COPASI is a package for modeling and simulation of biochemical networks, 
popular in the field of systems biology.

COPASI is a stand-alone program that simulates models of biochemical 
networks using ODE solvers or Gillespie's stochastic simulation 
algorithm.  COPASI is compatible with models in SBML format.  It also 
performs several analyses, such as steady state, stability, parameter 
sensitivity, elementary modes, Lyapunov exponents, optimization, and 
parameter estimation. Data can be visualized in plots, histograms and 
animations of network diagrams.  COPASI's GUI is based on QT, but a 
command line version is also included that allows for processing 
computations in batch mode.

COPASI is a collaboration between research groups at the Virginia 
Bioinformatics Institute, University of Heidelberg, University of 
Manchester and previously in the EML-Research.