BeatBox is a unified cardiac simulation environment that can be used to perform biophysically and anatomically realistic cardiac simulations. BeatBox provides:
BeatBox is free software and is distributed under version 3 (or later) of the GNU public licence.
BeatBox is written in C language and can be run on Unix systems. Once compiled you will not be required to access the C code unless you intend to extend the functionality of BeatBox itself. Instead, you will be able to use BeatBox scripts. Examples and instructions on how to use and write these are included in the documentation bundled in with the distribution.
BeatBox will work on Macs (tested on Leopard and Snow Leopard OS X)
and standard Linux: tested on Fedora and Red Hat Linux, though any
Linux should work. It also works on HECTOR (UK national HPC facility)
and has been tested on a number of other European HPC facilities.
The instructions below are given on the assumption
bash is used; modify them accordingly if you are
using a different command-line shell.
To compile BeatBox you will require:
autoconfpackage to configure BeatBox for your computer (only if you need to change the code substantially).
gcccompiler for the sequential version.
mpicc(MPI parallel) compiler as provided by MPICH or OpenMPI for the parallel version.
In order to use BeatBox for your system you will have to download and compile the distribution but this follows a fairly standard installation procedure assuming your computer satisfies the previously stated requirements.
You can download one of the following distributions:
Unpack this file, say by command
tar xvfz beatbox-1.2.tar.gz(if it is version 1.2 you have downloaded) and follow the instructions in
READMEin the resulting directory (
beatbox-1.2in this example).
Geometries are to be downloaded separately: geometry.tgz
Please let us know how you get on with compiling and running the code and if there are any other improvements we could make to the code to make it easier to use.
If you produce any publications based on the BeatBox code we would be grateful if you could include the following acknowledgement:
M. Antonioletti, V. N. Biktashev, A. Jackson, S. R. Kharche, T. Stary, I. V. Biktasheva, "BeatBox -- HPC Simulation Environment for Biophysically and Anatomically Realistic Cardiac Electrophysiology", PLoS ONE 12(5): e0172292, 2017, DOI: 0.1371/journal.pone.0172292
A quick start guide can be
found also in the the distrbibution bundle as
doc/beatbox_quickstart.html. This contains instructions
on compiling, installing and running the software. There is also a
description of a few simple tests, which can be run without going into
all details of the BeatBox functionality, and which can be used as
templates for other simple simulations.
A more detailed user manual can be found in
doc/beatbox.html which has a more detailed description of
BeatBox and its functionality.
BeatBox is under active developments, and certainly contains many errors and things to improve. We would be very interested to receive any comments and suggestions from the users.
There is BeatBox users mailing list, for the purpose of notification of users of any news from the developers, for feedback from users to the developers and for any Beatbox related discussions. Subscription is free and carries no obligations. You can subscribe by sending an email to firstname.lastname@example.org with an empty subject line and with contents of two lines,
subscribe BEATBOX-USERS Joe Bloggs(don't forget to substitute your name for Joe Bloggs's!) or online, via
https://www.jiscmail.ac.uk/BEATBOX-USERS--- click there on "Subscribe or Unsubscribe" under "Options".
See also the BeatBox Users Workshop materials
You can also contact the developers directly:Vadim Biktashev: V dot N dot Biktashev at exeter dot ac dot uk