Andre's CellML Software

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This is a project for Andre to share CellML related tools he works on that other people might find useful.



Related Projects


IDL specified API for manipulating and processing CellML 1.0 and 1.1. Includes C++ implementation. Accessible from a C++ program, or from any language for which a CORBA language mapping is available Also, a Java wrapper of the API is available.


OpenCell is a user interface for working with CellML models. Features: * Integrate models made up of ODEs. * Supports CellML 1.0 and 1.1, allowing you to build complex models using imports. * Plot and edit graphs. * And more ...

Biological Pathway Exchange Language

A Data Exchange Format for Biological Pathway Information

Cellmlviewer - A framework for visualizing annotated biological and biophysical concepts covered in

CellML is an implementation-independent simulation modelling language which is mainly used for understanding the dynamics of complex biological processes. Even though the CellML model structure and mathematics provide a powerful method for describing the dynamics of biological processes, the language has limited support for capturing higher level biological information. The biological knowledge is implicit in the mathematics and structure of the model. The objective is to develop a framework for

Dougal-cellml - Dougal's CellML workspaces

For working on CellML models within Hg, outside of the Physiome Model Repository

Cellml-test-models - Some models that are useful for testing CellML and related tools

Models for testing CellML and CellML tools. For example, models with known analytical solutions, that can be used for validating numerical solution approaches.

Cellml-spec-git1 - Mirror of CellML spec v1.2 source

CellML is a standard for representing mathematical models, based significantly on the use of MathML.

Black-box-cellml - Code for working with CellML models with embedded machine learning components

Code for working with CellML models with embedded machine learning components. This is based off the draft best current practice document available at The source code is stored in git. You can view view the project in gitweb at

Simengine - Faster ODEs in MATLAB for multi-core and CUDA GPUs with simEngine

Faster ODEs for multi-core and CUDA GPUssimEngine is the faster and easier way to solve nonlinear dynamical systems with MATLAB. simEngine combines intuitive expression of differential equation-based systems with highly optimized compiled code to produce simulation executables that perform up to 10× faster than MATLAB’s standard ODE solvers. simEngine also creates “embarrassingly parallel� simulations for multi-core and GPU hardware automatically. With simEngine you'll be able to do more

cellml-core-spec - CellML Core Specification Draft Development

CellML Core Specification Draft Development