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Review
. 2018 Sep 10;373(1758):20170382.
doi: 10.1098/rstb.2017.0382.

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

Gopal P Sarma  1 , Chee Wai Lee  2 , Tom Portegys  3 , Vahid Ghayoomie  4 , Travis Jacobs  5 , Bradly Alicea  6 , Matteo Cantarelli  2 , Michael Currie  7   8 , Richard C Gerkin  9 , Shane Gingell  10 , Padraig Gleeson  11 , Richard Gordon  12   13 , Ramin M Hasani  14 , Giovanni Idili  2 , Sergey Khayrulin  2   15   16 , David Lung  14 , Andrey Palyanov  15   16 , Mark Watts  8 , Stephen D Larson  17
Affiliations
Review

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

Gopal P Sarma et al. Philos Trans R Soc Lond B Biol Sci. .

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.

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Conflict of interest statement

S.D.L., M.C. and G.I. are also co-founders of MetaCell LLC, LTD, a software company that has made financial and in-kind donations to the OpenWorm project pre-2016 and the OpenWorm Foundation since its inception.

Figures

Figure 1.
Figure 1.
Overview of OpenWorm simulation stack. (a) A component diagram describing the relationships between inputs and outputs of sub-projects within OpenWorm. (b) A highly simplified schematic view of the system of equations executed in the combined c302/Sibernetic system.
Figure 2.
Figure 2.
(a) Top view of the robot. (b) Three-dimensional-printed body parts. (c) Side view of the robot. (d) Segment sub-assembly.
Figure 3.
Figure 3.
Schematic view of the scientific value of modelling and simulation in biology, as applied in OpenWorm.
See this image and copyright information in PMC

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