BeatBox-HPC simulation environment for biophysically and anatomically realistic cardiac electrophysiology

Area of Science:

• Computational Biology
• Biophysics
• Cardiovascular Research

Background:

• Cardiac electrophysiology research requires sophisticated simulation tools.
• Existing tools may necessitate low-level coding for complex experimental setups.
• Multi-scale modeling from cellular to whole-organ levels is crucial.

Purpose of the Study:

• To present the BeatBox simulation environment for cardiac electrophysiology.
• To detail its capabilities for in-silico experimental setup and execution.
• To describe its computational methods and parallelization strategies.

Main Methods:

• BeatBox utilizes a flexible script language interface and robust computational tools.
• It supports multi-scale modeling (0D to 3D) and anatomically realistic whole-heart simulations.
• Parallel processing via Message Passing Interface (MPI) is integrated for enhanced performance.

Main Results:

• BeatBox allows in-silico experiments without low-level recoding.
• It accommodates various components: cell excitation, tissue models, and stimulation protocols.
• Runtime measurements include cardiac re-entry tracing, ECG, and variable sampling.

Conclusions:

• BeatBox provides an open, flexible framework for cardiac electrophysiology research.
• Its multi-scale capabilities and ease of use facilitate new developments.
• The environment supports efficient, parallelized simulations on Unix-based platforms.