BeatBox - HPC Environment for Biophysically and Anatomically Realistic Cardiac Simulations

尽管经过了一个多世纪的研究，但人们对心律失常的触发机制知之甚少。即使是现代实验方法也不能提供足够的时间和空间分辨率来追踪心脏组织样本中纤颤的发展，更不用说体内的心脏了。人类遗传学的进步提供了某些基因对细胞活动影响的信息，但不能解释纤维性颤动产生的最终机制。因此，对于一些遗传性心脏病，首先出现的症状是死亡。心脏组织电活动的计算机模拟已经使我们对心脏颤动和心源性猝死的理解有所发展，随着我们接近全心脏建模的最终目标，它们的影响预计会显著增加。模拟动作电位在心脏组织中的传播在计算上是昂贵的，因为每个细胞都需要大量的方程和巨大的空间和时间尺度。这个问题的复杂性包括描述单个细胞通过组织的不均匀性激发到整个心脏的复杂几何结构的离子电流。心脏组织计算模型的及时运行越来越依赖于高性能计算（HPC）的有效使用。目前最先进的心脏模拟工具受到现代，详细模型的可用性或其易用性的限制。当前模型实现的杂乱导致许多研究人员开发他们自己的ad-hoc软件，这既阻碍了他们有效地利用HPC的能力，也阻碍了他们流畅地协作。因此，它阻碍了科学进步。该项目的目的是开发一个高性能计算环境，用于生物物理和解剖学上真实的心脏活动模拟，这是一个可适应和可扩展的框架，高性能计算可以被研究人员利用。

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 have already 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 dependent on the effective use of High Performance Computing (HPC). Current state of the art cardiac simulation tools are limited either by the availability of modern, detailed models, or by their 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, therefore, impeding scientific progress.The aim of this project is to develop an HPC environment for biophysically and anatomically realistic simualtion of cardiac activity, an adaptable and extensible framework with which High Performance Computing may be harnessed by researchers.