The Mathematical Institute, University of Oxford, Eprints Archive

Chaste: a test-driven approach to software development for biological modelling

Pitt-Francis, J and Pathmanathan, P. and Bernabeu, M O and Bordas, R and Cooper, J and Fletcher, A G and Mirams, G R and Murray, P J and Osbourne, J and Walter, A and Chapman, S. J. and Garny, A. and van Leeuwen, I. M. M. and Maini, P. K. and Rodriguez, B and Waters, S. L. and Whiteley, J. P. and Byrne, H. M. and Gavaghan, D. J. (2009) Chaste: a test-driven approach to software development for biological modelling. Computer Physics Communications, 180 (12). pp. 2452-2471.

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Abstract

Chaste (‘Cancer, heart and soft-tissue environment’) is a software library and a set of test suites for computational simulations in the domain of biology. Current functionality has arisen from modelling in the fields of cancer, cardiac physiology and soft-tissue mechanics. It is released under the LGPL 2.1 licence.

Chaste has been developed using agile programming methods. The project began in 2005 when it was reasoned that the modelling of a variety of physiological phenomena required both a generic mathematical modelling framework, and a generic computational/simulation framework. The Chaste project evolved from the Integrative Biology (IB) e-Science Project, an inter-institutional project aimed at developing a suitable IT infrastructure to support physiome-level computational modelling, with a primary focus on cardiac and cancer modelling.

Item Type:Article
Uncontrolled Keywords:Cardiac electrophysiology; Intestinal crypt simulation
Subjects:A - C > Biology and other natural sciences
Research Groups:Centre for Mathematical Biology
ID Code:846
Deposited By:Philip Maini
Deposited On:11 Nov 2009 07:46
Last Modified:15 Jul 2013 13:54

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