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Better together: Elements of successful scientific software development in a distributed collaborative community

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 Schneidman-Duhovny, Dina

PLoS computational biology, 2020-05, Vol.16 (5), p.e1007507-e1007507 [Periódico revisado por pares]

United States: Public Library of Science

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Título:
Better together: Elements of successful scientific software development in a distributed collaborative community
Autor: 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
Schneidman-Duhovny, Dina
Assuntos: 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 ; Integrated software ; 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 ; 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
É parte de: PLoS computational biology, 2020-05, Vol.16 (5), p.e1007507-e1007507
Notas: ObjectType-Article-1
SourceType-Scholarly Journals-1
ObjectType-Feature-3
content type line 23
ObjectType-Review-2
LA-UR-20-24100
USDOE
89233218CNA000001
The Rosetta software has been licensed to numerous non-profit and for-profit organizations. Rosetta Licensing is managed by UW CoMotion, and royalty proceeds are managed by the RosettaCommons. Under institutional participation agreements between the University of Washington, acting on behalf of the RosettaCommons, their respective institutions may be entitled to a portion of revenue received on licensing Rosetta software including programs described here. Baker, Malmström, Yarov-Yarovoy, Gront, Meiler, Whitehead, Schueler-Furman, King, Gray, Sgourakis, Lindert, Strauss, Karanicolas, Bonneau, Sammond, Kortemme, and Bradley are unpaid board members of the RosettaCommons. As members of the Scientific Advisory Board of Cyrus Biotechnology, Baker and Gray are granted stock options. Yifan Song, Indigo C. King, Steven M. Lewis, Brandon Frenz, Karen Khar and Ryan Pavlovicz are currently employed at Cyrus Biotechnology with granted stock options. Cyrus Biotechnology distributes the Rosetta software. Brian D. Weitzner and Scott E. Boyken hold equity in Lyell Immunopharma. Vikram K. Mulligan is a co-founder of and shareholder in Menten Biotechnology Labs, Inc. The content of this manuscript is relevant to work performed at Lyell and Menten. Neil P. King is a co-founder and shareholder of Icosavax, Inc., a biotech company developing nanoparticle vaccines. Justin B. Siegel is a co-founder and shareholder of Digestiva, Inc. and PvP Biologics Inc. David Baker is a co-founder, shareholder, or advisor to the following companies: ARZEDA, PvP Biologics, Cyrus Biotechnology, Cue Biopharma, Icosavax, Neoleukin Therapeutics, Lyell Immunotherapeutics, Sana Biotechnology, and A-Alpha Bio.
Membership of the RosettaCommons Consortium is listed in the S1 List.
Descrição: 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.
Editor: United States: Public Library of Science
Idioma: Inglês

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Better together: Elements of successful scientific software development in a distributed collaborative community

United States: Public Library of Science

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