Complex Pathway Simulator

Stable version: Version 4.4 (Build 26) released May 8, 2008

What's new in Version 4.4 (Build 26)

Licensing
COPASI is a software application for simulation and analysis of biochemical networks. COPASI is free for Non−Commercial Use. Commercial use of COPASI is available through a Non-Exclusive Software License Agreement. Please see commercial access for details on how to purchase the package online.

Development Releases
We are now offering frequent development releases which can be found in our download area. The latest development version of COPASI is Version 4.2.24 (development) released January 9, 2008. Development versions contain new features and bug fixes. However, they are not as thoroughly tested as stable releases and therefor may be not as reliable.

UPDATED 04/03/2008: COPASI's documentation in PDF format (5.04 Mb) and HTML format.

COPASI paper published:
An article describing COPASI has been published. People who are publishing scientific results obtained with the help of COPASI are asked to reference this paper:

• Hoops, S., Sahle, S., Gauges, R., Lee, C., Pahle, J., Simus, N., Singhal, M., Xu, L., Mendes, P., and Kummer, U. (2006). COPASI — a COmplex PAthway SImulator. Bioinformatics 22, 3067-74.

Current Features:

• 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.
• Analysis:
  • Stochastic and deterministic time course simulation
  • Steady state analysis (including stability).
  • Metabolic control analysis/sensitivity analysis.
  • Elementary mode analysis .
  • Mass conservation 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.
  • Plots and Histograms.
• Command Line (CopasiSE) for batch processing.
• SBML import (L1V1+2, L2V1-3) and export (L1V2, L2V1-3).
• Loading of Gepasi files.
• Export to Berkeley Madonna, XPPAUT, and C source code of the ODE system generated from the model.
• Versions for MS Windows, Linux, Mac OS X, and Solaris SPARC.

Currently known problems:

• COPASI does not run on MS Windows™ 95 (it does run on Win98 and above, though)

	By the Mendes group at VBI and Kummer group at EML Research.
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