BioHackrXiv

@biohackrxiv.fediscience.org.ap.brid.gy

BioHackrXiv is a preprint server powered by OSF. It was created with the aim of reporting on the work done during BioHackathons, CodeFests, Sprints or similar […]

🌉 bridged from ⁂ https://fediscience.org/@biohackrxiv, follow @ap.brid.gy to interact

@biohackrxiv.fediscience.org.ap.brid.gy Oct 10, 2026, 7:21 AM

"DBCLS BioHackathon 2026 report: An interactive, harmonised BioSample metadata resource for biological sample discovery" https://doi.org/10.37044/osf.io/hm9fn_v1

#biohackathon #BH26JP #BioSamples #bioinformatics

"The BioSample database contains tens of […]

[Original post on fediscience.org]

Figure 2: Screenshots of the sample search and visualization system. (A) Results of selecting liver asthe tissue and searching for liver samples from human RNA-seq experiments. (B) Heatmap showing the number of human RNA-seq samples to which the selected ontology terms were mapped, with 10 disease terms and 10 drug terms specified. (C) Distribution of the experimental conditions investigated under Kras knockout in mouse RNA-seq samples, with Kras specified as the knockout gene. (D) Line graph showing the annual number of submissions of human lung RNA-seq samples.

@biohackrxiv.fediscience.org.ap.brid.gy Sep 29, 2026, 3:29 PM

first 2027 #biohackathon listed is #SnakemakeHackathon2027 https://index.biohackrxiv.org/tag/SnakemakeHackathon2027

@biohackrxiv.fediscience.org.ap.brid.gy Sep 26, 2026, 8:57 AM

"DBCLS BioHackathon 2026 report: RDF publication of Marchantia polymorpha gene annotations, and agent-assisted preparation of DDBJ submissions" https://doi.org/10.37044/osf.io/xev4p_v1

#BH26JP #biohackathon #rdf

"First, gene annotations of the liverwort […]

[Original post on fediscience.org]

Figure 2: The bisbibenzyl route under salt stress. (a) Pathway schematic with enzyme steps coloured by the strongest induction among the expressed paralogs of that step. (b) log2 fold change of individual genes over a 100 mM NaCl time course, grouped by step.

@biohackrxiv.fediscience.org.ap.brid.gy Sep 22, 2026, 10:02 AM

"BioHackrXiv: Creating a federated publishing platform" https://doi.org/10.37044/osf.io/jh3m7_v1

"Overall goals are to have improved metadata and allow independence from OSF - though we
can operate in parallel. Ideally BioHackrXiv would be a template for a federated solution for
scientific […]

@biohackrxiv.fediscience.org.ap.brid.gy Sep 20, 2026, 2:10 PM

"DBCLS BioHackathon 2026 report: Extending TogoMCP beyond RDF Portal while making its schema guides check their own answers" https://doi.org/10.37044/osf.io/t25ng_v1

#biohackathon #mcp #rdf #BH26JP #qlever

"In the first six days of the event we published eleven releases (v2.12.2 to v2.20.0) […]

@biohackrxiv.fediscience.org.ap.brid.gy Sep 20, 2026, 2:07 PM

"DBCLS BioHackathon 2026 report: Open, Reproducible Extraction of Data-Entity References from the Biomedical Literature – with Entry-Level Resolution via Identifiers.org / TogoID" https://doi.org/10.37044/osf.io/p87z6_v1

#biohackathon #identifier #BH26JP […]

[Original post on fediscience.org]

Figure 3:Data Reuse Dashboard: database usage drill-down

@biohackrxiv.fediscience.org.ap.brid.gy Sep 20, 2026, 2:05 PM

"Logica, an intelligent platform for semantic interoperability" https://doi.org/10.37044/osf.io/92bc5_v2

#biohackathon #semantics #hl7fhir #BH26JP

"Logica is an interoperability platform that separates clinical meaning from physical data representation and separates language-model […]

@biohackrxiv.fediscience.org.ap.brid.gy Sep 19, 2026, 7:03 AM

"DBCLS BioHackathon 2026 report: QPX: Pathway analysis environment for non-model organisms" https://doi.org/10.37044/osf.io/7egfm_v1

#biohackathon #pathway #bioinformatics #BH26JP #rice #arabidopsis

"We report progress on Quest for Pathways with eXpression […]

[Original post on fediscience.org]

Part of Figure 1: Arabidopsis-to-rice pathway liftover: whole pathway and N-module detail.

The selection shows the "PathLift" arrow between the original Arabidopsis pathway and the new, pathlifted Oryza sativa pathway. They highlighted a complex with a purple line, which is detailed in the bottom part of the original figure.

@biohackrxiv.fediscience.org.ap.brid.gy Sep 18, 2026, 5:29 PM

"DBCLS BioHackathon 2026 report: Variant representation in RDF for precision medicine" https://doi.org/10.37044/osf.io/su8kx_v1

#biohackathon #BH26JP #rdf #precisionMedicine

"For the life science semantic web community, the provision of genomic variants ready for tools and applications is […]

@biohackrxiv.fediscience.org.ap.brid.gy Sep 18, 2026, 5:23 PM

"Building InterMine databases from RDF Portal" https://doi.org/10.37044/osf.io/dqm3j_v1

#biohackathon #rdf #intermine #BH26JP

"The public HumanMine has not had a data release since February 2022. RDF Portal, operated by the Database Division for Life […]

[Original post on fediscience.org]

Figure 1:How a mine gets its data. (a) Today each HumanMine source has its own loader, written and maintained as code by the mine’s developers. (b) With RDF Portal and rdfc2im, the work for each dataset moves upstream: RDF Portal holds each dataset’s RDF and an rdf-config model written in rdf-config’s common form, made once and reused by every consumer. rdfc2im is one tool for all sources, and what remains for each source is a curated mapping, kept as data with the evidence for every row. Tags show scope (per source, per dataset, shared, reused), effort (manual, automatic) and form (code, template, data).

@biohackrxiv.fediscience.org.ap.brid.gy Sep 18, 2026, 5:18 PM

"OSIRIS-MCP: Towards secure conversational access to research information in OSIRIS" https://doi.org/10.37044/osf.io/36g4c_v3

#biohackathon #osiris #mcp #BH26JP

"We developed a prototype Model Context Protocol (MCP) connector for OSIRIS, an open-source […]

[Original post on fediscience.org]

Figure 1:Architecture and trust boundaries of OSIRIS MCP. The language-model client communicatesonly with the read-only connector. OSIRIS retains responsibility for permissions, query construction,and access to the authoritative database.

@biohackrxiv.fediscience.org.ap.brid.gy Sep 4, 2026, 3:38 PM

Upcoming biohackathons:

- DBCLS BioHackathon, Matsuyama, Japan, 2026: https://index.biohackrxiv.org/tag/BH26JP
- BioHackathon Germany 2026, Göttingen, Germany, 2026: https://index.biohackrxiv.org/tag/BHG26
- BioHackathon Europe 2026, Barcelona, Spain, 2026 […]

@biohackrxiv.fediscience.org.ap.brid.gy Sep 4, 2026, 3:34 PM

"AI-Assisted Variant Review Across Asia: Country-Level Expert Panels, Regional Collaboration, and Global Knowledge Sharing" https://doi.org/10.37044/osf.io/e5g6s_v1

#biohackathon #ai #MHA26 #rareDisease

'We argue that the most useful near-term role of […]

[Original post on fediscience.org]

@biohackrxiv.fediscience.org.ap.brid.gy Aug 29, 2026, 12:08 PM

"Enhancing e!DAL-PGP: A Modern Data Submission Platform for Plant Science Research Data" https://doi.org/10.37044/osf.io/9mj78_v1

#biohackathon #BH25DE #fairData #plants

"The @deNBI Service e!DAL-PGP (Arend et al., 2016, p. Arend2020) serves as a critical […]

[Original post on fediscience.org]