"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 […]

"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 […] [Original post on fediscience.org]

"Maintaining and refining the Tidyomics ecosystem: enhancing core packages and interoperability for EuroBioc2026" https://doi.org/10.37044/osf.io/cd9s6_v1 "First, we introduce tidyAnnData, a new package that expands interoperability between the tidyverse and […] [Original post on fediscience.org]

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 […] [Original post on fediscience.org]

"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 […]

"Rendering SSSOM ontology mappings as RDF named graphs and RDF 1.2 triple terms" https://doi.org/10.37044/osf.io/auhzg_v1 "At the GOBLIN hackathon we explored rendering it as RDF with the individual mapping as first-class object, via two complementary serializations: named graphs (TriG […]

"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 […]

"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 […] [Original post on fediscience.org]

"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 […] [Original post on fediscience.org]

"INTOXICOM Workshop Report: Systems Biology Models for Toxicology" https://doi.org/10.37044/osf.io/zf2qj_v1 "The workshop took place under the INTOXICOM Implementation Study workshop series (Integrating the toxicology community into ELIXIR 2024) and aimed to […] [Original post on fediscience.org]

"INTOXICOM Workshop Report: Advancing FAIRtoxicology research output across Europe: ELIXIR & FAIRsharing studies" https://doi.org/10.37044/osf.io/64dfv_v1 "As part of the INTOXICOM Implementation Study for the ELIXIR Toxicology Communitya series of workshops is organized. The first INTOXICOM […]

"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 […]

"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 […] [Original post on fediscience.org]

"GA4GH VRS for the Semantic Web" https://doi.org/10.37044/osf.io/qy4td_v1 "We implemented an RDF Schema in ShEx, using OWL ontologies in the OBO Foundry such asthe NCI Thesaurus (NCIT), the Semanticscience Integrated Ontology (SIO), and the GenomeVariation Ontology (GVO). We based our modelling […]

"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 […]

"Evolving FAIR Image Analysis in Galaxy for Cross-domain and AI-ready Applications" https://doi.org/10.37044/osf.io/tsxby_v1 "he project addressed three major challenges:1. Improving semantic annotation for image analysis resources.2. Introducing content-based reproducibility validation […]

good luck to the participants of the SWAT4HCLS Biohackathon 2026 in the coming week! https://index.biohackrxiv.org/tag/SWAT4HCLS26 Use the hashtag to post your progress and have it show up on the BioHackRxiv #fediwall: https://guide.biohackrxiv.org/fediwall/ #SWAT4HCLS26

SWAT4HCLS Biohackathon 2026

Preprints for BioHackathons

index.biohackrxiv.org

"Towards Federated Learning Across Biobanks: Prototype Software from the 2026 Carnegie Mellon University–NVIDIA Hackathon" https://doi.org/10.37044/osf.io/5psfj_v1 "The Carnegie Mellon University-NVIDIA Federated Learning Hackathon for Biomedical […] [Original post on fediscience.org]

"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 […]

good luck to the hackers at #SnakemakeHackathon2026 !

"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]

"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 […] [Original post on fediscience.org]

"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 […] [Original post on fediscience.org]

"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 […] [Original post on fediscience.org]

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 - […]

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 - […]

"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 […]

"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 […]

"Increasing FAIRness in agrosystem sciences and plantphenomics" https://doi.org/10.37044/osf.io/cy65w_v1 "As part of the de.NBI BioHackathon 2023, we here report about our progress on increasingFAIR-compliance in agrosystem sciences and plant phenomics. Through the collaborative effortsof the […]

"Decoding Complex Genotype-Phenotype Interactions byDiscretizing the Genome" https://doi.org/10.37044/osf.io/xhkc3_v1 "ere, we introduce a new methodology for genotype-phenotype mapping based ongenomic hashes, unique representations of local genomic background. Each hash correspondsto a […]