Unit Testing, Model Validation, and Biological Simulation

摘要

The growth of the software industry has gone hand in hand with thedevelopment of tools and cultural practices for ensuring the reliability ofcomplex pieces of software. These tools and practices are now acknowledged tobe essential to the management of modern software. As computational models andmethods have become increasingly common in the biological sciences, it isimportant to examine how these practices can accelerate biological softwaredevelopment and improve research quality. In this article, we give a focusedcase study of our experience with the practices of unit testing and test-drivendevelopment in OpenWorm, an open-science project aimed at modelingCaenorhabditis elegans. We identify and discuss the challenges of incorporatingtest-driven development into a heterogeneous, data-driven project, as well asthe role of model validation tests, a category of tests unique to softwarewhich expresses scientific models.