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OpenWorm: an open-science approach to modeling Caenorhabditis elegans.

Szigeti, B; Gleeson, P; Vella, M; Khayrulin, S; Palyanov, A; Hokanson, J; Currie, M; ... Larson, S; + view all (2014) OpenWorm: an open-science approach to modeling Caenorhabditis elegans. Front Comput Neurosci , 8 , Article 137. 10.3389/fncom.2014.00137. Green open access

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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.

Type: Article
Title: OpenWorm: an open-science approach to modeling Caenorhabditis elegans.
Location: Switzerland
Open access status: An open access version is available from UCL Discovery
DOI: 10.3389/fncom.2014.00137
Publisher version: http://dx.doi.org/10.3389/fncom.2014.00137
Language: English
Additional information: Copyright © 2014 Szigeti, Gleeson, Vella, Khayrulin, Palyanov, Hokanson, Currie, Cantarelli, Idili and Larson. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
Keywords: C. elegans, complex systems simulation, emergent behavior, integrative modeling, open science
UCL classification: UCL
UCL > Provost and Vice Provost Offices
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences > Div of Biosciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences > Div of Biosciences > Neuro, Physiology and Pharmacology
URI: https://discovery.ucl.ac.uk/id/eprint/1451516
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