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

• Published in: PLoS computational biology Vol. 16; no. 5; p. e1007507
• Main Authors: 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
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 04.05.2020; Public Library of Science (PLoS)
• 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; United States; Poland; New York; La Jolla California; United States > US; Nashville Tennessee; Baltimore Maryland
• ISSN: 1553-7358; 1553-734X; 1553-7358
• DOI: 10.1371/journal.pcbi.1007507

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.