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

Author:

Sarma Gopal P.1ORCID,Lee Chee Wai2,Portegys Tom3,Ghayoomie Vahid4,Jacobs Travis5,Alicea Bradly6ORCID,Cantarelli Matteo2,Currie Michael78,Gerkin Richard C.9ORCID,Gingell Shane10,Gleeson Padraig11ORCID,Gordon Richard1213,Hasani Ramin M.14,Idili Giovanni2,Khayrulin Sergey21516,Lung David14,Palyanov Andrey1516ORCID,Watts Mark8ORCID,Larson Stephen D.2ORCID

Affiliation:

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

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’.

Funder

NeuroLinx

Amazon Web Services

Open Source Brain

National Institute of Biomedical Imaging and Bioengineering

National Institutes of Health

Google Summer of Code

Publisher

The Royal Society

Subject

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

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