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
🌉 bridged from ⁂ https://fediscience.org/@biohackrxiv, follow @ap.brid.gy to interact
"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 […]
"This paper presents the current status of trait data standardizationbetween the two organizations and outlines a direction for standardization. Trait data […]
Original post on fediscience.org
fediscience.org
December 24, 2025 at 9:33 AM
"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 […]
"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 […]
"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 […]
Original post on fediscience.org
fediscience.org
December 19, 2025 at 3:18 PM
"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 […]
"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 […]
"ere, we introduce a new methodology for genotype-phenotype mapping based ongenomic hashes, unique representations of local genomic background. Each hash correspondsto a […]
Original post on fediscience.org
fediscience.org
December 18, 2025 at 6:26 PM
"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 […]
"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 […]
"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 […]
Original post on fediscience.org
fediscience.org
December 18, 2025 at 6:32 AM
"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 […]
"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 […]
"For the metadata, validation will ensure structural and semantic compliance to the base RO-Crate specification and the ARC family of RO-Crate profiles […]
Original post on fediscience.org
fediscience.org
December 18, 2025 at 4:48 AM
"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 […]
"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 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 […]
Original post on fediscience.org
fediscience.org
November 29, 2025 at 8:40 AM
"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 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 […]
"these projects and pipelines showcase methods for constructing KGs from existing biomedical datasets andexemplify the practical […]
Original post on fediscience.org
fediscience.org
November 29, 2025 at 8:39 AM
"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 […]
"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 […]
"Scop3PTM Next was developed during BioHackathon Europe 2025 to address the need for integrated visualization of protein-centric data […]
Original post on fediscience.org
fediscience.org
November 26, 2025 at 5:57 PM
"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 […]
"Scop3PTM Next was developed during BioHackathon Europe 2025 to address the need for integrated visualization of protein-centric data […]
Call for Biohackathon topics: "SWAT4HCLS Biohackathon 2026, Amsterdan, The Netherlands" https://www.swat4ls.org/swat4hcls-biohackathon-2026/
#biohackathon #swat4hcls26 #SWAT4HCLS
#biohackathon #swat4hcls26 #SWAT4HCLS
SWAT4HCLS Biohackathon 2026
www.swat4ls.org
November 20, 2025 at 12:59 PM
Call for Biohackathon topics: "SWAT4HCLS Biohackathon 2026, Amsterdan, The Netherlands" https://www.swat4ls.org/swat4hcls-biohackathon-2026/
#biohackathon #swat4hcls26 #SWAT4HCLS
#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 […]
"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 […]
Original post on fediscience.org
fediscience.org
November 7, 2025 at 4:06 AM
"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 […]
"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 […]
"Ontologies provide structured vocabularies and relationships essential for organizing biological knowledge, yet their symbolic nature limits integration with modern […]
Original post on fediscience.org
fediscience.org
November 6, 2025 at 5:38 PM
"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 […]
"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 […]
"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 […]
Original post on fediscience.org
fediscience.org
November 6, 2025 at 5:45 AM
"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 […]
"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 […]
"We present the first comprehensive semantic formalization of MIRAGE guidelines through an integrated RDF […]
Original post on fediscience.org
fediscience.org
November 5, 2025 at 4:23 PM
"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 […]
"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 […]
"At the DBCLS BioHackathon 2025, we converted metatranscriptomic analytical shell scripts into Common Workflow Language (CWL) containerized with Docker […]
Original post on fediscience.org
fediscience.org
November 4, 2025 at 9:58 PM
"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 […]
"At the DBCLS BioHackathon 2025, we converted metatranscriptomic analytical shell scripts into Common Workflow Language (CWL) containerized with Docker […]
our preview website has been revamped: https://preview.biohackrxiv.org/
#biohackrxiv #preprint #biohackathon
#biohackrxiv #preprint #biohackathon
November 4, 2025 at 2:39 PM
our preview website has been revamped: https://preview.biohackrxiv.org/
#biohackrxiv #preprint #biohackathon
#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 […]
"SRAKE achieves a 20-fold improvement in ingestion speed, maintains constant memory usage through zero-copy streaming, and provides standards-compliant interfaces following […]
Original post on fediscience.org
fediscience.org
November 4, 2025 at 2:19 PM
"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 […]
"SRAKE achieves a 20-fold improvement in ingestion speed, maintains constant memory usage through zero-copy streaming, and provides standards-compliant interfaces following […]
Reposted by BioHackrXiv
hi, this is the Mastodon account for the BioHackrXiv preprint server! We will be posting new preprints via this account
#introduction
#introduction
November 3, 2025 at 4:56 PM
hi, this is the Mastodon account for the BioHackrXiv preprint server! We will be posting new preprints via this account
#introduction
#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 […]
"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 […]
Original post on fediscience.org
fediscience.org
November 4, 2025 at 5:11 AM
"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 […]
"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
#introduction
November 3, 2025 at 4:56 PM
hi, this is the Mastodon account for the BioHackrXiv preprint server! We will be posting new preprints via this account
#introduction
#introduction