bmoreau/copasi

COPASI is a software application for simulation and analysis of biochemical networks and their dynamics.

COPASI: biochemical network simulator

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 carries out several analyses of the network and its dynamics and has extensive support for parameter estimation and optimization. COPASI provides means to visualize data in customizable plots, histograms and animations of network diagrams. (list of features).

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Download COPASI

Precompiled versions of COPASI are available for all operating systems on the COPASI Homepage.

Building COPASI

COPASI's sources are available from our github repository. These sources are written in standard C++ and will compile on Linux, OS X and Windows.

Dependencies

To start compiling COPASI we recommend to use the copasi-dependencies package.The dependency package compiles all the dependencies necessary for COPASI, they include clapack, cppunit, expat, raptor libSEDML, libsbml, SBW as well as the Qt libraries QWT, QWT3D and the Qt MML widget. Instructions for building the dependencies are described here:

• General Instructions
• Linux build instructions

Compiling COPASI

Once the dependencies have been built, COPASI is easily compiled using CMake:

git clone https://github.com/copasi/COPASI
mkdir build_copasi
cd build_copasi
cmake -DBUILD_GUI=OFF -DCMAKE_INSTALL_PREFIX=~/copasi -DCOPASI_DEPENDENCY_DIR=../copasi-dependencies/bin ../COPASI
make
make install 

In the above ../copasi-dependencies is the location of the compiled copasi-dependencies project. The option BUILD_GUI=OFF builds only the command line version of COPASI (aka CopasiSE). To build the graphical frontend (aka CopasiUI), and having Qt 4 installed, the option would need to be BUILD_GUI=ON. The option CMAKE_INSTALL_PREFIX=~/copasi specifies, that COPASI ought to be installed in the current users home directory in a subfolder copasi.

There are many more compile options available, options for building the language bindings as well as options to enable some experimental features that are not yet available in the stable builds that are released publicly. To view the complete set of options, start the graphical cmake frontend in the continuing from the above command this would be done with:

cmake-gui ../COPASI

Feedback

To submit feedback, or bug reports, please use the COPASI Tracker, or our mailing list.

License

The packages available on this page are provided under the Artistic License 2.0, which is an OSI approved license. This license allows non-commercial and commercial use free of charge.