OpenWorm: an open-science approach to modeling Caenorhabditis elegans

Front Comput Neurosci. 2014 Nov 3;8:137. doi: 10.3389/fncom.2014.00137. eCollection 2014.

Abstract

OpenWorm is an international collaboration with the aim of understanding how the behavior of Caenorhabditis elegans (C. elegans) emerges from its underlying physiological processes. The project has developed a modular simulation engine to create computational models of the worm. The modularity of the engine makes it possible to easily modify the model, incorporate new experimental data and test hypotheses. The modeling framework incorporates both biophysical neuronal simulations and a novel fluid-dynamics-based soft-tissue simulation for physical environment-body interactions. The project's open-science approach is aimed at overcoming the difficulties of integrative modeling within a traditional academic environment. In this article the rationale is presented for creating the OpenWorm collaboration, the tools and resources developed thus far are outlined and the unique challenges associated with the project are discussed.

Keywords: C. elegans; complex systems simulation; emergent behavior; integrative modeling; open science.