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.
