iiinova — where your digital self keeps evolving

Reposted by Sebastian Lobentanzer

Gregor Sturm @grst.bsky.social · 29/05/2026

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/

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Reposted by Sebastian Lobentanzer

Claire @nlitb.bsky.social · 14/04/2026

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

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Sebastian Lobentanzer @slobentanzer.bsky.social · 13/02/2026

Thanks for your interest, reviewers are assigned now

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Sebastian Lobentanzer @slobentanzer.bsky.social · 11/02/2026

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...

github.com

[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...

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Sebastian Lobentanzer @slobentanzer.bsky.social · 27/10/2025

This paper is the result of a very fruitful collaboration with Medical Bioinformatics Rostock (Georg Fuellen) and a very talented medical student (Hans Jarchow, this study's first author). Many thanks to all collaborators for the enjoyable experience!

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Sebastian Lobentanzer @slobentanzer.bsky.social · 27/10/2025

We find that current LLMs have a varied profile of proficiency. They seem very aligned with "first do no harm," very rarely recommending potentially harmful interventions. On the other side of the spectrum, they show very mixed performance on the comprehensiveness and usefulness of their answers.

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Sebastian Lobentanzer @slobentanzer.bsky.social · 27/10/2025

In short, they still are not ready for autonomous deployment. But the picture is complex.

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Sebastian Lobentanzer @slobentanzer.bsky.social · 27/10/2025

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

rdcu.be

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

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Sebastian Lobentanzer @slobentanzer.bsky.social · 02/09/2025

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...

denbi.de

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...

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Reposted by Sebastian Lobentanzer

Malte Kuehl @maltekuehl.com · 28/08/2025

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).

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Sebastian Lobentanzer @slobentanzer.bsky.social · 28/08/2025

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.

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Sebastian Lobentanzer @slobentanzer.bsky.social · 29/07/2025

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 👇

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Sebastian Lobentanzer @slobentanzer.bsky.social · 16/07/2025

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!

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Reposted by Sebastian Lobentanzer

Bioconductor @bioconductor.bsky.social · 11/07/2025

💻🧬 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

biohackathon-europe.org

Projects

BioHackathon Europe projects

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Sebastian Lobentanzer @slobentanzer.bsky.social · 13/06/2025

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

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Reposted by Sebastian Lobentanzer

pyOpenSci @pyopensci.org · 12/06/2025

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 · 29/05/2025

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?

invt.io

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

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Sebastian Lobentanzer @slobentanzer.bsky.social · 19/05/2025

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!

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Reposted by Sebastian Lobentanzer

Saez-Rodriguez Group @saezlab.bsky.social · 09/04/2025

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

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Reposted by Sebastian Lobentanzer

Deutsches Zentrum für Diabetesforschung (DZD) @diabresearch-dzd.bsky.social · 27/03/2025

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.

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Sebastian Lobentanzer @slobentanzer.bsky.social · 27/03/2025

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.

ebi.ac.uk

BioChatter and the future of LLM driven bioscience -

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Reposted by Sebastian Lobentanzer

Computational Health Center @comphealthmunich.bsky.social · 25/03/2025

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.

jobs.helmholtz-muenchen.de

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

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Sebastian Lobentanzer @slobentanzer.bsky.social · 25/03/2025

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. :)

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Sebastian Lobentanzer @slobentanzer.bsky.social · 20/02/2025

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!

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Reposted by Sebastian Lobentanzer

EMBL-EBI Training @training.ebi.embl.org · 13/02/2025

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

Saez-Rodriguez Group @saezlab.bsky.social · 05/02/2025

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 · 30/01/2025

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 · 23/01/2025

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.

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Reposted by Sebastian Lobentanzer

Michael Sars Centre @msarscentre.bsky.social · 22/01/2025

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 👏

tinyurl.com

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...

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Reposted by Sebastian Lobentanzer

EMBL-EBI @ebi.embl.org · 22/01/2025

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 · 22/01/2025

It should be, sorry about that! I’ll contact the editor.

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Reposted by Sebastian Lobentanzer

Eric Topol @erictopol.bsky.social · 22/01/2025

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

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pyOpenSci @pyopensci.org · 16/01/2025

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: buff.ly/3P4MnOY

Graphic celebrating Inessa Pawson, recipient of the NumFOCUS Community Leadership Award 2024. The design features a professional photo of Inessa alongside details of her contributions, including roles as a NumPy Steering Council member, scikit-learn survey team co-lead, Scientific Python SPEC Steering Committee member, and organizer for SciPy US and PyCon US Maintainers Summit since 2020. The graphic highlights her passions: incentive design, collaborative intelligence, and jazz. Includes pyOpenSci branding and URL

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Sebastian Lobentanzer @slobentanzer.bsky.social · 16/01/2025

I feel like this is already possible on editorial discretion. It is the reviewers' time and expertise that is critical to the process of peer-review, but the editor is needed to contextualise reviews and make decisions. If the editor has no clue, the journal may not be the right venue.

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Reposted by Sebastian Lobentanzer

Stegle Lab @steglelab.bsky.social · 15/01/2025

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

benchmarks.elsa-ai.eu

Overview - Health - ELSA Benchmarks Platform

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Reposted by Sebastian Lobentanzer

Victor Javier @vjsanchez.bsky.social · 27/11/2024

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

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