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BeatBox - HPC Environment for Biophysically and Anatomically Realistic Cardiac Simulations

BeatBox - 用于生物物理和解剖学真实心脏模拟的 HPC 环境

基本信息

批准号：
EP/I029664/2
负责人：
Vadim Biktashev
金额：
$ 16.57万
依托单位：
UNIVERSITY OF EXETER
依托单位国家：
英国
项目类别：
Research Grant
财政年份：
2012
资助国家：
英国
起止时间：
2012 至无数据
项目状态：
已结题

来源：
https://gtr.ukri.org/projects?ref=EP%2FI029664%2F2
关键词：
BeatBox HPC Environment Biophysically Anatomically

项目摘要

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.

尽管经过一个多世纪的研究，心律失常的触发机制仍知之甚少。即使现代实验方法也无法提供足够的时间和空间分辨率来追踪心脏组织样本中颤动的发展，更不用说体内心脏了。人类遗传学的进展提供了有关某些基因对细胞活动影响的信息，但没有解释纤维颤动产生的机制。因此，对于一些遗传性心脏病，首先出现的症状就是死亡。心脏组织电活动的计算机模拟已经促进了我们对心颤和心源性猝死的理解的发展，随着我们接近全心建模的最终目标，其影响预计将显着增加。由于每个细胞有大量方程以及所需的巨大空间和时间尺度，对动作电位通过心脏组织的传播进行建模的计算成本很高。问题的复杂性包括对通过组织的不均匀性到整个心脏的复杂几何形状激发单个细胞的离子电流的描述。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。当前最先进的心脏模拟工具要么受到现代详细模型的可用性，要么受到其易用性的限制。当前模型实现的杂项导致许多研究人员开发自己的临时软件，从而阻碍他们有效利用 HPC 的力量，也无法流畅地协作。因此，它阻碍了科学进步。该项目的目的是开发一个 HPC 环境，用于对心脏活动进行生物物理和解剖学上的真实模拟，这是一个适应性强且可扩展的框架，研究人员可以利用该框架来利用高性能计算。