Better together: Elements of successful scientific software development in a distributed collaborative community
Many scientific disciplines rely on computational methods for data analysis, model generation, and prediction. Implementing these methods is often accomplished by researchers with domain expertise but without formal training in software engineering or computer science. This arrangement has led to un...
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| Veröffentlicht in: | PLoS computational biology 2020-05, Vol.16 (5), p.e1007507 |
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| creator | Koehler Leman, Julia Weitzner, Brian D Renfrew, P Douglas Lewis, Steven M Moretti, Rocco Watkins, Andrew M Mulligan, Vikram Khipple Lyskov, Sergey Adolf-Bryfogle, Jared Labonte, Jason W Krys, Justyna Bystroff, Christopher Schief, William Gront, Dominik Schueler-Furman, Ora Baker, David Bradley, Philip Dunbrack, Roland Kortemme, Tanja Leaver-Fay, Andrew Strauss, Charlie E M Meiler, Jens Kuhlman, Brian Gray, Jeffrey J Bonneau, Richard |
| description | Many scientific disciplines rely on computational methods for data analysis, model generation, and prediction. Implementing these methods is often accomplished by researchers with domain expertise but without formal training in software engineering or computer science. This arrangement has led to underappreciation of sustainability and maintainability of scientific software tools developed in academic environments. Some software tools have avoided this fate, including the scientific library Rosetta. We use this software and its community as a case study to show how modern software development can be accomplished successfully, irrespective of subject area. Rosetta is one of the largest software suites for macromolecular modeling, with 3.1 million lines of code and many state-of-the-art applications. Since the mid 1990s, the software has been developed collaboratively by the RosettaCommons, a community of academics from over 60 institutions worldwide with diverse backgrounds including chemistry, biology, physiology, physics, engineering, mathematics, and computer science. Developing this software suite has provided us with more than two decades of experience in how to effectively develop advanced scientific software in a global community with hundreds of contributors. Here we illustrate the functioning of this development community by addressing technical aspects (like version control, testing, and maintenance), community-building strategies, diversity efforts, software dissemination, and user support. We demonstrate how modern computational research can thrive in a distributed collaborative community. The practices described here are independent of subject area and can be readily adopted by other software development communities. |
| doi_str_mv | 10.1371/journal.pcbi.1007507 |
| format | Article |
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(LANL), Los Alamos, NM (United States)</creatorcontrib><title>Better together: Elements of successful scientific software development in a distributed collaborative community</title><title>PLoS computational biology</title><addtitle>PLoS Comput Biol</addtitle><description>Many scientific disciplines rely on computational methods for data analysis, model generation, and prediction. Implementing these methods is often accomplished by researchers with domain expertise but without formal training in software engineering or computer science. This arrangement has led to underappreciation of sustainability and maintainability of scientific software tools developed in academic environments. Some software tools have avoided this fate, including the scientific library Rosetta. We use this software and its community as a case study to show how modern software development can be accomplished successfully, irrespective of subject area. 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The practices described here are independent of subject area and can be readily adopted by other software development communities.</description><subject>Biochemistry</subject><subject>Biology</subject><subject>Biology and Life Sciences</subject><subject>Biophysics</subject><subject>Cancer</subject><subject>Chemistry</subject><subject>Collaboration</subject><subject>community</subject><subject>Computational biology</subject><subject>Computational Biology - methods</subject><subject>Computer and Information Sciences</subject><subject>Computer applications</subject><subject>Computer programs</subject><subject>Computer science</subject><subject>Consortia</subject><subject>Cooperative Behavior</subject><subject>Data Analysis</subject><subject>Documentation</subject><subject>Engineering</subject><subject>Engineering and Technology</subject><subject>Gene Library</subject><subject>Humans</subject><subject>Immunology</subject><subject>Interdisciplinary 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(LANL), Los Alamos, NM (United States)</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Gale In Context: Canada</collection><collection>Gale In Context: Science</collection><collection>ProQuest Central (Corporate)</collection><collection>Biotechnology Research Abstracts</collection><collection>Calcium & Calcified Tissue Abstracts</collection><collection>Neurosciences Abstracts</collection><collection>Nucleic Acids Abstracts</collection><collection>Health & Medical Collection</collection><collection>ProQuest Central (purchase pre-March 2016)</collection><collection>Medical Database (Alumni Edition)</collection><collection>Computing Database (Alumni Edition)</collection><collection>Technology Research Database</collection><collection>ProQuest SciTech Collection</collection><collection>ProQuest Technology Collection</collection><collection>ProQuest Natural Science Collection</collection><collection>Hospital Premium Collection</collection><collection>Hospital Premium Collection (Alumni Edition)</collection><collection>ProQuest Central (Alumni) (purchase pre-March 2016)</collection><collection>ProQuest Central (Alumni Edition)</collection><collection>ProQuest Central UK/Ireland</collection><collection>Advanced Technologies & Aerospace Collection</collection><collection>ProQuest Central Essentials</collection><collection>Biological Science Collection</collection><collection>ProQuest Central</collection><collection>Technology Collection</collection><collection>Natural Science Collection</collection><collection>ProQuest One Community College</collection><collection>ProQuest Central Korea</collection><collection>Engineering Research Database</collection><collection>Health Research Premium Collection</collection><collection>Health Research Premium Collection (Alumni)</collection><collection>ProQuest Central Student</collection><collection>SciTech Premium Collection</collection><collection>ProQuest Computer Science Collection</collection><collection>Computer Science Database</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>ProQuest Biological Science Collection</collection><collection>Computing Database</collection><collection>Health & Medical Collection (Alumni Edition)</collection><collection>Medical Database</collection><collection>Biological Science Database</collection><collection>Advanced Technologies & Aerospace Database</collection><collection>ProQuest Advanced Technologies & Aerospace Collection</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Publicly Available Content Database</collection><collection>ProQuest One Academic Eastern Edition (DO NOT USE)</collection><collection>ProQuest One Academic</collection><collection>ProQuest One Academic UKI Edition</collection><collection>ProQuest Central China</collection><collection>ProQuest Central Basic</collection><collection>Genetics Abstracts</collection><collection>MEDLINE - Academic</collection><collection>OSTI.GOV - Hybrid</collection><collection>OSTI.GOV</collection><collection>PubMed Central (Full Participant titles)</collection><collection>DOAJ Directory of Open Access Journals</collection><jtitle>PLoS computational biology</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Koehler Leman, Julia</au><au>Weitzner, Brian D</au><au>Renfrew, P Douglas</au><au>Lewis, Steven M</au><au>Moretti, Rocco</au><au>Watkins, Andrew M</au><au>Mulligan, Vikram Khipple</au><au>Lyskov, Sergey</au><au>Adolf-Bryfogle, Jared</au><au>Labonte, Jason W</au><au>Krys, Justyna</au><au>Bystroff, Christopher</au><au>Schief, William</au><au>Gront, Dominik</au><au>Schueler-Furman, Ora</au><au>Baker, David</au><au>Bradley, Philip</au><au>Dunbrack, Roland</au><au>Kortemme, Tanja</au><au>Leaver-Fay, Andrew</au><au>Strauss, Charlie E M</au><au>Meiler, Jens</au><au>Kuhlman, Brian</au><au>Gray, Jeffrey J</au><au>Bonneau, Richard</au><au>Schneidman-Duhovny, Dina</au><aucorp>RosettaCommons Consortium</aucorp><aucorp>RosettaCommons Consortium</aucorp><aucorp>Los Alamos National Lab. (LANL), Los Alamos, NM (United States)</aucorp><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Better together: Elements of successful scientific software development in a distributed collaborative community</atitle><jtitle>PLoS computational biology</jtitle><addtitle>PLoS Comput Biol</addtitle><date>2020-05-04</date><risdate>2020</risdate><volume>16</volume><issue>5</issue><spage>e1007507</spage><pages>e1007507-</pages><issn>1553-7358</issn><issn>1553-734X</issn><eissn>1553-7358</eissn><abstract>Many scientific disciplines rely on computational methods for data analysis, model generation, and prediction. Implementing these methods is often accomplished by researchers with domain expertise but without formal training in software engineering or computer science. This arrangement has led to underappreciation of sustainability and maintainability of scientific software tools developed in academic environments. Some software tools have avoided this fate, including the scientific library Rosetta. We use this software and its community as a case study to show how modern software development can be accomplished successfully, irrespective of subject area. Rosetta is one of the largest software suites for macromolecular modeling, with 3.1 million lines of code and many state-of-the-art applications. Since the mid 1990s, the software has been developed collaboratively by the RosettaCommons, a community of academics from over 60 institutions worldwide with diverse backgrounds including chemistry, biology, physiology, physics, engineering, mathematics, and computer science. Developing this software suite has provided us with more than two decades of experience in how to effectively develop advanced scientific software in a global community with hundreds of contributors. Here we illustrate the functioning of this development community by addressing technical aspects (like version control, testing, and maintenance), community-building strategies, diversity efforts, software dissemination, and user support. We demonstrate how modern computational research can thrive in a distributed collaborative community. The practices described here are independent of subject area and can be readily adopted by other software development communities.</abstract><cop>United States</cop><pub>Public Library of Science</pub><pmid>32365137</pmid><doi>10.1371/journal.pcbi.1007507</doi><orcidid>https://orcid.org/0000-0001-6380-2324</orcidid><orcidid>https://orcid.org/0000-0002-5693-3593</orcidid><orcidid>https://orcid.org/0000-0002-1909-0961</orcidid><orcidid>https://orcid.org/0000000163802324</orcidid><orcidid>https://orcid.org/0000000336394673</orcidid><orcidid>https://orcid.org/0000000256933593</orcidid><orcidid>https://orcid.org/0000000219090961</orcidid><oa>free_for_read</oa></addata></record> |
| fulltext | fulltext |
| identifier | ISSN: 1553-7358 |
| ispartof | PLoS computational biology, 2020-05, Vol.16 (5), p.e1007507 |
| issn | 1553-7358 1553-734X 1553-7358 |
| language | eng |
| recordid | cdi_plos_journals_2460759859 |
| source | MEDLINE; DOAJ Directory of Open Access Journals; Public Library of Science (PLoS) Journals Open Access; EZB-FREE-00999 freely available EZB journals; PubMed Central |
| subjects | Biochemistry Biology Biology and Life Sciences Biophysics Cancer Chemistry Collaboration community Computational biology Computational Biology - methods Computer and Information Sciences Computer applications Computer programs Computer science Consortia Cooperative Behavior Data Analysis Documentation Engineering Engineering and Technology Gene Library Humans Immunology Interdisciplinary research Laboratories Macromolecules Maintainability MATHEMATICS AND COMPUTING Medical research Methods modeling Models, Molecular People and Places Product development protein structure Proteins Research - trends Research Personnel Review Rosetta Science Policy Scientific software Social aspects Social Behavior Software Software - trends Software development Software development tools Software engineering Software packages Suites (Software) Sustainability User-Computer Interface Version control |
| title | Better together: Elements of successful scientific software development in a distributed collaborative community |
| url | https://sfx.bib-bvb.de/sfx_tum?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2025-01-02T20%3A29%3A21IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-gale_plos_&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=Better%20together:%20Elements%20of%20successful%20scientific%20software%20development%20in%20a%20distributed%20collaborative%20community&rft.jtitle=PLoS%20computational%20biology&rft.au=Koehler%20Leman,%20Julia&rft.aucorp=RosettaCommons%20Consortium&rft.date=2020-05-04&rft.volume=16&rft.issue=5&rft.spage=e1007507&rft.pages=e1007507-&rft.issn=1553-7358&rft.eissn=1553-7358&rft_id=info:doi/10.1371/journal.pcbi.1007507&rft_dat=%3Cgale_plos_%3EA632940723%3C/gale_plos_%3E%3Curl%3E%3C/url%3E&disable_directlink=true&sfx.directlink=off&sfx.report_link=0&rft_id=info:oai/&rft_pqid=2460759859&rft_id=info:pmid/32365137&rft_galeid=A632940723&rft_doaj_id=oai_doaj_org_article_39b3fd5bfd834abfb5347fc6af6789bc&rfr_iscdi=true |