{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,16]],"date-time":"2026-04-16T11:14:54Z","timestamp":1776338094247,"version":"3.51.2"},"reference-count":23,"publisher":"Oxford University Press (OUP)","issue":"11","license":[{"start":{"date-parts":[[2024,10,22]],"date-time":"2024-10-22T00:00:00Z","timestamp":1729555200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100005416","name":"Research Council of Norway","doi-asserted-by":"publisher","award":["187615"],"award-info":[{"award-number":["187615"]}],"id":[{"id":"10.13039\/501100005416","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,11,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>Since high-throughput techniques became a staple in biological science laboratories, computational algorithms, and scientific software have boomed. However, the development of bioinformatics software usually lacks software development quality standards. The resulting software code is hard to test, reuse, and maintain. We believe that the root of inefficiency in implementing the best software development practices in academic settings is the individualistic approach, which has traditionally been the norm for recognizing scientific achievements and, by extension, for developing specialized software. Software development is a collective effort in most software-heavy endeavors. Indeed, the literature suggests teamwork directly impacts code quality through knowledge sharing, collective software development, and established coding standards. In our computational biology research groups, we sustainably involve all group members in learning, sharing, and discussing software development while maintaining the personal ownership of research projects and related software products. We found that group members involved in this endeavor improved their coding skills, became more efficient bioinformaticians, and obtained detailed knowledge about their peers\u2019 work, triggering new collaborative projects. We strongly advocate for improving software development culture within bioinformatics through collective effort in computational biology groups or institutes with three or more bioinformaticians.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>Additional information and guidance on how to get started is available at https:\/\/ferenckata.github.io\/ImprovingSoftwareTogether.github.io\/.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btae632","type":"journal-article","created":{"date-parts":[[2024,10,22]],"date-time":"2024-10-22T18:05:43Z","timestamp":1729620343000},"source":"Crossref","is-referenced-by-count":3,"title":["Improving bioinformatics software quality through teamwork"],"prefix":"10.1093","volume":"40","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-3006-4297","authenticated-orcid":false,"given":"Katalin","family":"Ferenc","sequence":"first","affiliation":[{"name":"Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo , Oslo 0318,","place":["Norway"]}]},{"given":"Ieva","family":"Rauluseviciute","sequence":"additional","affiliation":[{"name":"Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo , Oslo 0318,","place":["Norway"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8847-9295","authenticated-orcid":false,"given":"Ladislav","family":"Hovan","sequence":"additional","affiliation":[{"name":"Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo , Oslo 0318,","place":["Norway"]}]},{"given":"Vipin","family":"Kumar","sequence":"additional","affiliation":[{"name":"Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo , Oslo 0318,","place":["Norway"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6280-3130","authenticated-orcid":false,"given":"Marieke L","family":"Kuijjer","sequence":"additional","affiliation":[{"name":"Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo , Oslo 0318,","place":["Norway"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5127-5459","authenticated-orcid":false,"given":"Anthony","family":"Mathelier","sequence":"additional","affiliation":[{"name":"Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo , Oslo 0318,","place":["Norway"]},{"name":"Department of Medical Genetics, Institute of Clinical Medicine, Oslo University Hospital and University of Oslo , Oslo 0450,","place":["Norway"]},{"name":"Department of Pharmacy, University of Oslo , Oslo 0371,","place":["Norway"]}]}],"member":"286","published-online":{"date-parts":[[2024,10,22]]},"reference":[{"key":"2024110520354605400_btae632-B1","doi-asserted-by":"publisher","first-page":"50","DOI":"10.1145\/2160718.2160733","article-title":"Managing technical debt","volume":"55","author":"Allman","year":"2012","journal-title":"Commun ACM"},{"key":"2024110520354605400_btae632-B2","doi-asserted-by":"publisher","first-page":"110848","DOI":"10.1016\/j.jss.2020.110848","article-title":"Software engineering practices for scientific software development: a systematic mapping study","volume":"172","author":"Arvanitou","year":"2021","journal-title":"J Syst Softw"},{"key":"2024110520354605400_btae632-B3","doi-asserted-by":"publisher","first-page":"e1004668","DOI":"10.1371\/journal.pcbi.1004668","article-title":"A quick introduction to version control with git and GitHub","volume":"12","author":"Blischak","year":"2016","journal-title":"PLoS Comput Biol"},{"key":"2024110520354605400_btae632-B4","doi-asserted-by":"publisher","first-page":"44","DOI":"10.5334\/jors.35","article-title":"Walking the talk: adopting and adapting sustainable scientific software development processes in a small biology lab","volume":"4","author":"Crusoe","year":"2016","journal-title":"JORS"},{"key":"2024110520354605400_btae632-B5","author":"Cunningham","year":", . 29\u201330"},{"key":"2024110520354605400_btae632-B6","doi-asserted-by":"publisher","author":"Ferenc","year":"2022","DOI":"10.1101\/2022.03.10.483804"},{"key":"2024110520354605400_btae632-B7","doi-asserted-by":"publisher","first-page":"4","DOI":"10.1109\/MIC.2014.88","article-title":"Better software, better research","volume":"18","author":"Goble","year":"2014","journal-title":"IEEE Internet Comput"},{"key":"2024110520354605400_btae632-B8","doi-asserted-by":"publisher","first-page":"e1008119","DOI":"10.1371\/journal.pcbi.1008119","article-title":"Ten simple rules to increase computational skills among biologists with code clubs","volume":"16","author":"Hagan","year":"2020","journal-title":"PLoS Comput Biol"},{"key":"2024110520354605400_btae632-B9","doi-asserted-by":"publisher","author":"Hannay","DOI":"10.1109\/SECSE.2009.5069155"},{"key":"2024110520354605400_btae632-B10","volume-title":"The Pragmatic Programmer","author":"Hunt","year":"1999"},{"key":"2024110520354605400_btae632-B11","doi-asserted-by":"publisher","first-page":"120","DOI":"10.1109\/MS.2007.155","article-title":"A software chasm: software engineering and scientific computing","volume":"24","author":"Kelly","year":"2007","journal-title":"IEEE Softw"},{"key":"2024110520354605400_btae632-B12","doi-asserted-by":"publisher","first-page":"e2002050","DOI":"10.1371\/journal.pbio.2002050","article-title":"All biology is computational biology","volume":"15","author":"Markowetz","year":"2017","journal-title":"PLoS Biol"},{"key":"2024110520354605400_btae632-B13","doi-asserted-by":"publisher","first-page":"410","DOI":"10.1038\/d41586-022-01901-x","article-title":"Ex-Google chief\u2019s venture aims to save neglected science software","volume":"607","author":"Matthews","year":"2022","journal-title":"Nature"},{"key":"2024110520354605400_btae632-B14","doi-asserted-by":"publisher","first-page":"1856","DOI":"10.1126\/science.314.5807.1856","article-title":"A scientist\u2019s nightmare: software problem leads to five retractions","volume":"314","author":"Miller","year":"2006","journal-title":"Science"},{"key":"2024110520354605400_btae632-B15","doi-asserted-by":"publisher","first-page":"480","DOI":"10.1016\/j.infsof.2009.11.004","article-title":"A teamwork model for understanding an agile team: a case study of a scrum project","volume":"52","author":"Moe","year":"2010","journal-title":"Inf Softw Technol"},{"key":"2024110520354605400_btae632-B16","doi-asserted-by":"publisher","author":"Nguyen-Hoan","year":"2010","DOI":"10.1145\/1852786.1852802"},{"key":"2024110520354605400_btae632-B17","doi-asserted-by":"publisher","first-page":"e839","DOI":"10.7717\/peerj-cs.839","article-title":"Improving bioinformatics software quality through incorporation of software engineering practices","volume":"8","author":"Noor","year":"2022","journal-title":"PeerJ Comput Sci"},{"key":"2024110520354605400_btae632-B18","author":"Posner"},{"key":"2024110520354605400_btae632-B19","doi-asserted-by":"publisher","first-page":"e0205898","DOI":"10.1371\/journal.pone.0205898","article-title":"A large-scale analysis of bioinformatics code on GitHub","volume":"13","author":"Russell","year":"2018","journal-title":"PLoS One"},{"key":"2024110520354605400_btae632-B20","doi-asserted-by":"publisher","first-page":"e1003285","DOI":"10.1371\/journal.pcbi.1003285","article-title":"Ten simple rules for reproducible computational research","volume":"9","author":"Sandve","year":"2013","journal-title":"PLoS Comput Biol"},{"key":"2024110520354605400_btae632-B21","doi-asserted-by":"publisher","first-page":"18","DOI":"10.1109\/MS.2008.85","article-title":"Developing scientific software","volume":"25","author":"Segal","year":"2008","journal-title":"IEEE Softw"},{"key":"2024110520354605400_btae632-B22","doi-asserted-by":"publisher","first-page":"e1005412","DOI":"10.1371\/journal.pcbi.1005412","article-title":"Ten simple rules for making research software more robust","volume":"13","author":"Taschuk","year":"2017","journal-title":"PLoS Comput Biol"},{"key":"2024110520354605400_btae632-B23","doi-asserted-by":"publisher","author":"Umarji","DOI":"10.1109\/CSEET.2009.44"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btae632\/59970913\/btae632.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/40\/11\/btae632\/60431645\/btae632.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/40\/11\/btae632\/60431645\/btae632.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,11,5]],"date-time":"2024-11-05T20:35:54Z","timestamp":1730838954000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/doi\/10.1093\/bioinformatics\/btae632\/7831429"}},"subtitle":[],"editor":[{"given":"Inanc","family":"Birol","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2024,10,22]]},"references-count":23,"journal-issue":{"issue":"11","published-print":{"date-parts":[[2024,11,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btae632","relation":{},"ISSN":["1367-4811"],"issn-type":[{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2024,11]]},"published":{"date-parts":[[2024,10,22]]},"article-number":"btae632"}}