Sebastian Lobentanzer
@slobentanzer.bsky.social
Accessible AI Research | Open Source
Computational Biology | Pharmacology
Research Software Engineering
PI @ Helmholtz Munich (Computational Health)
@slolab.ai
Computational Biology | Pharmacology
Research Software Engineering
PI @ Helmholtz Munich (Computational Health)
@slolab.ai
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
October 27, 2025 at 3:14 PM
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
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...
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
September 2, 2025 at 1:48 PM
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...
www.denbi.de/de-nbi-event...
Reposted by Sebastian Lobentanzer
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).
🤖🧬 New biomedical MCP server added to the registry:
BioCypher Knowledge Graph MCP
Check it out at https://biocontext.ai/registry/biocypher/biocypher-mcp
BioCypher Knowledge Graph MCP
Check it out at https://biocontext.ai/registry/biocypher/biocypher-mcp
August 28, 2025 at 3:14 PM
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).
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.
🤖🧬 New biomedical MCP server added to the registry:
BioCypher Knowledge Graph MCP
Check it out at https://biocontext.ai/registry/biocypher/biocypher-mcp
BioCypher Knowledge Graph MCP
Check it out at https://biocontext.ai/registry/biocypher/biocypher-mcp
August 28, 2025 at 3:17 PM
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.
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 👇
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 12:46 PM
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 👇
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!
💻🧬 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
In-person registration closes Tuesday, July 15
Project: github.com/elixir-europ...
#BioHackathon #Bioinformatics #Bioconductor
Projects
BioHackathon Europe projects
biohackathon-europe.org
July 16, 2025 at 2:50 PM
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!
Reposted by Sebastian Lobentanzer
💻🧬 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
In-person registration closes Tuesday, July 15
Project: github.com/elixir-europ...
#BioHackathon #Bioinformatics #Bioconductor
Projects
BioHackathon Europe projects
biohackathon-europe.org
July 11, 2025 at 3:15 PM
💻🧬 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
In-person registration closes Tuesday, July 15
Project: github.com/elixir-europ...
#BioHackathon #Bioinformatics #Bioconductor
Reposted by Sebastian Lobentanzer
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
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
June 12, 2025 at 7:48 PM
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
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
May 29, 2025 at 1:41 PM
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 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!
📢 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!
Join us & shape the future of AI for science - register & submit an abstract below:
🔗 haicon.cc
👋 See you in Karlsruhe!
May 19, 2025 at 2:09 PM
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!
Reposted by Sebastian Lobentanzer
Congrats & Good luck to our @slobentanzer.bsky.social as he starts his group @diabresearch-dzd.bsky.social & @comphealthmunich.bsky.social - he is hiring 👇
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.
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
April 9, 2025 at 7:53 AM
Congrats & Good luck to our @slobentanzer.bsky.social as he starts his group @diabresearch-dzd.bsky.social & @comphealthmunich.bsky.social - he is hiring 👇
Reposted by Sebastian Lobentanzer
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.
@comphealthmunich.bsky.social. We look forward to working together to advance #biomedical science by developing open source, user-friendly #AI software.
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.
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
March 27, 2025 at 2:18 PM
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.
@comphealthmunich.bsky.social. We look forward to working together to advance #biomedical science by developing open source, user-friendly #AI software.
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.
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 -
BioChatter and the future of LLM driven bioscience -
www.ebi.ac.uk
March 27, 2025 at 1:10 PM
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.
Many thanks to @ebi.embl.org for organising this series and inviting me! Please reach out to me for collab or jobs.
Reposted by Sebastian Lobentanzer
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.
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
March 25, 2025 at 12:37 PM
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.
His group focuses on „Accessible Biomedical AI Research“ - and he‘s hiring!
Open positions on slolab.ai and: bit.ly/slolab.
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. :)
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. :)
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.
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
March 25, 2025 at 1:29 PM
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. :)
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. :)
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!
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 🖥️🧬🧪
Registration is free but essential for each webinar: www.ebi.ac.uk/training/eve...
#GeneSky 🖥️🧬🧪
February 20, 2025 at 3:24 PM
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!
Reposted by Sebastian Lobentanzer
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 🖥️🧬🧪
Registration is free but essential for each webinar: www.ebi.ac.uk/training/eve...
#GeneSky 🖥️🧬🧪
February 13, 2025 at 10:56 AM
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 🖥️🧬🧪
Registration is free but essential for each webinar: www.ebi.ac.uk/training/eve...
#GeneSky 🖥️🧬🧪
Reposted by Sebastian Lobentanzer
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...
February 5, 2025 at 9:15 AM
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...
Reposted by Sebastian Lobentanzer
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
January 22, 2025 at 10:57 AM
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 👏
Reposted by Sebastian Lobentanzer
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...
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...
January 22, 2025 at 10:26 AM
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...
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...
January 22, 2025 at 3:38 PM
Reposted by Sebastian Lobentanzer
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
www.nature.com/articles/s41...
@slobentanzer.bsky.social @juliosaezrod.bsky.social
January 22, 2025 at 3:06 PM
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
www.nature.com/articles/s41...
@slobentanzer.bsky.social @juliosaezrod.bsky.social
Reposted by Sebastian Lobentanzer
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
Read more: https://buff.ly/3P4MnOY
January 16, 2025 at 5:20 PM
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
Read more: https://buff.ly/3P4MnOY
Reposted by Sebastian Lobentanzer
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
Register to participate: benchmarks.elsa-ai.eu?ch=4
Overview - Health - ELSA Benchmarks Platform
benchmarks.elsa-ai.eu
January 15, 2025 at 9:27 AM
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
Register to participate: benchmarks.elsa-ai.eu?ch=4
Reposted by Sebastian Lobentanzer
I love Zulip; it works very well for organizing the different projects in the lab. Highly recommended! @zulip.bsky.social
November 27, 2024 at 7:34 AM
I love Zulip; it works very well for organizing the different projects in the lab. Highly recommended! @zulip.bsky.social