Simulation tools

In addition to the simulation abilities of the complete environments there are also some simulation specific tools available.

API Generator for ODE Solution (AGOS)

AGOS is a tool developed at FISIOCOMP, Universidade Federal de Juiz de Fora, Brazil. It provides an on-line tool that automatically builds up an object-oriented C++ class library that allows its users to manipulate and numerically solve Initial Value Problems based on ODE systems described by the CellML and MathML standards. Further information about AGOS can be found in this article.

CellMLSimulator

This is a tool built on top of the C Code Generation Service (CCGS) from the CellML API implementation. It uses the CellML simulation and graphing metadata to decide what simulations need to be performed using the models specified in the metadata and then (optionally) produces the described plots. CellMLSimulator is an open source application developed by David Nickerson and is available from SourceForge.net.

Cell Electrophysiology Simulation Environment (CESE)

CESE is a Java framework for performing computational electrophysiological simulations. See the CESE website for notes on status of CellML support.

Chaste

Chaste is a general purpose simulation package aimed at multi-scale, computationally demanding problems arising in biology and physiology. Current functionality includes tissue and cell level electrophysiology, discrete tissue modelling, and soft tissue modelling. The package is being developed by a team mainly based in the Computational Biology Group at Oxford University Computing Laboratory, and development draws on expertise from software engineering, high performance computing, mathematical modelling and scientific computing.

Chaste uses CellML to specify cardiac ionic cell models, which are automatically translated into optimised C++ code using PyCml.

OpenCMISS

OpenCMISS is a mathematical modelling environment that enables the application of finite element analysis techniques to a variety of complex bioengineering simulations - multi-scale, multi-physics models such as coupling of cardiac electrophysiology, muscle contraction, tissue mechanics and fluid mechanics. Its design takes advantage high performance distributed memory computing hardware. CellML models are used by OpenCMISS to specify parts of the overall model, usually relating to electrophysiology or tissue mechanical properties.  OpenCMISS uses the CellML API to process CellML models. OpenCMISS development is done by international collaboration accross a number of leading institutions in this field.

runMatLabCellML

runMatLabCellML (written by David Cumin, Auckland Bioengineering Institute) — runs a CellML model as exported from COR. To use this utility, first load a CellML model in COR and export it as MatLab.