TY - JOUR

T1 - OpenWorm

T2 - Overview and recent advances in integrative biological simulation of Caenorhabditis elegans

AU - Sarma, Gopal P.

AU - Lee, Chee Wai

AU - Portegys, Tom

AU - Ghayoomie, Vahid

AU - Jacobs, Travis

AU - Alicea, Bradly

AU - Cantarelli, Matteo

AU - Currie, Michael

AU - Gerkin, Richard C.

AU - Gingell, Shane

AU - Gleeson, Padraig

AU - Gordon, Richard

AU - Hasani, Ramin M.

AU - Idili, Giovanni

AU - Khayrulin, Sergey

AU - Lung, David

AU - Palyanov, Andrey

AU - Watts, Mark

AU - Larson, Stephen D.

N1 - © 2018 The Author(s).

PY - 2018/9/10

Y1 - 2018/9/10

N2 - 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'.

AB - 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'.

KW - Bioinformatics

KW - Biological simulation

KW - Caenorhabditis elegans

KW - Computational neuroscience

KW - Computational physiology

KW - Software engineering

KW - Animals

KW - Models, Biological

KW - Connectome/instrumentation

KW - Caenorhabditis elegans/physiology

KW - biological simulation

KW - computational physiology

KW - computational neuroscience

KW - MODELS

KW - bioinformatics

KW - ION-CHANNEL

KW - software engineering

KW - NEUROBIOLOGY

UR - http://www.scopus.com/inward/record.url?scp=85054088349&partnerID=8YFLogxK

U2 - 10.1098/rstb.2017.0382

DO - 10.1098/rstb.2017.0382

M3 - Article

C2 - 30201845

AN - SCOPUS:85054088349

VL - 373

JO - Philosophical Transactions of the Royal Society B: Biological Sciences

JF - Philosophical Transactions of the Royal Society B: Biological Sciences

SN - 0800-4622

IS - 1758

M1 - 20170382

ER -