Chaste: an open source C++ library for computational physiology and biology.
AuthorsMirams, Gary R
Arthurs, Christopher J
Bernabeu, Miguel O
Fletcher, Alexander G
Harvey, Daniel G
Marsh, Megan E
Osborne, James M
Gavaghan, David J
KAUST Grant NumberKUK-C1-013-04
MetadataShow full item record
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.
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.
SponsorsThis 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.
PublisherPublic Library of Science (PLoS)
JournalPLoS Computational Biology
PubMed Central IDPMC3597547
CollectionsPublications Acknowledging KAUST Support
- CHASTE: incorporating a novel multi-scale spatial and temporal algorithm into a large-scale open source library.
- Authors: Bernabeu MO, Bordas R, Pathmanathan P, Pitt-Francis J, Cooper J, Garny A, Gavaghan DJ, Rodriguez B, Southern JA, Whiteley JP
- Issue date: 2009 May 28
- Cellular cardiac electrophysiology modeling with Chaste and CellML.
- Authors: Cooper J, Spiteri RJ, Mirams GR
- Issue date: 2014
- Chaste: using agile programming techniques to develop computational biology software.
- Authors: Pitt-Francis J, Bernabeu MO, Cooper J, Garny A, Momtahan L, Osborne J, Pathmanathan P, Rodriguez B, Whiteley JP, Gavaghan DJ
- Issue date: 2008 Sep 13
- On-lattice agent-based simulation of populations of cells within the open-source Chaste framework.
- Authors: Figueredo GP, Joshi TV, Osborne JM, Byrne HM, Owen MR
- Issue date: 2013 Apr 6
- Verification of computational models of cardiac electro-physiology.
- Authors: Pathmanathan P, Gray RA
- Issue date: 2014 May