COPASI
Release

COPASI 4.4.28 (development) Released

Stefan Hoops: 2008-12-05 02:58:00 +0000

The COPASI team announces the immediate availability of the development release COPASI 4.4.28 (development).

A new development release of COPASI has been made available. Please visit our non-commercial or commercial pages to download the latest development release.

COPASI 4.4.28 (development) has the following new features:

  • Graphical User Interface (CopasiUI)
    • COPASI can display graphical layouts of the reaction network. It is able to overlay simulation results of time courses onto them. Layouts can be imported through SBML files which contain them in the SBML layout extension format.
    • Added 3D bar chart display to all color coded matrices.
    • Enhanced the object selection dialog to support selecting individual matrix elements.
    • COPASI is now able to exchange SBML models with the Systems Biology Workbench. The exchange of models works in both directions.
    • The initial time for autonomous models is set and kept at 0. Autonomous models are models which do not depend explicitly on time, i.e., time does not appear in any rate law, ODE, or assignment.
    • The COPASI specific file dialog has been replaced with the standard dialog of the operating system COPASI is running on.
    • It is now possible to hide or show all curves within one plot by clicking a single button.
    • The results for the optimization task now feature an update button which allows the user to modify the model.
    • Added save button to the result of the elementary flux mode task.
    • Added save button to the parameter overview.
  • Simulation Engine
    • Added time scale separation analysis.
    • We added the capability to use matrix elements in mathematical formulas. This enables e.g. optimization of control coefficients.
    • Scans of optimizations and parameter estimation calculations are now possible.
  • SBML
    • COPASI imports the invalid RDF/XML used in SBML Level 2 Versions 2-3.
    • MIRIAM annotation is now exported to SBML as valid RDF in the COPASI name space in the annotation element and as invalid RDF/XML required in SBML Level 2 Versions 2-3.

In addition several bugs have been fixed, a full list can be found in the changelog.