Chaste: using agile programming techniques to develop computational biology software.

Full Abstract

Cardiac modelling is the area of physiome modelling where the available simulation software is perhaps most mature, and it therefore provides an excellent starting point for considering the software requirements for the wider physiome community. In this paper, we will begin by introducing some of the most advanced existing software packages for simulating cardiac electrical activity. We consider the software development methods used in producing codes of this type, and discuss their use of numerical algorithms, relative computational efficiency, usability, robustness and extensibility. We then go on to describe a class of software development methodologies known as test-driven agile methods and argue that such methods are more suitable for scientific software development than the traditional academic approaches. A case study is a project of our own, Cancer, Heart and Soft Tissue Environment, which is a library of computational biology software that began as an experiment in the use of agile programming methods. We present our experiences with a review of our progress thus far, focusing on the advantages and disadvantages of this new approach compared with the development methods used in some existing packages. We conclude by considering whether the likely wider needs of the cardiac modelling community are currently being met and suggest that, in order to respond effectively to changing requirements, it is essential that these codes should be more malleable. Such codes will allow for reliable extensions to include both detailed mathematical models--of the heart and other organs--and more efficient numerical techniques that are currently being developed by many research groups worldwide.

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Author information

Author/s: Pitt-Francis, Joe (J); Bernabeu, Miguel O (MO); Cooper, Jonathan (J); Garny, Alan (A); Momtahan, Lee (L); Osborne, James (J); Pathmanathan, Pras (P); Rodriguez, Blanca (B); Whiteley, Jonathan P (JP); Gavaghan, David J (DJ);

Affiliation: Oxford University Computing Laboratory, Wolfson Building, University of Oxford, Parks Road, Oxford OX1 3QD, UK. joe.pitt-francis(-atsign-)comlab.ox.ac.uk

Grants: BB/E024955/1 (Agency:United Kingdom Biotechnology and Biological Sciences Research Council) ; G0700278 (Agency:United Kingdom Medical Research Council)

Journal and publication information

Publication Type: Journal Article; Research Support, Non-U.S. Gov't

Journal: Philosophical transactions. Series A, Mathematical, physical, and engineering sciences (Philos Transact A Math Phys Eng Sci), published in England. (Language: eng)

Reference: 2008-Sep; vol 366 (issue 1878) : pp 3111-36

Dates: Created 2008/07/28; Completed 2008/09/30;

PMID: 18565813, status: MEDLINE (last retrieval date: 11/6/2008)

Sourced from the National Library of Medicine. Abstract text and other information may be subject to copyright.

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MeSH headings (categories)

This article was linked to the MESH Headings shown below.

Computational Biology - statistics & numerical data
Computer Simulation
Computer Systems
Electrophysiology
Heart - physiology

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