#biohackathon — Public Fediverse posts

"4th BioHackathon Germany report: Exploring Gamification Strategies to Enhance Bioinformatics Training" https://doi.org/10.37044/osf.io/dfwm9_v1

#biohackathon #BH25DE #gamification #training

"While gamification can enhance engagement, implementing it without trivializing scientific content remains challenging. As part of the Biohackathon Germany 2025, we explored strategies to adapt gamification for bioinformatics education. We curated a resource matrix evaluating 20 digital tools based on cost, implementation effort, and pedagogical impact. To guide instructors, we formulated the “Ten Simple Rules for Gamification in Bioinformatics and Life Sciences Education,” emphasizing a shift from superficial point systems to deep, competency-driven mechanics rooted in authentic data and high-stakes narratives." https://index.biohackrxiv.org/2026/08/10/dfwm9.html

"4th BioHackathon Germany report: Exploring Gamification Strategies to Enhance Bioinformatics Training" https://doi.org/10.37044/osf.io/dfwm9_v1

#biohackathon #BH25DE #gamification #training

"While gamification can enhance engagement, implementing it without trivializing scientific content remains challenging. As part of the Biohackathon Germany 2025, we explored strategies to adapt gamification for bioinformatics education. We curated a resource matrix evaluating 20 digital tools based on cost, implementation effort, and pedagogical impact. To guide instructors, we formulated the “Ten Simple Rules for Gamification in Bioinformatics and Life Sciences Education,” emphasizing a shift from superficial point systems to deep, competency-driven mechanics rooted in authentic data and high-stakes narratives." https://index.biohackrxiv.org/2026/08/10/dfwm9.html

"Variant annotation in RDF for clinical trials matching" Variant annotation in RDF for clinical trials matching

#biohackathon #BH25JP #rdf #clinicalTrial

"Precision oncology depends on semantic, interoperable representations of genomic variants (GV) - particularly structural variants (SVs) - to match patients with clinical trials. In this exploratory project, we investigated the use of RDF and the GA4GH VRS Schema to standardize variant annotations and integrate them with clinical trial data. Our work, developed in collaboration with the Pangenome Graphs and Platform for Precision Medicine groups, prototypes an RDF-based data harmonization that paves the way for improved semantic interoperability in precision medicine, especially for cancer research and AI-driven discovery." https://index.biohackrxiv.org/2026/08/09/2hbqf.html

"Variant annotation in RDF for clinical trials matching" Variant annotation in RDF for clinical trials matching

#biohackathon #BH25JP #rdf #clinicalTrial

"Precision oncology depends on semantic, interoperable representations of genomic variants (GV) - particularly structural variants (SVs) - to match patients with clinical trials. In this exploratory project, we investigated the use of RDF and the GA4GH VRS Schema to standardize variant annotations and integrate them with clinical trial data. Our work, developed in collaboration with the Pangenome Graphs and Platform for Precision Medicine groups, prototypes an RDF-based data harmonization that paves the way for improved semantic interoperability in precision medicine, especially for cancer research and AI-driven discovery." https://index.biohackrxiv.org/2026/08/09/2hbqf.html

"Variant representation in RDF" https://doi.org/10.37044/osf.io/jazsb_v1

"we detected an emerging number of novel RDF models to represent variant information in genomic datasets potentially hindering data reuse. We tackled the question how semantic representations can enhance the interoperability of variant data for clinical applications." https://index.biohackrxiv.org/2026/08/09/jazsb.html

#biohackathon #SWAT4HCLS25 #RDF #genetics

"Variant representation in RDF" https://doi.org/10.37044/osf.io/jazsb_v1

"we detected an emerging number of novel RDF models to represent variant information in genomic datasets potentially hindering data reuse. We tackled the question how semantic representations can enhance the interoperability of variant data for clinical applications." https://index.biohackrxiv.org/2026/08/09/jazsb.html

#biohackathon #SWAT4HCLS25 #RDF #genetics

"Schema-Driven Generation of Synthetic HL7 FHIR RDF Data from Shape Expressions (ShEx)" https://doi.org/10.37044/osf.io/3gak2_v1

#biohackathon #GOBLINHack26 #hl7fhir #shex

"We describe how synthetic HL7 FHIR data in RDF was produced directly from Shape Expressions (ShEx), using the authoritative FHIR R4 ShEx schema as the sole source of domain structure. Rather than encoding clinical knowledge in a domain-specific simulator, we drive generation from the published shapes: a schema-driven generator (rudof generate) consumes them, and a small configuration file controls scale, cardinalities, and value generation." https://index.biohackrxiv.org/2026/07/29/3gak2.html

"Measure before you rewrite: ablation-driven redesign of LLM-facing RDF schema documentation in TogoMCP" https://doi.org/10.37044/osf.io/6v5ra_v1

#biohackathon #BH25JP #llm #mcp

"MIE files are per-database YAML documents that TogoMCP supplies to a large language model at query time so it can compose SPARQL against the DBCLS RDF Portal. Ours had grown to eleven sections, semi-automatically generated for each of 36 databases and reviewed by hand." http://index.biohackrxiv.org/2026/07/26/6v5ra.html

"Measure before you rewrite: ablation-driven redesign of LLM-facing RDF schema documentation in TogoMCP" https://doi.org/10.37044/osf.io/6v5ra_v1

#biohackathon #BH25JP #llm #mcp

"MIE files are per-database YAML documents that TogoMCP supplies to a large language model at query time so it can compose SPARQL against the DBCLS RDF Portal. Ours had grown to eleven sections, semi-automatically generated for each of 36 databases and reviewed by hand." http://index.biohackrxiv.org/2026/07/26/6v5ra.html

In our most recent Travel Fellowship Blog Post https://www.open-bio.org/2026/06/17/2026-06-17-francesco-micocci-bits2026/ undergraduate Francesco Maria Antonio Micocci won Best Poster at #BITS2026 and joined the #BioHackathon in Padova, Italy

In our most recent Travel Fellowship Blog Post https://www.open-bio.org/2026/06/17/2026-06-17-francesco-micocci-bits2026/ undergraduate Francesco Maria Antonio Micocci won Best Poster at #BITS2026 and joined the #BioHackathon in Padova, Italy

BioHackrXiv authors can use Citation Typing Ontology (CiTO) citation intent annotations to express why they are citing the articles they cite. And many have! See https://doi.org/10.37044/OSF.IO/6RJVC and https://doi.org/10.5281/ZENODO.10072013

With 2026 being the fifth year of this feature, let's celebrate this with a citation network based on CiTO!

#research #openscience #preprint #biohackathon

BioHackrXiv authors can use Citation Typing Ontology (CiTO) citation intent annotations to express why they are citing the articles they cite. And many have! See https://doi.org/10.37044/OSF.IO/6RJVC and https://doi.org/10.5281/ZENODO.10072013

With 2026 being the fifth year of this feature, let's celebrate this with a citation network based on CiTO!

#research #openscience #preprint #biohackathon

"BiocExecute: Make package functions or workflows executable from the command line" https://doi.org/10.37044/osf.io/ywsmq_v1

"R2G2 integrates R with Galaxy, and Rapp (r-lib,2024) lets an R script run as if it were a command-line program. What is missing is a path from a Bioconductor package to such tools that follows the project’s own packaging conventions. BiocExecute fills that gap" https://index.biohackrxiv.org/2026/06/19/ywsmq.html

#biohackathon #bioconductor #EuroBioC2026

"BiocExecute: Make package functions or workflows executable from the command line" https://doi.org/10.37044/osf.io/ywsmq_v1

"R2G2 integrates R with Galaxy, and Rapp (r-lib,2024) lets an R script run as if it were a command-line program. What is missing is a path from a Bioconductor package to such tools that follows the project’s own packaging conventions. BiocExecute fills that gap" https://index.biohackrxiv.org/2026/06/19/ywsmq.html

#biohackathon #bioconductor #EuroBioC2026

"Eurobioc2026 BiocContainer Report" https://doi.org/10.37044/osf.io/acxky_v1

"Containers enhance reproducibility and provide an easy and convenient way to share the setups used to run an analysis. As part of the EuroBioc 2026 Hackathon, this working group got together with the aim of offering user-friendly and straightforward ways to create containers given the desired R packages, data and scripts, and importantly, coupled to the used Bioconductor release. This resulted in an R package called SimpleBiocContainer which offers a minimal set of functions to do this." https://index.biohackrxiv.org/2026/06/15/acxky.html

#biohackathon #EuroBioc2026 #containers #BioConductor #R

"Eurobioc2026 BiocContainer Report" https://doi.org/10.37044/osf.io/acxky_v1

"Containers enhance reproducibility and provide an easy and convenient way to share the setups used to run an analysis. As part of the EuroBioc 2026 Hackathon, this working group got together with the aim of offering user-friendly and straightforward ways to create containers given the desired R packages, data and scripts, and importantly, coupled to the used Bioconductor release. This resulted in an R package called SimpleBiocContainer which offers a minimal set of functions to do this." https://index.biohackrxiv.org/2026/06/15/acxky.html

#biohackathon #EuroBioc2026 #containers #BioConductor #R

"Bioconductor Spatial Data and Image Analysis Hackathon" https://doi.org/10.37044/osf.io/9ej32_v1

"We report the outcomes of the Bioconductor Spatial Data and Image Analysis Hackathon, held in Venice, Italy in April 2026. Twenty-seven researchers and software developers organized into four teams to advance R/Bioconductor capabilities for spatial omics and image analysis." https://index.biohackrxiv.org/2026/06/14/9ej32.html

#biohackathon #VeniceHackathon2026

"Bioconductor Spatial Data and Image Analysis Hackathon" https://doi.org/10.37044/osf.io/9ej32_v1

"We report the outcomes of the Bioconductor Spatial Data and Image Analysis Hackathon, held in Venice, Italy in April 2026. Twenty-seven researchers and software developers organized into four teams to advance R/Bioconductor capabilities for spatial omics and image analysis." https://index.biohackrxiv.org/2026/06/14/9ej32.html

#biohackathon #VeniceHackathon2026

"2nd SpatialData Hackathon: Frameworks, Formats and Interoperability" https://doi.org/10.37044/osf.io/s6bph_v1

"The event gathered experts to advance spatial omics through four hackathon tracks: (i) R interoperability, (ii) accessibility and performance of visualization tools, (iii) design modernization for the SpatialData framework, and (iv) file formats and transformations (NGFF)." https://index.biohackrxiv.org/2026/06/07/s6bph.html

#SpatialData2 #biohackathon

"2nd SpatialData Hackathon: Frameworks, Formats and Interoperability" https://doi.org/10.37044/osf.io/s6bph_v1

"The event gathered experts to advance spatial omics through four hackathon tracks: (i) R interoperability, (ii) accessibility and performance of visualization tools, (iii) design modernization for the SpatialData framework, and (iv) file formats and transformations (NGFF)." https://index.biohackrxiv.org/2026/06/07/s6bph.html

#SpatialData2 #biohackathon

"Snakemake Hackathon 2026" https://doi.org/10.37044/osf.io/h6zqj_v1

"Nonetheless, the platform’s continued evolution faces several open challenges: improving core performance on heterogeneous high-performance-computing (HPC) resources, extending the plugin architecture for domain-specific extensions, and lowering the entry barrier for novice users while preserving full reproducibility. Here we report on the Snakemake Hackathon 2026, convened in Munich, Germany (9–13 March 2026) with more than 40 participants representing academia, industry, and national-level research infrastructure." https://index.biohackrxiv.org/2026/04/27/h6zqj.html

#SnakemakeHackathon2026 #biohackathon #snakemake

"Snakemake Hackathon 2026" https://doi.org/10.37044/osf.io/h6zqj_v1

"Nonetheless, the platform’s continued evolution faces several open challenges: improving core performance on heterogeneous high-performance-computing (HPC) resources, extending the plugin architecture for domain-specific extensions, and lowering the entry barrier for novice users while preserving full reproducibility. Here we report on the Snakemake Hackathon 2026, convened in Munich, Germany (9–13 March 2026) with more than 40 participants representing academia, industry, and national-level research infrastructure." https://index.biohackrxiv.org/2026/04/27/h6zqj.html

#SnakemakeHackathon2026 #biohackathon #snakemake

"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

"Minimal information standardization of phenomic experimental data in animals" https://doi.org/10.37044/osf.io/ncrkm_v1

"The current landscape of animal phenomics is characterized by a substantial lack of stan-dardization, hindering data reuse, reproducibility, and interoperability across studies, all ofwhich are particularly important in light of the 3Rs principles for animal experiments (replace, reduce, refine) (Hubrecht & Carter, 2019). Within ELIXIR, the Domestic Animals Genome andPhenome Focus Group (since December 2025 an ELIXIR community) emerged to establishstandardized practices that enhance the quality and interoperability of animal research data" http://index.biohackrxiv.org/2026/04/10/ncrkm.html

#phenomics #3r #biohackathon #BioHackEU25

new blog post: "SWAT4HCLS 2026 Amsterdam this week" https://doi.org/10.59350/mztnx-y1770 https://chem-bla-ics.linkedchemistry.info/2026/03/22/swat4hcls-2026-amsterdam-this-week.html

"Tomorrow, SWAT4HCLS 2026 will start, again in Amsterdam. The first SWAT4LS I attended was also in Amsterdam, and the second meeting in Amsterdam I was also there. And I was in Cambridge (see this post), Antwerp (no post), and at least to one of the two Leiden meetings (also no posts, it seems)."

Replies show up in the blog post.

#biohackathon #swat4hcls

new blog post: "SWAT4HCLS 2026 Amsterdam this week" https://doi.org/10.59350/mztnx-y1770 https://chem-bla-ics.linkedchemistry.info/2026/03/22/swat4hcls-2026-amsterdam-this-week.html

"Tomorrow, SWAT4HCLS 2026 will start, again in Amsterdam. The first SWAT4LS I attended was also in Amsterdam, and the second meeting in Amsterdam I was also there. And I was in Cambridge (see this post), Antwerp (no post), and at least to one of the two Leiden meetings (also no posts, it seems)."

Replies show up in the blog post.

#biohackathon #swat4hcls

@rupdecat @biohackrxiv and many more #biohackathon meetings with reports here: http://index.biohackrxiv.org/meetings/ :)

@rupdecat @biohackrxiv and many more #biohackathon meetings with reports here: http://index.biohackrxiv.org/meetings/ :)

"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

"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

"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 :)

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

"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 andpromoted 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 registeringthem in WikiPathways with functional annotations. In parallel, we deployed WikiPathwaysnode data into Elasticsearch to enable fast and flexible search and integration of pathwayinformation." https://doi.org/10.37044/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/

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

"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

"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

Hi, #biohackathon 2025 is starting here in / near Berlin. People are a bit surprised this is my first (f2f) biohackathon attendance :-)

"AI for Computational Biology: Highlights from the first BioAI Hackathon at University of Warsaw" https://doi.org/10.37044/osf.io/vbw4t_v1

"Nine interdisciplinary and multi-institutional teams addressed the following problems: disease-gene prioritization, microbiome analysis, drug-protein interactions, alternative splicing prediction, chromatin architecture study and toxicological profiling. Using cutting-edge tools such as graph neural networks (GNNs), large language models (LLMs), and multi-omics integration frameworks, participants developed scalable and reproducible analytical pipelines. The results include: a disease gene prioritization framework using GNNs, a microbiome dynamics analysis for poultry health prediction and the construction of chromatin structure-aware regulatory networks. All projects follow the open science principles and display translational potential." https://index.biohackrxiv.org//2025/07/03/vbw4t.html

#biohackathon #BIOAI25

"Enhancing Digital Infrastructures and Data Handling Practices for Single Specimen Barcoding - the 2024 BGE Barcoding Hackathon" https://doi.org/10.37044/osf.io/xb4ut_v1

"The 2024 BGE Barcoding Hackathon, hosted by the Biodiversity Genomics Europe (BGE) project in Leiden, Netherlands, focused on advancing digital infrastructures and data handling practices for single specimen barcoding. This event brought together 24 participants from various consortium member institutes to enhance workflows in DNA barcoding, which complements genome sequencing efforts within BGE. The hackathon was structured around four thematic pillars: Data Generation and Processing, BOLD Release Candidate, Wider Data Integration, and Reference Data Curation. Participants worked on optimizing barcode generation pipelines, developing a new version of the Barcode of Life Data Systems (BOLD) data publishing platform, harmonizing data standards for better integration with databases like ENA and UNITE, and automating curation processes for DNA barcoding records." https://index.biohackrxiv.org//2025/06/30/xb4ut.html

#biohackathon #BGEBH24

@ljcastro @ZBMED @NFDI will there be a #biohackathon again?

I "added" DOI support to the BioHackrXiv Index, so that I now can extract DOIs from preprints and put them in the index. With CiTO annotation that also shows up in the JSON feed :) For example, for this #BH25JP preprint https://doi.org/10.37044/osf.io/8kap3_v1 this looks like this: https://index.biohackrxiv.org/2025/09/30/8kap3.html

#preprint #biohackathon

Oh no - the water spill seems to have wiped the edge of my 2017 Iwate #BioHackathon sticker http://2017.biohackathon.org/ ~ which was significantly older than the laptop 😢

the first DBCLS BioHackathon 2024 preprints are appearing online! I saw some social media coverage and the projects sounded awesome. And now I can start reading up on the details of the work done.

I also spotted the first preprint from the meeting with CiTO annotation (cito:citesAsDataSource)! Thanks, Julie Koblitz! https://doi.org/10.37044/osf.io/qxpn8

#biohackathon #CiTO