Chaste: incorporating a novel multi-scale spatial and temporal algorithm into a large-scale open source library

• Published in: Philosophical transactions of the Royal Society of London. Series A: Mathematical, physical, and engineering sciences Vol. 367; no. 1895; pp. 1907 - 1930
• Main Authors: Bernabeu, Miguel O., Bordas, Rafel, Pathmanathan, Pras, Pitt-Francis, Joe, Cooper, Jonathan, Garny, Alan, Gavaghan, David J., Rodriguez, Blanca, Southern, James A., Whiteley, Jonathan P.
• Format: Journal Article
• Language: English
• Published: London The Royal Society 28.05.2009
• Subjects: Algorithms; Cardiac Modelling; Computational Biology; Computer Graphics; Computer software; Electrophysiology; Linear systems; Modeling; Models, Biological; Numerical methods; Numerical schemes; Numerical Techniques; Odes; Scientific Computing; Simulations; Software Engineering; User-Computer Interface
• ISSN: 1364-503X; 1471-2962
• DOI: 10.1098/rsta.2008.0309

Recent work has described the software engineering and computational infrastructure that has been set up as part of the Cancer, Heart and Soft Tissue Environment (Chaste) project. Chaste is an open source software package that currently has heart and cancer modelling functionality. This software has been written using a programming paradigm imported from the commercial sector and has resulted in a code that has been subject to a far more rigorous testing procedure than that is usual in this field. In this paper, we explain how new functionality may be incorporated into Chaste. Whiteley has developed a numerical algorithm for solving the bidomain equations that uses the multi-scale (MS) nature of the physiology modelled to enhance computational efficiency. Using a simple geometry in two dimensions and a purpose-built code, this algorithm was reported to give an increase in computational efficiency of more than two orders of magnitude. In this paper, we begin by reviewing numerical methods currently in use for solving the bidomain equations, explaining how these methods may be developed to use the MS algorithm discussed above. We then demonstrate the use of this algorithm within the Chaste framework for solving the monodomain and bidomain equations in a three-dimensional realistic heart geometry. Finally, we discuss how Chaste may be developed to include new physiological functionality-such as modelling a beating heart and fluid flow in the heart-and how new algorithms aimed at increasing the efficiency of the code may be incorporated.