"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 the Model Context Protocol (MCP), an emerging open standard that specifies how LLMs call external functions, using metabolomics as a domain use case. We developed an MCP-based workflow that grounds tool descriptions in the EDAM ontology (Ison et al., 2013) (Black et al., 2022), improving reproducibility and semantic precision." https://osf.io/preprints/biohackrxiv/x5v6b_v1

#biohackathon #BioHack25EU #ontology #edam

"Evolving FAIR Image Analysis in Galaxy for Cross-domain and AI-ready Applications" https://doi.org/10.37044/osf.io/tsxby_v1

"The project addressed three major challenges:1. Improving semantic annotation for image analysis resources.2. Introducing content-based reproducibility validation mechanisms.3. Streamlining tools and training materials for accessible bioimage analysis.To achieve these goals, the project involved participants with heterogeneous backgroundsfrom different institutions, including ELIXIR, Euro-BioImaging, and the ISCC Foundation,joining both on-site and online." http://index.biohackrxiv.org/2026/03/31/tsxby.html

#biohackathon #BioHack25EU

"Tools to develop constraint-based models in R: adapting existing toolboxes" https://doi.org/10.37044/osf.io/ey4c5_v1

"In this project, we proposed the (re)development of an R based framework for developing and simulating constraint-based models. We proposed to expand the Sybil library for model simulation with the functionalities for model reconstruction and analysis available in the widely used RAVEN toolbox in Matlab." https://index.biohackrxiv.org/2026/03/13/ey4c5.html

#biohackathon #biohack25EU

"Bidirectional bridge: GitHub ⇄ bio.tools" https://doi.org/10.37044/osf.io/8ktd6_v1

"Here, we describe the tooling for a bidirectional bridge between the software developmentplatform GitHub and the ELIXIR bio.tools registry of life sciences software tools and dataresources. The developed bridge maps and improves metadata records across these twoplatforms, thereby benefiting both and helping make research software more FAIR: findable,accessible, interoperable and reusable" https://osf.io/preprints/biohackrxiv/8ktd6_v1

#BH25EU #BioHack25EU #biohackathon #ELIXIREurope #bioTools

"BioHackEU25 report: Scop3PTM Next - Interactive visualization of PTM data across sequence, structure and interactions" https://doi.org/10.37044/osf.io/xvrud_v1

"Scop3PTM Next was developed during BioHackathon Europe 2025 to address the need for integrated visualization of protein-centric data across sequence (and modification), interaction and structural contexts." https://index.biohackrxiv.org/2025/11/26/xvrud.html

#BioHack25EU #biohackathon #protein #bioinformatics