Unit Testing, Model Validation, and Biological Simulation

TL;DR

This paper explores how software testing practices like unit testing and model validation can enhance the development and reliability of biological simulation software, based on the OpenWorm project for modeling C. elegans.

Contribution

It provides a case study on implementing test-driven development and model validation in biological modeling software, highlighting challenges and benefits.

Findings

Test-driven development can improve software reliability in biological research.

Model validation tests are crucial for scientific accuracy in biological simulations.

Challenges include integrating testing into heterogeneous, data-driven projects.

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.