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COPASI 4.5 (Build 30)
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COPASI 4.4.29 (development)

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Complex Pathway Simulator

Stable version: COPASI 4.5 (Build 30) released April 14, 2009
What's new in Version 4.5 (Build 30)
Development version: COPASI 4.4.29 (development) released January 5, 2009
What's new in Version 4.4.29 (development)

COPASI is a software application for simulation and analysis of biochemical networks and their dynamics. COPASI is a stand-alone program that supports models in the SBML standard and can simulate their behavior using ODEs or Gillespie's stochastic simulation algorithm; arbitrary discrete events can be included in such simulations. COPASI also carries out several analyses of the network and the dynamics, such as steady state stability, parameter sensitivity, elementary flux modes, Lyapunov exponents. Any feature of a model can be optimized using a variety of diverse non-linear optimization algorithms. Parameter values can be estimated from data using a very customizable framework. COPASI is available in two versions: a graphical user interface (CopasiUI) and a command line version (CopasiSE) that only contains the calculation engine. COPASI provides means to visualize data in customizable plots, histograms and animations of network diagrams.

Licensing

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 4.4.29 (development) released January 5, 2009. 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 04/19/2009: COPASI's documentation in PDF format (4.42 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.
    • 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.
    • 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.

We keep a list of currently known problems in COPASI.


By the Mendes group at VBI and Kummer group at Heidelberg University.
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Created by: system. Last Modification: Wednesday 27 of January, 2010 09:45:02 EST by sven.