COPASI
Release

COPASI 4.10 (Build 55) Released

Stefan Hoops: 2013-05-16 05:58:00 +0000

The COPASI team announces the immediate availability of the stable release COPASI 4.10 (Build 55).

A new development release of COPASI has been made available. Please visit our free download page to retrieve this latest development release. Please note this version is released under the Artistic License 2.0, which is an OSI approved license. This license allows non-commercial and commercial use free of charge. This release is mainly a bug fix release which increases the stability and usability of COPASI. It therefore contains only few new features.

New features since the previous stable release:

New Features since 4.8 (Build 35)

  • Graphical User Interface (CopasiUI)
    • The start values and parameter boundaries are now displayed in optimization and parameter estimation results. Boundaries are additionally colored red if the result is very close.
    • If an unknown MIRIAM resource is found the user receives a message with instruction on how to update the MIRIAM resource database.
    • It is now possible to specify the line style and width of curves in a plot.
    • Improved GUI for defining plots
    • “Window” menu for easier access to plot windows
    • Logarithmic axis scaling can now be easily toggled on the plot windows
    • Improved default plots for parameter estimation results
    • Added User Interface for Linear Noise Approximation Task
    • Added User Interface for Cross Section Task
    • Added the capability to add validation data to the parameter estimation task.
    • The location of the last open or save file dialog is no remembered between sessions.
    • SBML documents can now be imported by dragging the file onto CopasiUI.
    • MIRIAM annotation which uses identifiers.org resources are now supported.
    • The web page describing a MIRIAM resource can now be openend in a Web browser by double clicking the entry in the GUI.
    • Method parameters are now remembered while working with one file. This allows easy switching between methods without the need to reenter the customized parameters.
    • Added capability to create an layout the current reaction network.
  • Simulation Engine
    • Added property DisplayName to all objects which allows to create more meaningful column headers in reports.
    • Added Linear Noise Approximation Task
    • Added Cross Section Task (for Poincaré type cross sections and bifurcation diagrams)
    • Added min() and max() functions to be used in mathematical expressions.
    • Added indicator functions for finding bifurcation points to the steady state task
    • Added value scaling for parameter estimation
  • SBML
    • Added support for exporting rates of compartments, species and global quantities
    • Export and Import of Level 3 Layout and Render information
    • support for exporting min, max, uniform and normal functions
    • Enabled export of models which use initial values of species, compartments or global quantities in mathematical expression.
  • Language Bindings
    • It is now possible to add tool specific annotation in XML format to many entities of the model (compartment, species, reaction, etc.)

A list of resolved issues can be found in the changelog for this release