BeatBox - HPC Simulation Environment for Biophysically and Anatomically Realistic Cardiac Electrophysiology

TL;DR

BeatBox is a versatile, open-source simulation environment enabling detailed, multi-scale cardiac electrophysiology modeling with flexible scripting and parallel computing capabilities, supporting realistic heart simulations without low-level coding.

Contribution

It introduces a flexible, script-based framework for cardiac electrophysiology simulations that integrates multi-scale models and parallel processing, enhancing usability and extensibility.

Findings

Supports multi-scale tissue modeling from cell to whole heart

Provides MPI parallelization for large-scale simulations

Includes tools for electrophysiological data analysis

Abstract

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.