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 C 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

Philos Trans R Soc Lond B Biol Sci. 2018 Sep 10;373(1758):20170382. doi: 10.1098/rstb.2017.0382.

Authors

Gopal P Sarma¹, Chee Wai Lee², Tom Portegys³, Vahid Ghayoomie⁴, Travis Jacobs⁵, Bradly Alicea⁶, Matteo Cantarelli², Michael Currie^{7

8}, Richard C Gerkin⁹, Shane Gingell¹⁰, Padraig Gleeson¹¹, Richard Gordon^{12

13}, Ramin M Hasani¹⁴, Giovanni Idili², Sergey Khayrulin^{2

15

16}, David Lung¹⁴, Andrey Palyanov^{15

16}, Mark Watts⁸, Stephen D Larson¹⁷

Affiliations

¹ School of Medicine, Emory University, Atlanta, GA, USA.
² The OpenWorm Foundation, New York, NY, USA.
³ Ernst and Young LLP, New York, NY, USA.
⁴ Laboratory of Systems Biology and Bioinformatics, University of Tehran, Tehran, Iran.
⁵ Melonport AG, Zug, Switzerland.
⁶ Orthogonal Research, Champaign, IL, USA.
⁷ Fling Inc., Bangkok, Thailand.
⁸ Raytheon Company, Waltham, MA, USA.
⁹ School of Life Sciences, Arizona State University, Tempe, AZ, USA.
¹⁰ Out of the BOTS, Inc., Queensland, Australia.
¹¹ Department of Neuroscience, Physiology and Pharmacology, University College London, London, UK.
¹² Embryogenesis Center, Gulf Specimen Marine Laboratory, Panacea, FL, USA.
¹³ C.S. Mott Center for Human Growth and Development, Department of Obstetrics and Gynecology, Wayne State University, Detroit, MI, USA.
¹⁴ Cyber-Physical Systems, Technische Universität Wien, Wien, Austria.
¹⁵ Laboratory of Complex Systems Simulation, A.P. Ershov Institute of Informatics Systems, Novosibirsk, Russia.
¹⁶ Laboratory of Structural Bioinformatics and Molecular Modeling, Novosibirsk State University, Novosibirsk, Russia.
¹⁷ The OpenWorm Foundation, New York, NY, USA stephen@openworm.org.

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'.

Keywords: Caenorhabditis elegans; bioinformatics; biological simulation; computational neuroscience; computational physiology; software engineering.

Publication types

Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Review

MeSH terms

Animals
Caenorhabditis elegans / physiology*
Connectome / instrumentation
Connectome / methods*
Models, Biological*

Abstract

Publication types

MeSH terms

Grants and funding