Chaste: using agile programming techniques to develop computational biology software

Joe Pitt-Francis, Miguel O Bernabeu, Jonathan Cooper, Alan Garny, Lee Momtahan, James Osborne, Pras Pathmanathan, Blanca Rodriguez, Jonathan P Whiteley, David J Gavaghan

Research output: Contribution to journalArticlepeer-review

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.

Original languageEnglish
Pages (from-to)3111-36
Number of pages26
JournalPhilosophical Transactions A: Mathematical, Physical and Engineering Sciences
Volume366
Issue number1878
DOIs
Publication statusPublished - 19 Jun 2008

Keywords

  • Computational Biology
  • Computer Simulation
  • Computer Systems
  • Electrophysiology
  • Heart
  • Humans
  • Models, Cardiovascular
  • Programming Languages
  • Software

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