id,title,description,date_created,date_modified,date_published,original_publication_date,publication_doi,provider,is_published,reviews_state,version,is_latest_version,preprint_doi,license,tags_list,tags_data,contributors_list,contributors_data,first_author,subjects_list,subjects_data,download_url,has_coi,conflict_of_interest_statement,has_data_links,has_prereg_links,prereg_links,prereg_link_info,last_updated
c8jw6_v1,"Persistence, metadata collection and re-architecture of BioHackrXiv","In this paper, we present the work executed on re-architecting BioHackrXiv during the international ELIXIR BioHackathon Europe 2023 in Barcelona, Spain. BioHackrXiv is a scholarly publication service for biohackathons and codefests that target biology and the biomedical sciences in the spirit of pre-publishing platforms.",2025-04-01T10:55:54.981234,2025-04-03T05:16:00.646444,2025-04-02T08:35:08.309125,2025-03-31T23:00:00,,biohackrxiv,1,accepted,1,1,https://doi.org/10.37044/osf.io/c8jw6_v1,CC-By Attribution 4.0 International,biohackathon; biohackrxiv; codefest; preprints,"[""biohackathon"", ""biohackrxiv"", ""codefest"", ""preprints""]",Arun Isaac; Yuhao Wang; Tazro Ohta; Leyla Jael Castro; Toshiaki Katayama; Pjotr Prins,"[{""id"": ""4jfmk"", ""name"": ""Arun Isaac"", ""index"": 0, ""orcid"": ""0000-0002-6810-8195"", ""bibliographic"": true}, {""id"": ""xvefb"", ""name"": ""Yuhao Wang"", ""index"": 1, ""orcid"": null, ""bibliographic"": true}, {""id"": ""edbh2"", ""name"": ""Tazro Ohta"", ""index"": 2, ""orcid"": ""0000-0003-3777-5945"", ""bibliographic"": true}, {""id"": ""8wu3p"", ""name"": ""Leyla Jael Castro"", ""index"": 3, ""orcid"": ""0000-0003-3986-0510"", ""bibliographic"": true}, {""id"": ""eqwyj"", ""name"": ""Toshiaki Katayama"", ""index"": 4, ""orcid"": null, ""bibliographic"": true}, {""id"": ""6uzra"", ""name"": ""Pjotr Prins"", ""index"": 5, ""orcid"": null, ""bibliographic"": true}]",Arun Isaac,Life Sciences; Bioinformatics,"[{""id"": ""66defcee6c7cdc67bcf54eb0"", ""text"": ""Life Sciences""}, {""id"": ""66defcf46c7cdc67bcf54ef3"", ""text"": ""Bioinformatics""}]",https://osf.io/download/67ebc644c955b9e749b252f8,0,,not_applicable,not_applicable,[],,2025-04-09T21:06:18.571318
5uhwz_v2,2024 OME-NGFF workflows hackathon,"The 2024 OME-NGFF Workflows Hackathon, held at the BioVisionCenter at the University of Zurich, brought together an international group of researchers and developers to develop the ecosystem around the open, scalable, and FAIR bioimage file format OME-Zarr. Over five days, participants tackled key challenges in four main areas: (1) advancing the OME-Zarr specification, (2) enabling workflow interoperability by integrating OME-Zarr image processing tasks across multiple open-source frameworks, (3) expanding Java support for Zarr v3 and enhancing the compatibility of OME-Zarr with the popular bioimage analysis software Fiji, and (4) improving the Python resources supporting OME-Zarr. The event led to the release of OME-Zarr 0.5, which formalizes the adoption of Zarr v3 and introduces a sharding strategy to reduce file system overhead. This report provides an overview of the key discussions, outcomes, and future directions emerging from the hackathon, with the goal of fostering continued community engagement in developing OME-Zarr as a robust open bioimaging standard.",2025-03-13T15:52:29.933088,2025-03-14T02:14:21.772524,2025-03-14T02:12:05.532132,,,biohackrxiv,1,accepted,2,1,https://doi.org/10.37044/osf.io/5uhwz_v2,CC-By Attribution 4.0 International,FAIR; NGFF; bioimaging; ome-zarr; workflows; zarr,"[""FAIR"", ""NGFF"", ""bioimaging"", ""ome-zarr"", ""workflows"", ""zarr""]",Joel Lüthi; Marvin Albert; Liviu Anita; Kola Babalola; Davis Bennett; John A. Bogovic; Lorenzo Cerrone; Rémy Dornier; Jan Eglinger; Vera Galinova,"[{""id"": ""6nsp3"", ""name"": ""Joel L\u00fcthi"", ""index"": 0, ""orcid"": ""0000-0003-3023-170X"", ""bibliographic"": true}, {""id"": ""9dcq2"", ""name"": ""Marvin Albert"", ""index"": 1, ""orcid"": null, ""bibliographic"": true}, {""id"": ""jgc8p"", ""name"": ""Liviu Anita"", ""index"": 2, ""orcid"": null, ""bibliographic"": true}, {""id"": ""ewrts"", ""name"": ""Kola Babalola"", ""index"": 3, ""orcid"": null, ""bibliographic"": true}, {""id"": ""s9x6d"", ""name"": ""Davis Bennett"", ""index"": 4, ""orcid"": null, ""bibliographic"": true}, {""id"": ""5sy2w"", ""name"": ""John A. Bogovic"", ""index"": 5, ""orcid"": null, ""bibliographic"": true}, {""id"": ""b4u5r"", ""name"": ""Lorenzo Cerrone"", ""index"": 6, ""orcid"": null, ""bibliographic"": true}, {""id"": ""p64na"", ""name"": ""R\u00e9my Dornier"", ""index"": 7, ""orcid"": null, ""bibliographic"": true}, {""id"": ""4weu2"", ""name"": ""Jan Eglinger"", ""index"": 8, ""orcid"": ""0000-0001-7234-1435"", ""bibliographic"": true}, {""id"": ""6hxf7"", ""name"": ""Vera Galinova"", ""index"": 9, ""orcid"": null, ""bibliographic"": true}]",Joel Lüthi,Physical Sciences and Mathematics; Life Sciences; Bioinformatics; Biology; Computer Sciences; Research Methods in Life Sciences,"[{""id"": ""66defcee6c7cdc67bcf54ead"", ""text"": ""Physical Sciences and Mathematics""}, {""id"": ""66defcee6c7cdc67bcf54eb0"", ""text"": ""Life Sciences""}, {""id"": ""66defcf46c7cdc67bcf54ef3"", ""text"": ""Bioinformatics""}, {""id"": ""66defd0b6c7cdc67bcf55002"", ""text"": ""Biology""}, {""id"": ""66defd146c7cdc67bcf5508e"", ""text"": ""Computer Sciences""}, {""id"": ""66defd266c7cdc67bcf551ba"", ""text"": ""Research Methods in Life Sciences""}]",https://osf.io/download/67d2ff4d86f2525b5800f0b1,1,"Many of the authors have been involved with the development of the OME-Zarr specification and tools in its ecosystem already before the hackathon.
Norman Rzepka and Hannes Spitz are affiliated with scalable minds, a company that builds, delivers, supports and integrates image analysis solutions. Norman Rzepka owns equity in scalable minds.
Matthew McCormick is the President of the Insight Software Consortium, a  NumFOCUS fiscally sponsored project that support the Insight Toolkit (ITK), a toolkit used in the OME-Zarr community, and currently works at Fideus Labs, which provides professional scientific software services including support for the OME-Zarr ecosystem.
Szymon Stoma and Filip Mroz are affiliated with Histopixel, a software house specializing in bioimage analysis. Szymon Stoma owns equity in Histopixel.
Maximilian Schulz works as a research software engineer at the
Institute of Human Biology (IHB) as part of Roche’s Pharma Research and Early Development (pRED).
Eric Perlman is the principal of Yikes LLC, a consultancy providing data management support to individual labs in the life science, including the use of OME-Zarr as a key component.",available,not_applicable,[],,2025-04-09T21:06:19.330460
83apv_v1,Simplifying and Standardizing the Creation of Data Use Agreements for Life Sciences and Beyond - BH Germany2024,"The primary goal of this project is to develop a web application for creating data usage agreements (DUA) in a way that allows automated evaluation of access permissions. Specifically, we want to adhere to the Open Digital Rights Language (ODRL) standard [1] and model permissions and prohibitions for the use of digital objects. ODRL is a policy expression language developed and adopted by the W3C. It provides a flexible and interoperable data model and vocabulary to enable fine-grained statements about the use of digital content and services. Recently, the Data Governance Act (DGA) was published as an implementation of the EU Data Act and defined roles for data intermediaries such as data trustees with certain prohibitions and obligations. The high expectations placed on the data trustee require that they have technical measures in place to facilitate the negotiation and enforcement of data use agreements. The “Ethical, Legal & Social Aspects” section of the NFDI (ELSA), has also issued a statement to the DGA [2], demonstrating the importance of this issue.

Usually, DUAs are negotiated individually between parties and are not stored in a machine-readable format, which prevents automated modeling and verification of access rights for digital objects. Our web application will allow to create a DUA step by step via a configurable graphical user interface using ODRL data model in the background. This enables legal laymen to create data use agreements without much effort. The use of ODRL allows to programmatically query the data use agreements and to answer access requests automatically. To this end, the resulting DUAs can be persisted and queried through an API e.g. according to the GAIA-X specifications of Eclipse Dataspace Components (EDC) [3, 4] to exchange data compliant to rules and policies. Additionally, we want to address the integration of ODRLs in FDOs, such as ARC-RO-Crate of the DataPlant consortia and discuss extensions of the RO-Crate profiles. At last, for legal review and formal signing, negotiated DUAs can be rendered as PDFs.

In summary, we will simplify the process of creating DUAs by adhering to international standards and will contribute to efforts to harmonize technical solutions, as the EOSC describes ODRL as a core metadata schema for legal interoperability [5]. DUAs can serve as a platform to gain the trust of data owners with protected, sensitive data and thus enable access to such resources. The project is in line with ELIXIR-DE/de.NBI's objective to improve the accessibility of resources and to ensure efficient, interoperable and secure resource sharing. It also aligns with the goals of the NFDI by handling sensitive data and enabling data protection. Especially when dealing with data from the health sector, but also handling agronomic data like land survey data or data from breeding programs.The project is a joint activity of the Leibniz IPK in Gatersleben (ELIXIR-DE/de.NBI Service Center GCBN), and the Justus-Liebig-University Giessen (ELIXIR-DE/de.NBI Service Center BiGi) and contributes to NFDI4Biodiversity, FAIRAgro, NFDI4Microbiota, DataPlant and FAIR-DS as well as to European initiatives such as EOSC and Gaia-X.",2025-03-10T09:06:18.052552,2025-03-11T08:45:23.300367,2025-03-11T08:33:33.750089,,,biohackrxiv,1,accepted,1,1,https://doi.org/10.37044/osf.io/83apv_v1,CC-By Attribution 4.0 International,ARC; DUA; ODRL; RO-Crate,"[""ARC"", ""DUA"", ""ODRL"", ""RO-Crate""]",Manuel Feser; Sebastian Beyvers; Daniel Arend; Constantin Breß; Maria Hansen; Christian Henke; Stephan Lesch; Carmen Scheuner; Heinrich Lukas Weil,"[{""id"": ""yg9br"", ""name"": ""Manuel Feser"", ""index"": 0, ""orcid"": ""0000-0001-6546-1818"", ""bibliographic"": true}, {""id"": ""9kcem"", ""name"": ""Sebastian Beyvers"", ""index"": 1, ""orcid"": null, ""bibliographic"": true}, {""id"": ""b89zu"", ""name"": ""Daniel Arend"", ""index"": 2, ""orcid"": ""0000-0002-2455-5938"", ""bibliographic"": true}, {""id"": ""bpfqw"", ""name"": ""Constantin Bre\u00df"", ""index"": 3, ""orcid"": null, ""bibliographic"": true}, {""id"": ""zat9c"", ""name"": ""Maria Hansen"", ""index"": 4, ""orcid"": null, ""bibliographic"": true}, {""id"": ""3sdtr"", ""name"": ""Christian Henke"", ""index"": 5, ""orcid"": null, ""bibliographic"": true}, {""id"": ""q86ur"", ""name"": ""Stephan Lesch"", ""index"": 6, ""orcid"": null, ""bibliographic"": true}, {""id"": ""v5qbf"", ""name"": ""Carmen Scheuner"", ""index"": 7, ""orcid"": null, ""bibliographic"": true}, {""id"": ""b4r82"", ""name"": ""Heinrich Lukas Weil"", ""index"": 8, ""orcid"": null, ""bibliographic"": true}]",Manuel Feser,Life Sciences; Law,"[{""id"": ""66defcee6c7cdc67bcf54eb0"", ""text"": ""Life Sciences""}, {""id"": ""66defcee6c7cdc67bcf54eb5"", ""text"": ""Law""}]",https://osf.io/download/67ceab987ba0c3c918040c8c,0,,not_applicable,not_applicable,[],,2025-04-09T21:06:23.665248
pzmue_v1,Secure Processing Environments as a Service in the de.NBI Cloud,"Sensitive human data is crucial for biomedical research, enabling faster drug development and better understanding of diseases. The Biohackathon Germany project utilized ELIXIR Europe's services and external tools to create Secure Processing Environments, ensuring high protection of sensitive data while facilitating research across Germany and Europe.",2025-03-07T14:30:30.113051,2025-03-11T09:24:01.867468,2025-03-11T09:15:42.207068,2025-03-06T23:00:00,,biohackrxiv,1,accepted,1,1,https://doi.org/10.37044/osf.io/pzmue_v1,CC-By Attribution 4.0 International,GA4GH; LS Login; Secure Processing Environment; Task Execution Service (TES); Workflow Execution Service (WES),"[""GA4GH"", ""LS Login"", ""Secure Processing Environment"", ""Task Execution Service (TES)"", ""Workflow Execution Service (WES)""]",Martin Braun; Alexander Kanitz; Jan Krüger; Landfried Kraatz; Jacobo Miranda; Carsten Schelp; Valentin Schneider-Lunitz; Sanjay Kumar Srikakulam; Xaver Stiensmeier; Nils Hoffmann,"[{""id"": ""qe34m"", ""name"": ""Martin Braun"", ""index"": 0, ""orcid"": null, ""bibliographic"": true}, {""id"": ""rzdg4"", ""name"": ""Alexander Kanitz"", ""index"": 1, ""orcid"": null, ""bibliographic"": true}, {""id"": ""hkcey"", ""name"": ""Jan Kr\u00fcger"", ""index"": 2, ""orcid"": null, ""bibliographic"": true}, {""id"": ""bmsf8"", ""name"": ""Landfried Kraatz"", ""index"": 3, ""orcid"": null, ""bibliographic"": true}, {""id"": ""fjz4b"", ""name"": ""Jacobo Miranda"", ""index"": 4, ""orcid"": null, ""bibliographic"": true}, {""id"": ""4mjfs"", ""name"": ""Carsten Schelp"", ""index"": 5, ""orcid"": null, ""bibliographic"": true}, {""id"": ""db5ag"", ""name"": ""Valentin Schneider-Lunitz"", ""index"": 6, ""orcid"": null, ""bibliographic"": true}, {""id"": ""dsc3k"", ""name"": ""Sanjay Kumar Srikakulam"", ""index"": 7, ""orcid"": null, ""bibliographic"": true}, {""id"": ""6b5yg"", ""name"": ""Xaver Stiensmeier"", ""index"": 8, ""orcid"": null, ""bibliographic"": true}, {""id"": ""3nsmv"", ""name"": ""Nils Hoffmann"", ""index"": 9, ""orcid"": ""0000-0002-6540-6875"", ""bibliographic"": true}]",Martin Braun,Life Sciences,"[{""id"": ""66defcee6c7cdc67bcf54eb0"", ""text"": ""Life Sciences""}]",https://osf.io/download/67cb032ed901de800ac9c1a6,0,,not_applicable,not_applicable,[],,2025-04-09T21:06:16.326583
hbw6m_v1,Development of FAIR image analysis workflows and training in Galaxy,"Although image analysis tools are available within the Galaxy platform, they remain underutilised. During the 2023 BioHackathon Europe, our efforts focused on enhancing the image analysis community in Galaxy by cataloguing and annotating tools and facilitating community discussions to establish naming conventions that promote standardisation. These initial efforts, detailed in the project outcomes, laid the foundation for the ongoing expansion of Galaxy’s image analysis capabilities.
Building on these achievements, this year’s work aimed to exploit and demonstrate the
Galaxy platform’s full potential to address the needs of the image analysis community.
This project involved developing FAIR (Findable, Accessible, Interoperable, and Reusable)
image analysis workflows, creating tutorials for the Galaxy Training Network (GTN) to provide
documentation, and fostering broader adoption and facilitating the
application of these workflows across scientific domains.",2025-03-07T14:29:53.326364,2025-03-13T01:18:01.029441,2025-03-13T01:09:40.720488,,,biohackrxiv,1,accepted,1,1,https://doi.org/10.37044/osf.io/hbw6m_v1,CC0 1.0 Universal,FAIR; Galaxy; image analysis; useGalaxy; workflows,"[""FAIR"", ""Galaxy"", ""image analysis"", ""useGalaxy"", ""workflows""]",Leonid Kostrykin; Boris Depoortere; Diana Chiang; Sven Klumpe; Riccardo Massei; Matúš Kalaš; Anne Fouilloux; Beatriz Serrano-Solano,"[{""id"": ""xzvhn"", ""name"": ""Leonid Kostrykin"", ""index"": 0, ""orcid"": null, ""bibliographic"": true}, {""id"": ""pj4qk"", ""name"": ""Boris Depoortere"", ""index"": 1, ""orcid"": null, ""bibliographic"": true}, {""id"": ""sm95k"", ""name"": ""Diana Chiang"", ""index"": 2, ""orcid"": null, ""bibliographic"": true}, {""id"": ""gm8hy"", ""name"": ""Sven Klumpe"", ""index"": 3, ""orcid"": ""0000-0002-8350-6503"", ""bibliographic"": true}, {""id"": ""7ncwp"", ""name"": ""Riccardo Massei"", ""index"": 4, ""orcid"": null, ""bibliographic"": true}, {""id"": ""jdwbh"", ""name"": ""Mat\u00fa\u0161 Kala\u0161"", ""index"": 5, ""orcid"": ""0000-0002-1509-4981"", ""bibliographic"": true}, {""id"": ""sjwy3"", ""name"": ""Anne Fouilloux"", ""index"": 6, ""orcid"": null, ""bibliographic"": true}, {""id"": ""6mpqb"", ""name"": ""Beatriz Serrano-Solano"", ""index"": 7, ""orcid"": ""0000-0002-5862-6132"", ""bibliographic"": true}]",Leonid Kostrykin,Physical Sciences and Mathematics; Life Sciences; Environmental Sciences; Earth Sciences,"[{""id"": ""66defcee6c7cdc67bcf54ead"", ""text"": ""Physical Sciences and Mathematics""}, {""id"": ""66defcee6c7cdc67bcf54eb0"", ""text"": ""Life Sciences""}, {""id"": ""66defd0a6c7cdc67bcf54ffb"", ""text"": ""Environmental Sciences""}, {""id"": ""66defd146c7cdc67bcf5508d"", ""text"": ""Earth Sciences""}]",https://osf.io/download/67cb02f7b11192ea7ffd8d34,0,,not_applicable,not_applicable,[],,2025-04-09T21:06:24.009360
p9u42_v1,BioHackEU24 report: ORCID and ROR identifiers in BioHackrXiv reports,"The first BioHackrXiv preprint was published in 2020, using a platform based on the idea of using Markdown, and just weeks ago, BioHackrXiv published their 100th preprint. Machine-readable etadata added to the Markdown that is added includes the title, keywords, the author names, their affiliations, and details about the Biohackathon event the preprint is related to. The metadata in 2000 already supported listing the ORCID identifier of the authors, but this was not added to the author list in the generated PDF. This report describes two improvements of the platform: visualization of the ORCID identifiers in the preprint PDF and support for Research Organization Registry (ROR) identifiers of the affiliations.",2025-03-06T05:35:02.847151,2025-03-11T08:17:22.420386,2025-03-11T08:14:27.373296,2025-03-05T23:00:00,,biohackrxiv,1,accepted,1,1,https://doi.org/10.37044/osf.io/p9u42_v1,CC-By Attribution 4.0 International,BioHackrXiv,"[""BioHackrXiv""]",Egon Willighagen; Tazro Ohta,"[{""id"": ""8s72v"", ""name"": ""Egon Willighagen"", ""index"": 0, ""orcid"": ""0000-0001-7542-0286"", ""bibliographic"": true}, {""id"": ""edbh2"", ""name"": ""Tazro Ohta"", ""index"": 1, ""orcid"": ""0000-0003-3777-5945"", ""bibliographic"": true}]",Egon Willighagen,Life Sciences,"[{""id"": ""66defcee6c7cdc67bcf54eb0"", ""text"": ""Life Sciences""}]",https://osf.io/download/67c936280d2fea4da5fd6e72,0,,not_applicable,not_applicable,[],,2025-04-09T21:06:14.464625
m7xr6_v1,Report: Workshop on connecting Knowledge Graphs with BioChatter,"The workshop on connecting Knowledge Graphs (KGs) with BioChatter convened experts from biology, computer science, and bioinformatics to tackle challenges in integrating and accessing dispersed datasets in plant sciences. The goal was to create user-friendly interfaces for querying these datasets using natural language, bypassing the need for expertise in semantic technologies or query languages like SPARQL or Cypher.

Key use cases included the BrAPI project, which aimed to simplify data retrieval from plant research datasets. While BioChatter effectively generated simple API queries, complex multi-step queries posed challenges, suggesting that programmatic approaches are better suited for such tasks. Integrating BrAPI with BioCypher enabled successful querying of KGs for questions like identifying studies involving specific plant varieties.

The RDF adapter use case focused on enhancing the Plant Phenotyping Experiment Ontology (PPEO) by converting it into a BioCypher-compatible KG, thereby improving data interoperability and enabling LLMs to generate context-aware responses. The Mobile Element Knowledge Graph use case explored the relationship between transposable elements and gene regulation networks, utilizing BioChatter to assist users unfamiliar with Cypher.

The Stress Knowledge Map (SKM) use case integrated a highly curated model of plant stress signaling with BioCypher and BioChatter, allowing natural language queries and improving access to complex biological data. The Chem and Plant KG use case aimed to integrate diverse scientific resources into a unified KG, enhancing data interoperability and accessibility.

Challenges included the need for human-readable concepts within KGs to improve LLM interaction and aligning LLMs with user demands. Future work will focus on refining KG schemas, improving LLM integration, and expanding documentation to support broader adoption and utility in scientific research. The workshop highlighted the potential of combining KGs with LLMs to enhance data accessibility and drive new insights in biological and agricultural sciences.",2025-03-05T10:34:49.010611,2025-03-11T09:14:21.616170,2025-03-11T09:09:15.313349,,,biohackrxiv,1,accepted,1,1,https://doi.org/10.37044/osf.io/m7xr6_v1,CC-By Attribution 4.0 International,,[],Cyril Pommier; Sebastian Beier; Pedro Miguel Barros; Johann Confais; Nicolas Francillonne; Hugo Miguel Costa Rodrigues; Hiromi Kajiya-Kanegae; Ryokei Tanaka; Bruno Eduardo  Costa; Raphaël Flores,"[{""id"": ""8qy46"", ""name"": ""Cyril Pommier"", ""index"": 0, ""orcid"": ""0000-0002-9040-8733"", ""bibliographic"": true}, {""id"": ""habky"", ""name"": ""Sebastian Beier"", ""index"": 1, ""orcid"": ""0000-0002-2177-8781"", ""bibliographic"": true}, {""id"": ""bgvh9"", ""name"": ""Pedro Miguel Barros"", ""index"": 2, ""orcid"": null, ""bibliographic"": true}, {""id"": ""hazrf"", ""name"": ""Johann Confais"", ""index"": 3, ""orcid"": ""0000-0003-2945-5036"", ""bibliographic"": true}, {""id"": ""jeyfp"", ""name"": ""Nicolas Francillonne"", ""index"": 4, ""orcid"": null, ""bibliographic"": true}, {""id"": ""cyqbe"", ""name"": ""Hugo Miguel Costa Rodrigues"", ""index"": 5, ""orcid"": null, ""bibliographic"": true}, {""id"": ""wxrtc"", ""name"": ""Hiromi Kajiya-Kanegae"", ""index"": 6, ""orcid"": ""0000-0002-5719-7559"", ""bibliographic"": true}, {""id"": ""b42wn"", ""name"": ""Ryokei Tanaka"", ""index"": 7, ""orcid"": null, ""bibliographic"": true}, {""id"": ""6gs7h"", ""name"": ""Bruno Eduardo  Costa"", ""index"": 8, ""orcid"": null, ""bibliographic"": true}, {""id"": ""uwmtv"", ""name"": ""Rapha\u00ebl Flores"", ""index"": 9, ""orcid"": null, ""bibliographic"": true}]",Cyril Pommier,Physical Sciences and Mathematics; Life Sciences; Plant Sciences; Computer Sciences; Artificial Intelligence and Robotics; Databases and Information Systems,"[{""id"": ""66defcee6c7cdc67bcf54ead"", ""text"": ""Physical Sciences and Mathematics""}, {""id"": ""66defcee6c7cdc67bcf54eb0"", ""text"": ""Life Sciences""}, {""id"": ""66defcef6c7cdc67bcf54ec4"", ""text"": ""Plant Sciences""}, {""id"": ""66defd146c7cdc67bcf5508e"", ""text"": ""Computer Sciences""}, {""id"": ""66defd206c7cdc67bcf5515a"", ""text"": ""Artificial Intelligence and Robotics""}, {""id"": ""66defd236c7cdc67bcf55182"", ""text"": ""Databases and Information Systems""}]",https://osf.io/download/67c828d3600ab9e7d6bb380c,0,,not_applicable,not_applicable,[],,2025-04-09T21:06:23.134979
5uhwz_v1,2024 OME-NGFF workflows hackathon,"The 2024 OME-NGFF Workflows Hackathon, held at the BioVisionCenter at the University of Zurich, brought together an international group of researchers and developers to develop the ecosystem around the open, scalable, and FAIR bioimage file format OME-Zarr. Over five days, participants tackled key challenges in four main areas: (1) advancing the OME-Zarr specification, (2) enabling workflow interoperability by integrating OME-Zarr image processing tasks across multiple open-source frameworks, (3) expanding Java support for Zarr v3 and enhancing the compatibility of OME-Zarr with the popular bioimage analysis software Fiji, and (4) improving the Python resources supporting OME-Zarr. The event led to the release of OME-Zarr 0.5, which formalizes the adoption of Zarr v3 and introduces a sharding strategy to reduce file system overhead. This report provides an overview of the key discussions, outcomes, and future directions emerging from the hackathon, with the goal of fostering continued community engagement in developing OME-Zarr as a robust open bioimaging standard.",2025-03-03T15:12:37.567239,2025-03-11T08:20:21.293972,2025-03-11T08:15:33.009850,,,biohackrxiv,1,accepted,1,0,https://doi.org/10.37044/osf.io/5uhwz_v1,CC-By Attribution 4.0 International,FAIR; NGFF; bioimaging; ome-zarr; workflows; zarr,"[""FAIR"", ""NGFF"", ""bioimaging"", ""ome-zarr"", ""workflows"", ""zarr""]",Joel Lüthi; Marvin Albert; Liviu Anita; Kola Babalola; Davis Bennett; John A. Bogovic; Lorenzo Cerrone; Rémy Dornier; Jan Eglinger; Vera Galinova,"[{""id"": ""6nsp3"", ""name"": ""Joel L\u00fcthi"", ""index"": 0, ""orcid"": ""0000-0003-3023-170X"", ""bibliographic"": true}, {""id"": ""9dcq2"", ""name"": ""Marvin Albert"", ""index"": 1, ""orcid"": null, ""bibliographic"": true}, {""id"": ""jgc8p"", ""name"": ""Liviu Anita"", ""index"": 2, ""orcid"": null, ""bibliographic"": true}, {""id"": ""ewrts"", ""name"": ""Kola Babalola"", ""index"": 3, ""orcid"": null, ""bibliographic"": true}, {""id"": ""s9x6d"", ""name"": ""Davis Bennett"", ""index"": 4, ""orcid"": null, ""bibliographic"": true}, {""id"": ""5sy2w"", ""name"": ""John A. Bogovic"", ""index"": 5, ""orcid"": null, ""bibliographic"": true}, {""id"": ""b4u5r"", ""name"": ""Lorenzo Cerrone"", ""index"": 6, ""orcid"": null, ""bibliographic"": true}, {""id"": ""p64na"", ""name"": ""R\u00e9my Dornier"", ""index"": 7, ""orcid"": null, ""bibliographic"": true}, {""id"": ""4weu2"", ""name"": ""Jan Eglinger"", ""index"": 8, ""orcid"": ""0000-0001-7234-1435"", ""bibliographic"": true}, {""id"": ""6hxf7"", ""name"": ""Vera Galinova"", ""index"": 9, ""orcid"": null, ""bibliographic"": true}]",Joel Lüthi,Physical Sciences and Mathematics; Life Sciences; Bioinformatics; Biology; Computer Sciences; Research Methods in Life Sciences,"[{""id"": ""66defcee6c7cdc67bcf54ead"", ""text"": ""Physical Sciences and Mathematics""}, {""id"": ""66defcee6c7cdc67bcf54eb0"", ""text"": ""Life Sciences""}, {""id"": ""66defcf46c7cdc67bcf54ef3"", ""text"": ""Bioinformatics""}, {""id"": ""66defd0b6c7cdc67bcf55002"", ""text"": ""Biology""}, {""id"": ""66defd146c7cdc67bcf5508e"", ""text"": ""Computer Sciences""}, {""id"": ""66defd266c7cdc67bcf551ba"", ""text"": ""Research Methods in Life Sciences""}]",https://osf.io/download/67c5c700fdb0164475f455bb,1,"Many of the authors have been involved with the development of the OME-Zarr specification and tools in its ecosystem already before the hackathon.
Norman Rzepka and Hannes Spitz are affiliated with scalable minds, a company that builds, delivers, supports and integrates image analysis solutions. Norman Rzepka owns equity in scalable minds.
Matthew McCormick is the President of the Insight Software Consortium, a  NumFOCUS fiscally sponsored project that support the Insight Toolkit (ITK), a toolkit used in the OME-Zarr community, and currently works at Fideus Labs, which provides professional scientific software services including support for the OME-Zarr ecosystem.
Szymon Stoma and Filip Mroz are affiliated with Histopixel, a software house specializing in bioimage analysis. Szymon Stoma owns equity in Histopixel.
Maximilian Schulz works as a research software engineer at the
Institute of Human Biology (IHB) as part of Roche’s Pharma Research and Early Development (pRED).
Eric Perlman is the principal of Yikes LLC, a consultancy providing data management support to individual labs in the life science, including the use of OME-Zarr as a key component.",available,not_applicable,[],,2025-04-09T21:06:21.719849
gzyxq_v1,BioHackGermany24 report: User-friendly ISA-based metadata annotation of life science experiments with ISA Wizard,"As a contribution to BioHackathon Germany 2024, the following report details the work conducted during that event for project 8: User-friendly ISA-based metadata annotation of life science experiments with ISA Wizard.",2025-02-07T15:32:21.488764,2025-02-07T16:09:22.852835,2025-02-07T16:07:19.165626,,,biohackrxiv,1,accepted,1,1,https://doi.org/10.37044/osf.io/gzyxq_v1,CC-By Attribution 4.0 International,ENA; FAIR; ISA; MIAPPE; Research Data Management; svelte,"[""ENA"", ""FAIR"", ""ISA"", ""MIAPPE"", ""Research Data Management"", ""svelte""]",Sebastian Beier; Patrick König,"[{""id"": ""habky"", ""name"": ""Sebastian Beier"", ""index"": 0, ""orcid"": ""0000-0002-2177-8781"", ""bibliographic"": true}, {""id"": ""2huzp"", ""name"": ""Patrick K\u00f6nig"", ""index"": 1, ""orcid"": ""0000-0002-8948-6793"", ""bibliographic"": true}]",Sebastian Beier,Life Sciences,"[{""id"": ""66defcee6c7cdc67bcf54eb0"", ""text"": ""Life Sciences""}]",https://osf.io/download/67a6279598502bfea0b38d71,0,,not_applicable,not_applicable,[],,2025-04-09T21:06:21.359918
5ue2s_v1,BioHackJP24 report: Running a WikiBlitz,"During BioHackathon 24 in Fukushima, we organized a WikiBlitz, a collaborative effort to integrate biodiversity observations from iNaturalist into the Wikimedia ecosystem. A WikiBlitz is inspired by the concept of a BioBlitz, where participants document as many species as possible within a limited time frame, while also contributing structured data to Wikidata, Wikimedia Commons, and Wikipedia. In this report, we describe the methodology and outcomes of this event, including the collection of 109 biodiversity observations and their subsequent verification and integration into Wikimedia platforms. We highlight the challenges and best practices for running a WikiBlitz, particularly around licensing and data quality, and demonstrate how tools such as iNaturalist2Commons and Wikidata queries can enhance the reuse of citizen science data. Finally, we provide a step-by-step tutorial to support future WikiBlitz events, ensuring broader participation and sustainable knowledge-sharing across platforms.",2025-02-05T16:42:08.649628,2025-02-07T03:42:08.007110,2025-02-07T03:41:08.466576,,,biohackrxiv,1,accepted,1,1,https://doi.org/10.37044/osf.io/5ue2s_v1,CC-By Attribution 4.0 International,bioblitz; crowdsourcing; inaturalist; wikidata; wikipedia,"[""bioblitz"", ""crowdsourcing"", ""inaturalist"", ""wikidata"", ""wikipedia""]",Andra Waagmeester; Yasunori Yamamoto; Shuya Ikeda; Núria Queralt Rosinach; Erick Antezana; Julia Koblitz,"[{""id"": ""4gq5j"", ""name"": ""Andra Waagmeester"", ""index"": 0, ""orcid"": ""0000-0001-9773-4008"", ""bibliographic"": true}, {""id"": ""a5w98"", ""name"": ""Yasunori Yamamoto"", ""index"": 1, ""orcid"": ""0000-0002-6943-6887"", ""bibliographic"": true}, {""id"": ""6w5kp"", ""name"": ""Shuya Ikeda"", ""index"": 2, ""orcid"": null, ""bibliographic"": true}, {""id"": ""awyjz"", ""name"": ""N\u00faria Queralt Rosinach"", ""index"": 3, ""orcid"": ""0000-0003-0169-8159"", ""bibliographic"": true}, {""id"": ""ac37u"", ""name"": ""Erick Antezana"", ""index"": 4, ""orcid"": ""0000-0002-2497-8236"", ""bibliographic"": true}, {""id"": ""sm6t9"", ""name"": ""Julia Koblitz"", ""index"": 5, ""orcid"": ""0000-0002-7260-2129"", ""bibliographic"": true}]",Andra Waagmeester,Life Sciences; Biology; Biodiversity; Research Methods in Life Sciences,"[{""id"": ""66defcee6c7cdc67bcf54eb0"", ""text"": ""Life Sciences""}, {""id"": ""66defd0b6c7cdc67bcf55002"", ""text"": ""Biology""}, {""id"": ""66defd186c7cdc67bcf550c5"", ""text"": ""Biodiversity""}, {""id"": ""66defd266c7cdc67bcf551ba"", ""text"": ""Research Methods in Life Sciences""}]",https://osf.io/download/67a3974a67017f92b30c5772,0,,available,not_applicable,[],,2025-04-09T21:06:19.344020