Research output: Contribution to journal › Article › peer-review
OpenWorm : Overview and recent advances in integrative biological simulation of Caenorhabditis elegans. / Sarma, Gopal P.; Lee, Chee Wai; Portegys, Tom et al.
In: Philosophical Transactions of the Royal Society B: Biological Sciences, Vol. 373, No. 1758, 20170382, 10.09.2018.Research output: Contribution to journal › Article › peer-review
}
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 -
ID: 16947477