German Network for Bioinformatics Infrastructure – de.NBI' is a national, academic and non-profit infrastructure supported by the Federal Ministry of Education and Research providing bioinformati...

www.denbi.de

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Reposted by Sebastian Lobentanzer

Malte Kuehl @maltekuehl.com · Aug 28

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 · Aug 28

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

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Sebastian Lobentanzer @slobentanzer.bsky.social · Aug 28

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 · Aug 28

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

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Sebastian Lobentanzer @slobentanzer.bsky.social · Jul 29

capitalism

Sebastian Lobentanzer @slobentanzer.bsky.social · Jul 29

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 · Jul 29

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...

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).

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Sebastian Lobentanzer @slobentanzer.bsky.social · Jul 16

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 · Jul 11

💻🧬 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

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Reposted by Sebastian Lobentanzer

Bioconductor @bioconductor.bsky.social · Jul 11

💻🧬 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

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Sebastian Lobentanzer @slobentanzer.bsky.social · Jun 13

No, there’s a .com in that one that probably shouldn’t be there

Reposted by Sebastian Lobentanzer

pyOpenSci @pyopensci.org · Jun 12

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

Illustration of a woman on a video call, with text that says pyOpenSci is seeking volunteer editors with a Physics background. Editors help review 2–4 packages a year and shape peer review policies. Diverse applicants encouraged. Apply link: bit.ly/pyOSEditor

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Sebastian Lobentanzer @slobentanzer.bsky.social · May 29

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

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Sebastian Lobentanzer @slobentanzer.bsky.social · May 19

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 · Feb 17

📢 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!

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Reposted by Sebastian Lobentanzer

Saez-Rodriguez Group @saezlab.bsky.social · Apr 9

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 · Mar 25

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

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Sebastian Lobentanzer @slobentanzer.bsky.social · Mar 27

Great work!

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Reposted by Sebastian Lobentanzer

Deutsches Zentrum für Diabetesforschung (DZD) @diabresearch-dzd.bsky.social · Mar 27

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 · Mar 25

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

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Sebastian Lobentanzer @slobentanzer.bsky.social · Mar 27

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.

BioChatter and the future of LLM driven bioscience -

www.ebi.ac.uk

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Reposted by Sebastian Lobentanzer

Computational Health Center @comphealthmunich.bsky.social · Mar 25

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

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Sebastian Lobentanzer @slobentanzer.bsky.social · Mar 25

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 · Mar 25

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

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Sebastian Lobentanzer @slobentanzer.bsky.social · Feb 20

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 · Feb 13

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 🖥️🧬🧪

Webinar series at EMBL-EBI
Large Language Models and their applications in Bioinformatics
26 February - 26 March 2025

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Reposted by Sebastian Lobentanzer

EMBL-EBI Training @training.ebi.embl.org · Feb 13

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 🖥️🧬🧪

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Reposted by Sebastian Lobentanzer

Saez-Rodriguez Group @saezlab.bsky.social · Feb 5

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...

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Sebastian Lobentanzer @slobentanzer.bsky.social · Jan 30

Good points, particularly on keeping up with developments and continuously experimenting. It's not an easy task for research groups, even large ones.

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Sebastian Lobentanzer @slobentanzer.bsky.social · Jan 23

The „iron rule“ of science: collect tons of data and report it objectively. But to be fair, the people who receive the credit nowadays are not the ones who suffer the tedium any more.

Reposted by Sebastian Lobentanzer

Michael Sars Centre @msarscentre.bsky.social · Jan 22

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

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Reposted by Sebastian Lobentanzer

EMBL-EBI @ebi.embl.org · Jan 22

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...

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Sebastian Lobentanzer @slobentanzer.bsky.social · Jan 22

rdcu.be/d68Ek

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