BeatBox-HPC simulation environment for biophysically and anatomically realistic cardiac electrophysiology.
BeatBox-HPC simulation environment for biophysically and anatomically realistic cardiac electrophysiology.
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DOI：
10.1371/journal.pone.0172292
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发表时间：
2017
期刊：
影响因子：
3.7
通讯作者：
Biktasheva IV
中科院分区：
文献类型：
--
作者：
Antonioletti M;Biktashev VN;Jackson A;Kharche SR;Stary T;Biktasheva IV
BeatBox 仿真环境将灵活的脚本语言用户界面与强大的计算工具相结合，以便设置心脏电生理学计算机模拟实验，而无需在低级别重新编码，从而可以将细胞激发、组织/解剖模型、刺激协议包含在 BeatBox 脚本中，并且可以顺序或并行 (MPI) 运行仿真，而无需重新编译。 BeatBox 是一款用 C 语言编写的免费软件，可在基于 Unix 的平台上运行。它提供全方位的多尺度组织建模，从 0 维单个细胞模拟、1 维纤维、2 维薄片和 3 维组织板，一直到解剖学上真实的整个心脏模拟，并提供运行时测量，包括心脏折返尖端/细丝追踪、心电图、任何变量的局部/全局样本等。BeatBox 解算器、细胞和组织/解剖模型 存储库通过强大而灵活的接口进行扩展，从而为该领域的新发展提供了一个开放的框架。在本文中，我们概述了 BeatBox 当前状态，并描述了主要计算方法和 MPI 并行化方法。
The BeatBox simulation environment combines flexible script language user interface with the robust computational tools, in order to setup cardiac electrophysiology in-silico experiments without re-coding at low-level, so that cell excitation, tissue/anatomy models, stimulation protocols may be included into a BeatBox script, and simulation run either sequentially or in parallel (MPI) without re-compilation. BeatBox is a free software written in C language to be run on a Unix-based platform. It provides the whole spectrum of multi scale tissue modelling from 0-dimensional individual cell simulation, 1-dimensional fibre, 2-dimensional sheet and 3-dimensional slab of tissue, up to anatomically realistic whole heart simulations, with run time measurements including cardiac re-entry tip/filament tracing, ECG, local/global samples of any variables, etc. BeatBox solvers, cell, and tissue/anatomy models repositories are extended via robust and flexible interfaces, thus providing an open framework for new developments in the field. In this paper we give an overview of the BeatBox current state, together with a description of the main computational methods and MPI parallelisation approaches.