BioHackathon Europe 2025, Berlin, Germany, 2025

  BioHackEU25 

2025-11-03 - 2025-11-07
https://biohackathon-europe.org/
https://biohackathon-europe.org/about/biohackrxiv/

BioHackathon Europe is an annual event that brings together bioinformaticians and computational biologists from around the world. It’s organised by ELIXIR Europe, and offers an intense week of hacking, with participants working on diverse and exciting projects. BioHackathon is a community-driven event, which provides an opportunity for members of the life sciences community to meet and work together on topics of common interest. The goal is to create code that addresses challenges in bioinformatics research.

Source

Previous BioHackathon Europe preprints

YAML instructions

biohackathon_name: "BioHackathon Europe 2025"
biohackathon_url: "https://biohackathon-europe.org/"
biohackathon_location: "Berlin, Germany, 2025"

Preprints

    Nov 29, 2025
    https://doi.org/10.37044/osf.io/gv2ac_v1

  • Mining the potential of knowledge graphs for metadata on training

    Training metadata in the life‑science community is increasingly standardized through Bioschemas, yet remains fragmented and under‑utilized. In this work we harvested training records from ELIXR’s TeSS platform and the Galaxy Training Network, converting them into a unified knowledge graph. A dedicated pipeline parses RDF/Turtle dumps, deduplicates entries, and builds rich indexes (keyword, provider, location, date, topic) that power a Model Context Protocol (MCP) server. The MCP offers live and offline search tools—including keyword, provider, location, date, topic, and SPARQL queries—enabling natural‑language access to training resources via LLM‑driven clients. User‑story driven evaluations demonstrate the system’s ability to generate custom learning paths, assemble trainer profiles, and link training data to external repositories. Findings highlight gaps in persistent identifiers (ORCID, ROR) and location granularity, informing recommendations for metadata providers. The project showcases how knowledge‑graph‑backed metadata can enhance discoverability, interoperability, and AI‑assisted exploration of scientific training materials. less than 1 minute read
    • Nov 26, 2025
    https://doi.org/10.37044/osf.io/xvrud_v1

  • BioHackEU25 report: Scop3PTM Next - Interactive visualization of PTM data across sequence, structure and interactions

    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. The project delivers an open-source library of modular JavaScript components, built with Vue.js and documented with Storybook, enabling reusable and interoperable visualizations. The framework provides 1D sequence tracks, contact-map networks and interactive 3D structural renders, using MolSpecView for rendering 3D structures linked to Nightingale 1D tracks. Together, these components offer a unified interface for exploring PTM features across multiple representational layers. This work establishes the basis for a community-oriented visualization library to support proteomics analysis. less than 1 minute read