title: OpenWorm: an open-science approach to modeling Caenorhabditis elegans.
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.
authors.affiliation: Neuroinformatics Doctoral Training Centre, University of Edinburgh Edinburgh, UK ; OpenWorm Project San Diego, CA, USA.
authors.forename: Balázs
authors.initials: B
authors.lastname: Szigeti
authors.affiliation: OpenWorm Project San Diego, CA, USA ; Department of Neuroscience, Physiology and Pharmacology, University College London London, UK.
authors.forename: Padraig
authors.initials: P
authors.lastname: Gleeson
authors.affiliation: OpenWorm Project San Diego, CA, USA ; Department of Physiology, Development and Neuroscience, University of Cambridge Cambridge, UK.
authors.forename: Michael
authors.initials: M
authors.lastname: Vella
authors.affiliation: OpenWorm Project San Diego, CA, USA ; Laboratory of Complex Systems Simulation, A.P. Ershov Institute of Informatics Systems Novosibirsk, Russia.
authors.forename: Sergey
authors.initials: S
authors.lastname: Khayrulin
authors.affiliation: OpenWorm Project San Diego, CA, USA ; Laboratory of Complex Systems Simulation, A.P. Ershov Institute of Informatics Systems Novosibirsk, Russia.
authors.forename: Andrey
authors.initials: A
authors.lastname: Palyanov
authors.affiliation: OpenWorm Project San Diego, CA, USA ; Department of Biomedical Engineering, Duke University Durham, NC, USA.
authors.forename: Jim
authors.initials: J
authors.lastname: Hokanson
authors.affiliation: OpenWorm Project San Diego, CA, USA.
authors.forename: Michael
authors.initials: M
authors.lastname: Currie
authors.affiliation: OpenWorm Project San Diego, CA, USA.
authors.forename: Matteo
authors.initials: M
authors.lastname: Cantarelli
authors.affiliation: OpenWorm Project San Diego, CA, USA.
authors.forename: Giovanni
authors.initials: G
authors.lastname: Idili
authors.affiliation: OpenWorm Project San Diego, CA, USA.
authors.forename: Stephen
authors.initials: S
authors.lastname: Larson
keywords: C. elegans; complex systems simulation; emergent behavior; integrative modeling; open science