Chaste: an open source C++ library for computational physiology and biology.

Handle URI:
http://hdl.handle.net/10754/596776
Title:
Chaste: an open source C++ library for computational physiology and biology.
Authors:
Mirams, Gary R; Arthurs, Christopher J; Bernabeu, Miguel O; Bordas, Rafel; Cooper, Jonathan; Corrias, Alberto; Davit, Yohan; Dunn, Sara-Jane; Fletcher, Alexander G; Harvey, Daniel G; Marsh, Megan E; Osborne, James M; Pathmanathan, Pras; Pitt-Francis, Joe; Southern, James; Zemzemi, Nejib; Gavaghan, David J
Abstract:
Chaste - Cancer, Heart And Soft Tissue Environment - is an open source C++ library for the computational simulation of mathematical models developed for physiology and biology. Code development has been driven by two initial applications: cardiac electrophysiology and cancer development. A large number of cardiac electrophysiology studies have been enabled and performed, including high-performance computational investigations of defibrillation on realistic human cardiac geometries. New models for the initiation and growth of tumours have been developed. In particular, cell-based simulations have provided novel insight into the role of stem cells in the colorectal crypt. Chaste is constantly evolving and is now being applied to a far wider range of problems. The code provides modules for handling common scientific computing components, such as meshes and solvers for ordinary and partial differential equations (ODEs/PDEs). Re-use of these components avoids the need for researchers to 're-invent the wheel' with each new project, accelerating the rate of progress in new applications. Chaste is developed using industrially-derived techniques, in particular test-driven development, to ensure code quality, re-use and reliability. In this article we provide examples that illustrate the types of problems Chaste can be used to solve, which can be run on a desktop computer. We highlight some scientific studies that have used or are using Chaste, and the insights they have provided. The source code, both for specific releases and the development version, is available to download under an open source Berkeley Software Distribution (BSD) licence at http://www.cs.ox.ac.uk/chaste, together with details of a mailing list and links to documentation and tutorials.
Citation:
Mirams GR, Arthurs CJ, Bernabeu MO, Bordas R, Cooper J, et al. (2013) Chaste: An Open Source C++ Library for Computational Physiology and Biology. PLoS Computational Biology 9: e1002970. Available: http://dx.doi.org/10.1371/journal.pcbi.1002970.
Publisher:
Public Library of Science (PLoS)
Journal:
PLoS Computational Biology
KAUST Grant Number:
KUK-C1-013-04
Issue Date:
14-Mar-2013
DOI:
10.1371/journal.pcbi.1002970
PubMed ID:
23516352
PubMed Central ID:
PMC3597547
Type:
Article
ISSN:
1553-7358
Sponsors:
This work was funded by: GlaxoSmithKline Grants and Affiliates Award to GRM and DJG; EPSRC e-Science pilot project in Integrative Biology (GR/S72023/01); EPSRC, Software for High Performance Computing project (EP/F011628/1); European Commission, Prediction of Drug Impact in Cardiac Toxicity (preDiCT), Framework 7 grant (DG-INFSO 224381); European Commission, Virtual Physiological Network of Excellence (VPH-NoE), Framework 7 grant (DG-INFSO 223920); 2020 Science: EPSRC and Microsoft Research, Cambridge through grant EP/I017909/1 (www.2020science.net); BBSRC grant to Oxford Centre for Integrative Systems Biology (BB/D020190/1); The Life Sciences Interface and Systems Biology Doctoral Training Centres, and the Systems Approaches to Biomedical Science Industrial Doctorate Centre (EP/E501605/1, EP/G50029/1 and EP/G037280/1). This publication was also based on work supported in part by Award No. KUK-C1-013-04, made by King Abdullah University of Science and Technology (KAUST). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Appears in Collections:
Publications Acknowledging KAUST Support

Full metadata record

DC FieldValue Language
dc.contributor.authorMirams, Gary Ren
dc.contributor.authorArthurs, Christopher Jen
dc.contributor.authorBernabeu, Miguel Oen
dc.contributor.authorBordas, Rafelen
dc.contributor.authorCooper, Jonathanen
dc.contributor.authorCorrias, Albertoen
dc.contributor.authorDavit, Yohanen
dc.contributor.authorDunn, Sara-Janeen
dc.contributor.authorFletcher, Alexander Gen
dc.contributor.authorHarvey, Daniel Gen
dc.contributor.authorMarsh, Megan Een
dc.contributor.authorOsborne, James Men
dc.contributor.authorPathmanathan, Prasen
dc.contributor.authorPitt-Francis, Joeen
dc.contributor.authorSouthern, Jamesen
dc.contributor.authorZemzemi, Nejiben
dc.contributor.authorGavaghan, David Jen
dc.date.accessioned2016-02-21T08:50:27Zen
dc.date.available2016-02-21T08:50:27Zen
dc.date.issued2013-03-14en
dc.identifier.citationMirams GR, Arthurs CJ, Bernabeu MO, Bordas R, Cooper J, et al. (2013) Chaste: An Open Source C++ Library for Computational Physiology and Biology. PLoS Computational Biology 9: e1002970. Available: http://dx.doi.org/10.1371/journal.pcbi.1002970.en
dc.identifier.issn1553-7358en
dc.identifier.pmid23516352en
dc.identifier.doi10.1371/journal.pcbi.1002970en
dc.identifier.urihttp://hdl.handle.net/10754/596776en
dc.description.abstractChaste - Cancer, Heart And Soft Tissue Environment - is an open source C++ library for the computational simulation of mathematical models developed for physiology and biology. Code development has been driven by two initial applications: cardiac electrophysiology and cancer development. A large number of cardiac electrophysiology studies have been enabled and performed, including high-performance computational investigations of defibrillation on realistic human cardiac geometries. New models for the initiation and growth of tumours have been developed. In particular, cell-based simulations have provided novel insight into the role of stem cells in the colorectal crypt. Chaste is constantly evolving and is now being applied to a far wider range of problems. The code provides modules for handling common scientific computing components, such as meshes and solvers for ordinary and partial differential equations (ODEs/PDEs). Re-use of these components avoids the need for researchers to 're-invent the wheel' with each new project, accelerating the rate of progress in new applications. Chaste is developed using industrially-derived techniques, in particular test-driven development, to ensure code quality, re-use and reliability. In this article we provide examples that illustrate the types of problems Chaste can be used to solve, which can be run on a desktop computer. We highlight some scientific studies that have used or are using Chaste, and the insights they have provided. The source code, both for specific releases and the development version, is available to download under an open source Berkeley Software Distribution (BSD) licence at http://www.cs.ox.ac.uk/chaste, together with details of a mailing list and links to documentation and tutorials.en
dc.description.sponsorshipThis work was funded by: GlaxoSmithKline Grants and Affiliates Award to GRM and DJG; EPSRC e-Science pilot project in Integrative Biology (GR/S72023/01); EPSRC, Software for High Performance Computing project (EP/F011628/1); European Commission, Prediction of Drug Impact in Cardiac Toxicity (preDiCT), Framework 7 grant (DG-INFSO 224381); European Commission, Virtual Physiological Network of Excellence (VPH-NoE), Framework 7 grant (DG-INFSO 223920); 2020 Science: EPSRC and Microsoft Research, Cambridge through grant EP/I017909/1 (www.2020science.net); BBSRC grant to Oxford Centre for Integrative Systems Biology (BB/D020190/1); The Life Sciences Interface and Systems Biology Doctoral Training Centres, and the Systems Approaches to Biomedical Science Industrial Doctorate Centre (EP/E501605/1, EP/G50029/1 and EP/G037280/1). This publication was also based on work supported in part by Award No. KUK-C1-013-04, made by King Abdullah University of Science and Technology (KAUST). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.en
dc.publisherPublic Library of Science (PLoS)en
dc.rightsThis is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.en
dc.subject.meshDatabases, Factualen
dc.titleChaste: an open source C++ library for computational physiology and biology.en
dc.typeArticleen
dc.identifier.journalPLoS Computational Biologyen
dc.identifier.pmcidPMC3597547en
dc.contributor.institutionComputational Biology, Department of Computer Science, University of Oxford, Oxford, United Kingdom. gary.mirams@cs.ox.ac.uken
kaust.grant.numberKUK-C1-013-04en

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