"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

🧬 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