title: Unit testing, model validation, and biological simulation.
abstract: The growth of the software industry has gone hand in hand with the development of tools and cultural practices for ensuring the reliability of complex pieces of software. These tools and practices are now acknowledged to be essential to the management of modern software. As computational models and methods have become increasingly common in the biological sciences, it is important to examine how these practices can accelerate biological software development and improve research quality. In this article, we give a focused case study of our experience with the practices of unit testing and test-driven development in OpenWorm, an open-science project aimed at modeling Caenorhabditis elegans. We identify and discuss the challenges of incorporating test-driven development into a heterogeneous, data-driven project, as well as the role of model validation tests, a category of tests unique to software which expresses scientific models.
authors.affiliation: School of Medicine, Emory University, Atlanta, USA.|OpenWorm Foundation, Boston, USA.
authors.forename: Gopal P
authors.initials: GP
authors.lastname: Sarma
authors.affiliation: Department of Bioengineering, Imperial College London, London, UK.|OpenWorm Foundation, Boston, USA.
authors.forename: Travis W
authors.initials: TW
authors.lastname: Jacobs
authors.affiliation: The University of Texas at Austin, Austin, USA.|OpenWorm Foundation, Boston, USA.
authors.forename: Mark D
authors.initials: MD
authors.lastname: Watts
authors.affiliation: Laboratory of Systems Biology and Bioinformatics, University of Tehran, Tehran, Iran.|OpenWorm Foundation, Boston, USA.
authors.forename: S Vahid
authors.initials: SV
authors.lastname: Ghayoomie
authors.affiliation: OpenWorm Foundation, Boston, USA.
authors.forename: Stephen D
authors.initials: SD
authors.lastname: Larson
authors.affiliation: School of Life Sciences, Arizona State University, Tempe, USA.|OpenWorm Foundation, Boston, USA.
authors.forename: Richard C
authors.initials: RC
authors.lastname: Gerkin
keywords: C. elegans; biology; model; quality control; software; testing; validation