🧬 5th BioHackathon Germany – Save the Date!
📍 Göttingen | 📅 Dec 7–11, 2026

Mark your calendars! We’re bringing together life scientists, bioinformaticians, and data stewards from around the globe for an intense week of collaborative hacking. 💻✨

Key Dates to Watch:
🚀 Mid-April: Project applications open

Don't miss your chance to innovate and build the future of life science data!
🔗 https://www.denbi.de/de-nbi-events/2051-5th-biohackathon-germany

#BioHackathon #Bioinformatics #OpenScience #deNBI #ELIXIR #LifeSciences

"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

"BH25DE report: On the path to machine-actionabletraining materials" https://doi.org/10.37044/osf.io/un6cd_v1

"We demonstrated contentfederationvia themTeSS-Xplatform, enabling cross-instanceexchange and preparing for future integration with the EOSC federation. To enhance interop-erability, we indexed relevant ontologies and curated semanticcrosswalksbetween establishedmetadata models, specificallyMoDALIAandSchema.org/Bioschemas."

#schema #bioschemas #BH25DE #biohackathon

"BioHackEU25 report: METRICS - Monitoring of KeyPerformance Indicators for ELIXIR Services" https://doi.org/10.37044/osf.io/2jgk4_v1

"As part of the BioHackathon Europe 2025, we report on the activities of the METRICS project, which addresses the need for consistent and transparent evaluation of services across ELIXIR and related initiatives using KPIs. The project brings together experts from multiple ELIXIR Nodes and scientific domains to identify, harmonise, and semantically model KPIs that reflect service quality, usage, sustainability, and impact."

#ELIXIREurope #BioHackathon #BioHackEU25

RE: https://waag.social/@henk/115886429344110445

sounds like a good spot for a #biohackathon too :)

"QPX: Pathway analysis environment" https://doi.org/10.37044/osf.io/m37f2_v1

"Building on our work at DBCLS BioHackathon 2023 (BH23), where we introduced QPX and promoted pathway modeling with WikiPathways (Pico et al., 2008) using PathVisio (Kutmon etal., 2015), we now focused on creating new pathway diagrams for diverse species and registering them in WikiPathways with functional annotations. In parallel, we deployed WikiPathways node data into Elasticsearch to enable fast and flexible search and integration of pathway information." https://osf.io/m37f2_v1

#biohackathon #BH25JP #wikipathways

2025 has come to an end. This year, we published 45 preprints resulting from 16 different biohackathons. Sometimes reports come in late, as we will see. A quick list of #biohackathon meetings with preprints in 2025:

- DBCLS BioHackathon 2023 #BH23JP: https://index.biohackrxiv.org/tag/BH23JP
- DBCLS BioHackathon 2024 #BH24JP: https://index.biohackrxiv.org/tag/BH24JP
- DBCLS BioHackathon 2025 #BH25JP: https://index.biohackrxiv.org/tag/BH25JP

- BioHackathon Europe 2023 #BH23EU: https://index.biohackrxiv.org/tag/BH23EU
- BioHackathon Europe 2024 #BH24EU: https://index.biohackrxiv.org/tag/BH24EU
- BioHackathon Europe 2025 #BioHackEU25: https://index.biohackrxiv.org/tag/BioHackEU25

- 2nd BioHackathon Germany 2023 #BH23DE: https://index.biohackrxiv.org/tag/BH23DE
- 3rd BioHackathon Germany 2024 #BH24DE: https://index.biohackrxiv.org/tag/BH24DE

- 16th International SWAT4HCLS Conference 2025 #SWAT4HCLS25: https://index.biohackrxiv.org/tag/SWAT4HCLS25

And seven others! A full overview is found on this page: https://index.biohackrxiv.org/meetings/

"BioHackEU25 Report Project 16: MiCoReCa (Microbiome Community Resource Catalogue) - Towards Centralized Curation And Integration Of Microbiome Bioinformatics Resources" https://doi.org/10.37044/osf.io/jfpsx_v1

"To address this critical gap, the ELIXIR Microbiome Community proposes the development of MiCoReCa (Microbiome Community Resource Catalogue), a comprehensive, dynamic, open-access catalogue of microbiome-related bioinformatics resources (tools, workflows, training, standards, and databases). Leveraging our community’s expertise, this initiative will utilize standardized ontologies like EDAM and cross-reference established platforms like bio.tools and WorkflowHub to create a centralized, findable inventory." https://index.biohackrxiv.org/2025/12/31/jfpsx.html

#biohackathon #elixireurope #BIoHackEU25

"Enhancement of the Interoperability of Trait Data on Genetic Resources between Japan and France" https://doi.org/10.37044/osf.io/hw2fj_v1

"This paper presents the current status of trait data standardizationbetween the two organizations and outlines a direction for standardization. Trait data forgenetic resources in Japan and France are managed using independently developed standards.The lack of mapping standards hinders data integration and interoperability. To support expertsin the mapping process, we developed a tool that translates trait terms."

#biohackathon #bh23jp

"Mining the potential of knowledge graphs for metadata on training" https://doi.org/10.37044/osf.io/gv2ac_v1

"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" https://index.biohackrxiv.org/2025/11/29/gv2ac.html

#biohackathon #BioHackEU25 #BH25EU #SPARQL #MCP

"A Blueprint for Open Science: How Transatlantic Teams Built and Deployed Knowledge Graphs to Enable Biological (AI) Models" https://doi.org/10.37044/osf.io/g4rk2_v1

"these projects and pipelines showcase methods for constructing KGs from existing biomedical datasets andexemplify the practical deployment of GraphRAG in real-world biomedical context, thereby advancing the biomedical sciences [..]" https://index.biohackrxiv.org/2025/11/26/g4rk2.html

#biohackathon #KGhack25 #KGhack #openscience #AWSOpen

"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

Call for Biohackathon topics: "SWAT4HCLS Biohackathon 2026, Amsterdan, The Netherlands" https://www.swat4ls.org/swat4hcls-biohackathon-2026/

#biohackathon #swat4hcls26 #swat4hcls

"DBCLS BioHackathon 2025 report on the WikiBlitz" https://doi.org/10.37044/osf.io/7s6da_v1

"As part of the DBCLS BioHackathon 2025, we organized a WikiBlitz to improve biodiversity knowledge by integrating iNaturalist, GBIF, Wikidata, and Wikipedia. Participants identified local flora and fauna, filling gaps in multilingual Wikipedia articles. This report summarizes the methodology, results, and insights, illustrating the usefulness of combining citizen science with digital platforms to enrich ecological data and promote biodiversity awareness." https://index.biohackrxiv.org/2025/10/24/7s6da.html

By @Andrawaag et al.

#biohackathon #bh25jp #wikidata #inaturalist #wikiblitz

"on2vec: Ontology Embeddings with Graph Neural Networks and Sentence Transformers" https://doi.org/10.37044/osf.io/4f763_v1

"Ontologies provide structured vocabularies and relationships essential for organizing biological knowledge, yet their symbolic nature limits integration with modern machine learning methods. Leveraging recent advances in graph neural networks (GNNs) and transformer-based language models, we present on2vec, a toolkit developed during the DBCLS BioHackathon 2025 for generating vector embeddings from OWL ontologies. on2vec integrates structural information from ontology hierarchies with semantic features from textual annotations using HuggingFace Sentence Transformers, producing domain-aware embeddings suitable for downstream biomedical applications and ontology-based reasoning tasks." https://index.biohackrxiv.org//2025/10/21/4f763.html

#biohackathon #ontology #BH25JP

"AI in Practice: Insights from a Community Survey of Biohackathon Participants" https://doi.org/10.37044/osf.io/pza7v_v1

"Findings reveal that most participants are frequent AI users, with tools like ChatGPT, Gemini, and Claude widely adopted, with ChatGPT as number one response. AI is primarily used to assist or draft tasks in coding, research, and writing, while full task automation remains uncommon, reflecting a preference for AI as a collaborative aid rather than a replacement." https://index.biohackrxiv.org//2025/10/12/pza7v.html

#biohackathon #AI #BH25JP

"Translating and Formalizing the MIRAGE Guidelines to a Prototype MIRAGE Ontology and DCAT3 Extension Vocabulary for Glycomics Data Management" https://doi.org/10.37044/osf.io/wj8bz_v1

"We present the first comprehensive semantic formalization of MIRAGE guidelines through an integrated RDF ontology framework comprising the MIRAGE Ontology and MIRAGE-DCAT3 vocabulary. The MIRAGE Ontology models glycan structures, biological specimens, analytical instruments, and experimental processes with formal OWL semantics and SHACL validation constraints." https://index.biohackrxiv.org//2025/09/30/wj8bz.html

#biohackathon #BH25JP #shacl #ontology

"DBCLS BioHackathon 2025 report: Creation and Publication Analytical Workflow of Creators' Interests" https://doi.org/10.37044/osf.io/qd5sz_v1

"At the DBCLS BioHackathon 2025, we converted metatranscriptomic analytical shell scripts into Common Workflow Language (CWL) containerized with Docker. Sub-workflows were created for metagenomic assembly, read mapping, and gene annotation, and validated with test datasets. The workflows, released on GitHub and WorkflowHub, improve reproducibility and address issues of reusability and software environment dependency." https://index.biohackrxiv.org//2025/09/30/qd5sz.html

#WorkflowHub #biohackathon #BH25JP #CommonWorkflowLanguage

our preview website has been revamped: https://preview.biohackrxiv.org/

#biohackrxiv #preprint #biohackathon

"A Standards-Compliant, Multi-Modal Platform for Offline Access to SRA Metadata" https://doi.org/10.37044/osf.io/9jau6_v1

"SRAKE achieves a 20-fold improvement in ingestion speed, maintains constant memory usage through zero-copy streaming, and provides standards-compliant interfaces following clig.dev guidelines. The platform introduces biomedical-specific semantic search using SapBERT embeddings via ONNX Runtime, implements comprehensive quality control thresholds for search results, and offers multiple access modalities including a CLI, REST API, MCP server for AI integration, and a simple web interface."

#biohackathon #BH25JP