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 Biocomplexity
Institute and Initiative  at University of Virginia, University of 
Heidelberg, University of Connecticut, and previously the University
of Manchester, Virginia Tech, and the EML-Research.