Antonioletti Mario, Biktashev Vadim N, Jackson Adrian, Kharche Sanjay R, Stary Tomas, Biktasheva Irina V
EPCC, The University of Edinburgh, Edinburgh, United Kingdom.
CEMPS, University of Exeter, Exeter, United Kingdom.
PLoS One. 2017 May 3;12(5):e0172292. doi: 10.1371/journal.pone.0172292. eCollection 2017.
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.
BeatBox模拟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，以便在无需底层重新编码的情况下设置心脏电生理计算机模拟实验，从而使细胞兴奋、组织/解剖模型、刺激方案能够包含在BeatBox脚本中，并且模拟可以顺序运行或并行（MPI）运行而无需重新编译。BeatBox是一个用C语言编写的免费软件，可在基于Unix的平台上运行。它提供了从0维单个细胞模拟、1维纤维、2维薄片和3维组织平板到解剖学上逼真的全心模拟的全谱多尺度组织建模，并具有运行时测量功能，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求解器、细胞以及组织/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框架。在本文中，我们概述了BeatBox的当前状态，并描述了主要的计算方法和MPI并行化方法。
