Beatbox - A Computer Simulation Environment for Computational Biology of the Heart

Abstract

Despite over a century's study, the trigger mechanisms of cardiac arrhythmias are poorly understood. Even modern experimental methods do not provide sufficient temporal and spacial resolution to trace the development of fibrillation in samples of cardiac tissue, not to mention the heart in vivo. Advances in human genetics provide information on the impact of certain genes on cellular activity, but do not explain the resultant mechanisms by which fibrillation arises. Thus, for some genetic cardiac diseases, the first presenting symptom is death. Computer simulations of electrical activity in cardiac tissue offer increasingly detailed insight into these phenomena, providing a view of cellular-level activity on the scale of a whole tissue wall. Already, advances in this field have led to developments in our understanding of heart fibrillation and sudden cardiac death and their impact is expected to increase significantly as we approach the ultimate goal of whole-heart modelling. Modelling the propagation of Action Potential through cardiac tissue is computationally expensive due to the huge number of equations per cell and the vast spacial and temporal scales required. The complexity of the problem encompasses the description of ionic currents underlying excitation of a single cell through the inhomogeneity of the tissue to the complex geometry of the whole heart. The timely running of computational models of cardiac tissue is increasingly dependant on the effective use of High Performance Computing (HPC), i.e. systems with parallel processors. Current state of the art cardiac simulation tools are limited either by the availability of modern, detailed models, or by their hardware portability or ease of use. The miscellany of current model implementations leads many researchers to develop their own ad-hoc software, preventing them from both utilising the power of HPC effectively, and from collaborating fluidly. It is, arguably, impeding scientific progress. This paper presents a roadmap for the development of Beatbox, a computer simulation environment for computational biology of the heart--an adaptable and extensible framework with which High Performance Computing may be harnessed by researchers.