OpenWorm: Overview and recent advances in integrative biological simulation of Caenorhabditis elegans

Gopal P. Sarma; Chee Wai Lee; Tom Portegys; Vahid Ghayoomie; Travis Jacobs; Bradly Alicea; Matteo Cantarelli; Michael Currie; Richard Gerkin; Shane Gingell; Padraig Gleeson; Richard Gordon; Ramin M. Hasani; Giovanni Idili; Sergey Khayrulin; David Lung; Andrey Palyanov; Mark Watts; Stephen D. Larson

doi:10.1098/rstb.2017.0382

OpenWorm: Overview and recent advances in integrative biological simulation of Caenorhabditis elegans

Gopal P. Sarma, Chee Wai Lee, Tom Portegys, Vahid Ghayoomie, Travis Jacobs, Bradly Alicea, Matteo Cantarelli, Michael Currie, Richard Gerkin, Shane Gingell, Padraig Gleeson, Richard Gordon, Ramin M. Hasani, Giovanni Idili, Sergey Khayrulin, David Lung, Andrey Palyanov, Mark Watts, Stephen D. Larson

Life Sciences, School of (SOLS)

Research output: Contribution to journal › Article › peer-review

53 Scopus citations

Abstract

The adoption of powerful software tools and computational methods from the software industry by the scientific research community has resulted in a renewed interest in integrative, large-scale biological simulations. These typically involve the development of computational platforms to combine diverse, process-specific models into a coherent whole. The OpenWorm Foundation is an independent research organization working towards an integrative simulation of the nematode Caenorhabditis elegans, with the aim of providing a powerful new tool to understand how the organism's behaviour arises from its fundamental biology. In this perspective, we give an overview of the history and philosophy of OpenWorm, descriptions of the constituent sub-projects and corresponding open-science management practices, and discuss current achievements of the project and future directions. This article is part of a discussion meeting issue 'Connectome to behaviour: modelling C. Elegans at cellular resolution'.

Original language	English (US)
Article number	20170382
Journal	Philosophical Transactions of the Royal Society B: Biological Sciences
Volume	373
Issue number	1758
DOIs	https://doi.org/10.1098/rstb.2017.0382
State	Published - 2018

Keywords

Bioinformatics
Biological simulation
Caenorhabditis elegans
Computational neuroscience
Computational physiology
Software engineering

ASJC Scopus subject areas

General Biochemistry, Genetics and Molecular Biology
General Agricultural and Biological Sciences

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10.1098/rstb.2017.0382

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Sarma, G. P., Lee, C. W., Portegys, T., Ghayoomie, V., Jacobs, T., Alicea, B., Cantarelli, M., Currie, M., Gerkin, R., Gingell, S., Gleeson, P., Gordon, R., Hasani, R. M., Idili, G., Khayrulin, S., Lung, D., Palyanov, A., Watts, M., & Larson, S. D. (2018). OpenWorm: Overview and recent advances in integrative biological simulation of Caenorhabditis elegans. Philosophical Transactions of the Royal Society B: Biological Sciences, 373(1758), Article 20170382. https://doi.org/10.1098/rstb.2017.0382

Sarma, GP, Lee, CW, Portegys, T, Ghayoomie, V, Jacobs, T, Alicea, B, Cantarelli, M, Currie, M, Gerkin, R, Gingell, S, Gleeson, P, Gordon, R, Hasani, RM, Idili, G, Khayrulin, S, Lung, D, Palyanov, A, Watts, M & Larson, SD 2018, 'OpenWorm: Overview and recent advances in integrative biological simulation of Caenorhabditis elegans', Philosophical Transactions of the Royal Society B: Biological Sciences, vol. 373, no. 1758, 20170382. https://doi.org/10.1098/rstb.2017.0382

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OpenWorm: Overview and recent advances in integrative biological simulation of Caenorhabditis elegans

Abstract

Keywords

ASJC Scopus subject areas

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