{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,12,24]],"date-time":"2025-12-24T02:47:09Z","timestamp":1766544429997,"version":"3.41.2"},"reference-count":12,"publisher":"Oxford University Press (OUP)","issue":"3","license":[{"start":{"date-parts":[[2025,3,11]],"date-time":"2025-03-11T00:00:00Z","timestamp":1741651200000},"content-version":"vor","delay-in-days":10,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,3,4]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>The BioArchLinux project was initiated to address challenges in bioinformatics software reproducibility and freshness. Relying on Arch Linux's user-driven ecosystem, we aim to create a comprehensive and continuously updated repository for life sciences research.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>BioArchLinux provides a PKGBUILD-based system for seamless software packaging and maintenance, enabling users to access the latest bioinformatics tools across multiple programming languages. The repository includes Docker images, Windows Subsystem for Linux (WSL) support, and Junest for nonroot environments, enhancing accessibility across platforms. Although being developed and maintained by a small core team, BioArchLinux is a fast-growing bioinformatics repository that offers a participatory and community-driven environment.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>The repository, documentation, and tools are freely available at https:\/\/bioarchlinux.org and https:\/\/github.com\/BioArchLinux. Users and developers are encouraged to contribute and expand this open-source initiative.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btaf106","type":"journal-article","created":{"date-parts":[[2025,3,11]],"date-time":"2025-03-11T13:44:56Z","timestamp":1741700696000},"source":"Crossref","is-referenced-by-count":4,"title":["BioArchLinux: community-driven fresh reproducible software repository for life sciences"],"prefix":"10.1093","volume":"41","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-3426-9273","authenticated-orcid":false,"given":"Guoyi","family":"Zhang","sequence":"first","affiliation":[{"name":"Evolution & Ecology Research Centre, School of Biological, Earth, Environmental Sciences, UNSW Sydney , Sydney, NSW 2052,","place":["Australia"]},{"name":"Australian Museum Research Institute, Australian Museum , 1 William St , Sydney, NSW 2010,","place":["Australia"]}]},{"given":"Pekka","family":"Ristola","sequence":"additional","affiliation":[{"name":"BioArchLinux Member , Helsinki, 00100,","place":["Finland"]}]},{"given":"Han","family":"Su","sequence":"additional","affiliation":[{"name":"BioArchLinux Member , Beijing, 100000,","place":["China"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9157-061X","authenticated-orcid":false,"given":"Bipin","family":"Kumar","sequence":"additional","affiliation":[{"name":"Obront Biotech Pvt. Ltd. , Hyderabad, 500007,","place":["India"]}]},{"given":"Boyu","family":"Zhang","sequence":"additional","affiliation":[{"name":"Beijing Forestry University , Beijing, 100083,","place":["China"]}]},{"given":"Yujin","family":"Hu","sequence":"additional","affiliation":[{"name":"Shenzhen Research Institute of Big Data , Shenzhen, 518172,","place":["China"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3374-2409","authenticated-orcid":false,"given":"Michael G","family":"Elliot","sequence":"additional","affiliation":[{"name":"Department of Evolution, University of Groningen , Groningen, 9700 AB,","place":["The Netherlands"]}]},{"given":"Viktor","family":"Drobot","sequence":"additional","affiliation":[{"name":"Pharm InnTech LLC , Moscow, 127299, Russia"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5789-6296","authenticated-orcid":false,"given":"Jie","family":"Zhu","sequence":"additional","affiliation":[{"name":"Microbiota I-Center (MagIC) , Hong Kong SAR 999077,","place":["China"]},{"name":"Li Ka Shing Institute of Health Sciences, Faculty of Medicine, The Chinese University of Hong Kong , Hong Kong SAR 999077,","place":["China"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2664-3357","authenticated-orcid":false,"given":"Jens","family":"Staal","sequence":"additional","affiliation":[{"name":"Department of Biomedical Molecular Biology, Ghent University , 9000,","place":["Belgium"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3947-4444","authenticated-orcid":false,"given":"Martin","family":"Larralde","sequence":"additional","affiliation":[{"name":"Leiden University Center for Infectious Diseases, Leiden University Medical Center (LUMC) , Leiden, 2300 RA,","place":["The Netherlands"]},{"name":"Structural and Computational Biology Unit, EMBL , Heidelberg, 69117,","place":["Germany"]}]},{"given":"Shun","family":"Wang","sequence":"additional","affiliation":[{"name":"JASP Team Member , Shenzhen, 518000,","place":["China"]}]},{"given":"Yun","family":"Yi","sequence":"additional","affiliation":[{"name":"BioArchLinux Member , Beijing, 100000,","place":["China"]}]},{"given":"Haoran","family":"Yu","sequence":"additional","affiliation":[{"name":"Xi\u2019an University , Xi\u2019an, 710065,","place":["China"]}]}],"member":"286","published-online":{"date-parts":[[2025,3,11]]},"reference":[{"key":"2025032023575500300_btaf106-B1","doi-asserted-by":"publisher","first-page":"452","DOI":"10.1038\/533452a","article-title":"1,500 scientists lift the lid on reproducibility","volume":"533","author":"Baker","year":"2016","journal-title":"Nature"},{"key":"2025032023575500300_btaf106-B2","doi-asserted-by":"publisher","first-page":"213","DOI":"10.1186\/s13059-024-03343-2","article-title":"Genomic reproducibility in the bioinformatics era","volume":"25","author":"Baykal","year":"2024","journal-title":"Genome Biol"},{"key":"2025032023575500300_btaf106-B5","doi-asserted-by":"publisher","first-page":"475","DOI":"10.1038\/s41592-018-0046-7","article-title":"Bioconda: sustainable and comprehensive software distribution for the life sciences","volume":"15","author":"Gr\u00fcning","year":"2018","journal-title":"Nat Methods"},{"volume-title":"It\u2019s Impossible to Conduct Research Without Software, Say 7 Out of 10 UK Researchers","year":"2014","author":"Hettrick","key":"2025032023575500300_btaf106-B7"},{"key":"2025032023575500300_btaf106-B8","doi-asserted-by":"publisher","first-page":"181","DOI":"10.1093\/bib\/bbp046","article-title":"Bioinformatics approaches for genomics and post genomics applications of next-generation sequencing","volume":"11","author":"Horner","year":"2010","journal-title":"Brief Bioinform"},{"key":"2025032023575500300_btaf106-B10","doi-asserted-by":"publisher","first-page":"221","DOI":"10.1109\/BIBE.2019.00047","article-title":"Towards reproducible bioinformatics: the OpenBio-C scientific workflow environment","author":"Kanterakis","year":"2019","journal-title":"2019 IEEE 19th Int Conf Bioinf Bioeng (BIBE)"},{"key":"2025032023575500300_btaf106-B12","doi-asserted-by":"publisher","first-page":"9","DOI":"10.1109\/SoHeal52568.2021.00008","article-title":"A quantitative assessment of package freshness in linux distributions","author":"Legay","year":"2021","journal-title":"2021 IEEE\/ACM 4th Int Workshop Softw Health Projects Ecosyst Commun (SoHeal)"},{"key":"2025032023575500300_btaf106-B14","doi-asserted-by":"publisher","first-page":"29207","DOI":"10.1109\/ACCESS.2022.3158675","article-title":"Reproducibility in computing research: an empirical study","volume":"10","author":"Raghupathi","year":"2022","journal-title":"IEEE Access"},{"year":"2024","author":"Repology Team","key":"2025032023575500300_btaf106-B15"},{"year":"2024","author":"Squillace","key":"2025032023575500300_btaf106-B16"},{"key":"2025032023575500300_btaf106-B18","doi-asserted-by":"publisher","first-page":"1999","DOI":"10.1109\/TBME.2016.2555481","article-title":"How modeling standards, software, and initiatives support reproducibility in systems biology and systems medicine","volume":"63","author":"Waltemath","year":"2016","journal-title":"IEEE Trans Biomed Eng"},{"year":"2016","author":"Yoo","key":"2025032023575500300_btaf106-B19"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btaf106\/62375471\/btaf106.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/41\/3\/btaf106\/62375471\/btaf106.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/41\/3\/btaf106\/62375471\/btaf106.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,3,23]],"date-time":"2025-03-23T02:14:02Z","timestamp":1742696042000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/doi\/10.1093\/bioinformatics\/btaf106\/8069455"}},"subtitle":[],"editor":[{"given":"Peter","family":"Robinson","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2025,3]]},"references-count":12,"journal-issue":{"issue":"3","published-print":{"date-parts":[[2025,3,4]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btaf106","relation":{},"ISSN":["1367-4811"],"issn-type":[{"type":"electronic","value":"1367-4811"}],"subject":[],"published-other":{"date-parts":[[2025,3]]},"published":{"date-parts":[[2025,3]]},"article-number":"btaf106"}}