"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 […]
🧬 5th BioHackathon Germany – Save the Date!
📍 Göttingen | 📅 Dec 7–11, 2026
Mark your calendars! We’re bringing together life scientists, bioinformaticians, and data stewards for an intense week of hacking. 💻✨
🚀 Mid-April: Project applications open
🔗 www.denbi.de/de-nbi-event...
#BioHackathon
Figure 3:Principal component analysis (PCA) of bio.tools entries with a GitHub repository basedon the numbers of contributors, forks (and network count), commits, pulls, releases, open issues,subscribers, watchers, stargazers and the average time to close issues. The colors represent thebio.toolsmaturitylevel, i.e.,Emerging,MatureorLegacy.
"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 […]
[Original post on fediscience.org]
RE: https://waag.social/@henk/115886429344110445
sounds like a good spot for a #biohackathon too :)
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
- […]
@elixir-nl.bsky.social joined the @elixir-europe.org #BioHackathon, collaborating with data experts from across Europe.
The NL community co-led/contributed to projects on interoperability, FAIR research software, metadata standards & multimodal data integration.
👉 www.health-ri.nl/en/news/elix...
Call for Biohackathon topics: "SWAT4HCLS Biohackathon 2026, Amsterdan, The Netherlands" https://www.swat4ls.org/swat4hcls-biohackathon-2026/
#biohackathon #swat4hcls26 #swat4hcls
ERGA Annotation Committee and online friends at @elixir-europe.org #Biohackathon @ergabiodiv.bsky.social final results!
ERGA Data Analysis Committee and online friends at @elixir-europe.org #Biohackathon @ergabiodiv.bsky.social #phyogenomics with BUSCO genes - final results!
"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 […]
"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 […]
ERGA Annotation Committee and online friends at @elixir-europe.org #Biohackathon @ergabiodiv.bsky.social
ERGA Data Analysis Committee and online friends at @elixir-europe.org #Biohackathon @ergabiodiv.bsky.social #phyogenomics with BUSCO genes
"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 […]
"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 […]
ERGA Data Analysis Committee at @elixir-europe.org #Biohackathon @ergabiodiv.bsky.social #phyogenomics with BUSCO genes
The #LongTREC consortium is well represented at #BioHackathon Europe in Berlin! Advancing open-source tools to accelerate innovation — perfectly aligned with our own goals more specifically in #LongReadTranscriptomics. Congratulations to all who took part! @anaconesa.bsky.social
"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 […]
New website (see link from main post). It shows in the left column the BioHackrXiv "BHX" logo with short explanation what BHX is. On the right is the new content. Users no longer have to select a BioHackathon, but all that information is now extracted from the paper.md itself. The "Getting Started" box explains the process. Under this box is now only the two options to provide the paper, Option 1 being the repository URL, and the Option 2 is to upload a .zip file.
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 […]
🎉 We are excited to join this year's #Biohackathon Europe in Bad Saarow!
Looking forward to a week of fruitful projects, networking, & fun—thanks to the @elixir-europe.org Hub & everyone joining onsite or online!
🚀 @sneumann.bsky.social, Michael Crusoe, Nils Hoffmann & many more from across Europe.
ERGA Data Analysis Committee at @elixir-europe.org #Biohackathon @ergabiodiv.bsky.social #phyogenomics with BUSCO genes
"A Lightweight PURL Resolver for Linked Life Science Data" https://doi.org/10.37044/osf.io/8kap3_v1
"To address this issue, we developed a lightweight Persistent Uniform Resource Locator (PURL) resolver during the BioHackathon Japan 2025. The resolver is implemented in PHP, chosen for its […]
Want to make better use of ontologies? Check out on2vec created at DBCLS #biohackathon 2025...
It turns ontologies into embeddings you can actually use in ML models. Perfect for biomedical data, knowledge graphs, etc. osf.io/preprints/bi... github.com/david4096/on...
🖥️ There is still time to register and join this year's BioHackathon Europe! Learn more about participating ERGA members and the projects they will develop: www.erga-biodiversity.eu/post/erga-at... #BioHackEU25 #biohackathon #bioinformartics #community @elixir-europe.org @biogeneurope.bsky.social
