Hackathon - System biology models and knowledge graphs

[Carissa Bleker]

Dear COMBINE members, 

If you are interested in integrating systems biology and knowledge graphs (and LLMs), please see the Biohackathon Germany project: 

"A common framework for transforming systems biology models into human- and AI-accessible knowledge graphs" (project 4). 

We will be working on developing BioCypher adapters for SBML and SBGN-ML to a common knowledge graph schema, that is both human and AI-accessible. 

The 4th BioHackathon Germany will be held 01-05 December 2025 in Walsrode, information and registration is here:

https://www.denbi.de/de-nbi-events/1840-4th-biohackathon-germany

Best, 

Carissa

[Carissa Bleker]

Dear all, 

Towards the goal of jointly developing a user-oriented, AI-ready knowledge graph representation for systems biology models, at the 4th BioHackathon Germany (1-5 December 2025 in Walsrode), we will be working on developing BioCypher adapters for SBML and SBGN-ML to a common knowledge graph schema. For more information, you can read the project "A common framework for transforming systems biology models into human- and AI-accessible knowledge graphs" description here: project 4.

To help guide and prioritise work at the hackathon (and  also any follow-up work/projects that may come from it), we ask for your input by answering the below questionnaire by 30 November 2025.

Note that all the questions in the questionnaire are optional, and if you are logged in with a Google account, you are able to return to edit or complete it. 

https://forms.gle/rVpKDe9PBB6qMGdV7 

Please also share the questionnaire with your research circles, the more input the better!

Thank you! (And apologies for the cross-posting.)

Kind regards, 

Carissa Bleker