COPASI: feature list

• Model:
  • Chemical reaction network.
  • Arbitrary kinetic functions.
  • ODEs for compartments, species, and global quantities.
  • Assignments for compartments, species, and global quantities.
  • Initial assignments for compartments, species, and global quantities.
  • SBML import (L1V1+2, L2V1-4) and export (L1V2, L2V1-4).
• Analysis:
  • Stochastic and deterministic time course simulation
  • Steady state analysis (including stability).
  • Metabolic control analysis/sensitivity analysis.
  • Elementary mode analysis .
  • Mass conservation analysis.
  • Time scale separation analysis
  • Calculation of Lyapunov exponents.
  • Parameter scans.
  • Optimization of arbitrary objective functions.
  • Parameter estimation using data from time course and/or steady state experiments simultaneously.
• Graphical User Interface (CopasiUI)
  • Sliders for interactive parameter changes.
  • Color-coded tables
  • 3D bar charts
  • Plots and Histograms.
  • Network diagram visualization of results.
• Command Line (CopasiSE) for batch processing.
• Versions for MS Windows, Linux, Mac OS X, and Solaris SPARC.
• Loading of legacy Gepasi files.
• Export to Berkeley Madonna, XPPAUT, and C source code of the ODE system generated from the model.
• Saving of mathematical formulas and ODEs in MathML or LaTeX

We keep a list of currently known problems in COPASI.

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