BioHackrXiv

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]

Figure 1: Curated crosswalks between MoDALIA and Schema.org metadata models for training materials. The figure shows schema.org on the left side, SSSOM icon below an bidirectional arrow in the middle in a screenshot of a MoDALIA predicate definition on the right.

"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]

Part of Figure 1:Photo of project poster for the mid-week presentation. The photo shows a A0 sheet notes from the meeting, including country flags, some key words, and the output of brainstorming.

"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]

Screenshot of the linked BioHackrXiv preprint, showing the top half of a preprint PDF page, showing the BioHackrXiv logo from the template, a table at the top listing a Arabidopsis thaliana pathway, and below that part of Figure 1 showing a "[p]athway diagram for for Caffeine synthesis inCoffea arabica. This diagram is already published in WikiPathways at https://www.wikipathways.org/pathways/WP5586.html".

"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 […]

"MCP server tools with RDF shapes" https://doi.org/10.37044/osf.io/8qeh5_v1

"In this paper, we present the work we have done during the Japan Biohackathon 2025 about implementing MCP servers supported by RDF data shapes to improve natural language interactions with large RDF datasets using […]

"BioHackEU25 report: Towards a Robust ValidationService for Data and Metadata in ARC RO-Crates" https://doi.org/10.37044/osf.io/zah28_v1

"For the metadata, validation will ensure structural and semantic compliance to the base RO-Crate specification and the ARC family of RO-Crate profiles […]

"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 […]

"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 […]

"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 […]

SWAT4HCLS Biohackathon 2026

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 […]

"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 […]

"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 […]

"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 […]

hi, this is the Mastodon account for the BioHackrXiv preprint server! We will be posting new preprints via this account

#introduction

"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 […]

hi, this is the Mastodon account for the BioHackrXiv preprint server! We will be posting new preprints via this account

#introduction