If you check the SBML software guide, you will find a bunch of programs that simulate ODE models in SBML. It is good to see a complete list, but most people would just like to use one of them. Choosing between these many programs is really a pain. I have experienced the pain and want to help others a little bit.

Choosing the SBML Simulator

My demands

I do not need a command-line tool because I already have my C library or the open-source library GSL to do that. I want to use a program with GUI, allowing me to see the graphical time-course output and to change parameters conveniently.


The SBML software guide provides a fairly complete list of available ODE simulators that are compatible with SBML. The SBW group present comparisons between several solvers, which focus on the robustness and accuracy of a program rather than on efficiency. That page further links to two other comparisons, one by the VCell group (feature comparison) and the other by the BioUML group. The google search may eventually direct you to these slides which may give you an idea on the efficiency.

My experiences

After going through these pages, I decide to try two programs: CellDesigner (using SOSlib) and Copasi. BioUML and ByoDyn also look good, but BioUML require Java6 which I have not installed and ByoDyn is a bit difficult to install as it requires several libraries.

CellDesigner and Copasi are generally comparable in features, accuracy and speed. While CellDesigner may be more friendly to biologists, Copasi is powerful in mathematical tools. For a person, like me, who focus on the mathematical aspect of the model, copsi is clearly the better choice.