Optimization is now available. At this time only with a few algorithms. More algorithms and parameter estimation to appear in the next version.
Command line version CopasiSE (Simulation Engine) is now available. This is useful for executing larger optimization problems in servers without graphical front-ends, and for being called from scripts.
When closing COPASI with an unsaved model, there is now a dialog box asking to confirm closing (allowing the user to cancel and save model if desired).
Improved kinetic function support allowing functions defined in a piecewise manner and with references to other functions.
Improved SBML support and upgrade to libsbml 2.3.2.
Enhanced report definition: user now has access to header and footer of a report; conversion between the old report tables and the new report structure has been implemented.
COPASI now allows users to define global parameters. This allows, for example, to change several kinetic constants simultaneously.
The user can now generate a standard steady state report (text file) with a simple button click.
Program icon was added to the binaries.
COPASI now warns that there are some features in imported SBML files that it does not support.
COPASI now has an autosave capability: model files are saved every 10 minutes.
Bug Fixes
COPASI would crash when doing a stochastic simulation if one of the reactions was a constant flux kinetic type.
If a user would change the Interval Time in the Time Course widget, and then immediately after would run the simulation, COPASI would crash.
A crash would ocurre if a user deleted a report definition and the simulation was still defined to use it. Currently, if a user intends to delete a report, a dialog box informs of the consequences and if the user accepts, all plots that would follow this definition are deleted.
After creating a new model, then switching to the trajectory task widget and then to the compartment widget, COPASI would crash.
When an object was removed but it previously had a slider, then activating the slider dialog would crash COPASI.
If the user specified too small an interval size for output, COPASI would stop with an overflow error.
Read-only files are now correctly handled: only save-as dialog is now displayed (as file cannot be overwritten anyway).
When exporting a model to SBML, the file dialog now has a default file name created from the main model's name.
The timestamp is now correctly written in SBML export files.
COPASI was not reading appropriately some units in SBML files.
The abbreviation for the time unit "minute" was corrected to "min" to adhere to the SI standard.
The activity status of plots is now read correctly from a COPASI file: non-active plots are now not drawn, only plots with active status are displayed.
All the result tables are now read-only.
If a file was saved with the "save as" option, the program would not change the file name displayed to the new file name.
The stochastic integrator was reporting more time points than requested by the user.
The standard time course plot was including fixed metabolite concentrations; this is no longer the case.
In some circumstances the integrator could enter an infinite loop.
Scan widgets did not have a "Task executable" check box.
In some rare circumstances COPASI would not really change the value of a parameter when the user had changed it in a edit box.
The behavior of the object select widget was enhanced.
Results saved to file with the "Save to file" button, are now tab separated files and the column name is more consistent with the table in COPASI.
If the compartment for a metabolite was changed, COPASI would not immediately adjust the concentration of the metabolite.
