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Change History | COPASI 4.0 (Build 18)

COPASI 4.0 (Build 18)

Version 4.0 (Build 18)

Release Date: June 16, 2006

New Features

  • Added task to calculate the Lyapunov exponent via the Wolf method.
  • Enabled scanning for MCA and Lyapunov exponent.
  • Added two hybrid simulation methods for calculating a Time Course.
  • Added two new optimization methods Levenberg-Marquardt and Evolutionary Strategies (SRES).
  • Redesign Optimization and Parameter Estimation widget to enable creation and editing of multiple parameters and constraints while simultaneously displaying the information for more condensed.
  • The objective function editor has been greatly enhanced.
  • The description of experimental data for Parameter Estimation can now copied to other experiments within one data file.
  • The GUI now displays the results of Parameter Estimation, which also can be saved from there.
  • Added plotting of fitted values and errors for Parameter Estimation.
  • Implemented logarithmically scaled plots.
  • Added a list last visited files, which can be found under the file menu.
  • Implemented export of Berkeley Madonna files and C source code. This feature is also accessible from the command line.
  • The parameter overview allows now changing of global parameters.
  • Implemented MathML rendering of kinetic functions and ODEs. The later may also be saved in MathML.
  • Added SBML support for non-autonomous models.
  • Made method parameters more human readable.

Bug Fixes

  • Fixed plotting and reporting for Scan.
  • The slider window behaves more civilized, it no longer stays on top.
  • The warning and error message handling has been fixed, i.e., no more spurious messages.
  • Fixed problem loading Gepasi file including metabolites named "PI".
  • When closing the application hitting cancel in the save dialog prevents COPASI from exiting.
  • Fixed problem leaving the GUI in a non functional state when deleting the last compartment, metabolite, reaction, or plot.
  • Fixed import of SBML containing NaN in the MathML.
  • Fixed problem editing and displaying the comment for the model.
  • Fixed resizing behavior in object selection widget.
  • COPASI no longer refuses to do Parameter Estimation of steady state experiments for non-autonomous models, instead it issues a warning.
  • Fixed SBML export of files with substance unit set to items (see FAQ).
  • Fixed crash in reaction widget when a function variable was not correctly mapped.
  • Default reports are associated with the correct task, for which they are intended.
  • Fixed crash in Parameter Estimation when the experimental data description is incorrect. Instead appropriate messages are created indicating the exact problem.
  • The Optimization widget now contains the previously missing update model check box.