Skip to main content

Chaste: A test−driven approach to software development for biological modelling

D.J.a c Pitt−Francis J.a Pathmanathan P.a Bernabeu M.O.a Bordas R.a Cooper J.a Fletcher A.G.b c Mirams G.R.d Murray P.b Osborne J.M.a c Walter A.b Chapman S.J.b Garny A.d van Leeuwen I.M.M.e Maini P.K.b c Rodríguez B.a Waters S.L.b Whiteley J.P.a b Byrne H.M.f Gavaghan

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. Program summary: Program title: Chaste. Catalogue identifier: AEFD_v1_0. Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AEFD_v1_0.html. Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland. Licensing provisions: LGPL 2.1. No. of lines in distributed program, including test data, etc.: 5 407 321. No. of bytes in distributed program, including test data, etc.: 42 004 554. Distribution format: tar.gz. Programming language: C++. Operating system: Unix. Has the code been vectorised or parallelized?: Yes. Parallelized using MPI. RAM:

Affiliation
Oxford University Computing Laboratory‚ University of Oxford‚ Wolfson Building‚ Parks Road‚ Oxford‚ OX1 3QD‚ United Kingdom; Mathematical Institute‚ 24−29 St. Giles‚ Oxford‚ OX1 3LB‚ United Kingdom; Oxford Centre for Integrative Systems Biology‚ South Parks Road‚ Oxford‚ OX1 3QU‚ United Kingdom; Department of Physiology‚ Anatomy and Genetics‚ University of Oxford‚ Sherrington Building‚ Parks Road‚ Oxford‚ OX1 3PT‚ United Kingdom; Department of Surgery‚ Molecular Oncology Ninewells Hospital‚ University of Dundee‚ Dundee‚ DD1 9SY‚ United Kingdom; School of Mathematical Sciences‚ University of Nottingham‚ University Park‚ Nottingham‚ NG7 2RD‚ United Kingdom
Journal
Computer Physics Communications
Note
cited By 102
Number
12
Pages
2452−2471
Volume
180
Year
2009