Parameter scans are now available. This was implemented in a very flexible way even allowing for repeats of stochastic simulations (useful to estimate distributions)
A new widget under Biochemical model allows one to see and edit all of the model parameters together, irrespective of their nature (e.g. kinetic constants, volumes, etc.)
Sliders can now work in logarithmic space
COPASI files now keep all of the information about sliders, so that they are recreated every time the file is loaded again.
Trajectories are now allowed to proceed backwards in time with the ODE solver LSODA (not in stochastic simulations, though)
COPASI now displays the file name of the current model on its title bar.
Double-clicking metabolite names in the compartment widget, or reaction names in the metabolite widget now brings up the definition page of the element double-clicked.
A bug appeared in release 12 that would not allow some kinetic parameters to be edited, this has been fixed.
Files saved through the Save as feature, or SBML export were being overwritten without warning to the user; there is now the standard warning.
Deleting a newly created kinetic type would crash Copasi; this no longer happens.
When selecting end time of a trajectory smaller than the beginning time, the program would crash. Now it does either carry out a backward integration (see new features) or warn the user that this is not possible (stochastic methods)
COPASI now warns the user when the COPASIDIR environment variable is not set.
Several minor bugs in table headers were fixed
The time unit chosen by the user was being ignored and second was always displayed. Now COPASI honors the time units specified by the user
In some places COPASI was not displaying units next to numeric values.
Some rare actions on the dialog that creates sliders would crash COPASI.
Slider creation is now more intuitive than previously.
Improved importing some SBML files that would previously crash COPASI.
If a user attempted to read an XML file that is not SBML, COPASI would crash; now it just ignores the file and returns an empty model.
Sample files in the OS X version were not reachable by the users.
Sometimes zooming into a plot would work correctly.
Under some circumstances the plot widget would crash after deleting a metabolite that was included in the plot. This no longer happens
Sometimes the object tree would not be initialized properly
COPASI would crash when loading an SBML file that had no rate laws. Now COPASI warns the user about this but will read the file.
When a user changes a volume, COPASI now keeps the concentration as before and adjust the number of particles to that concentration in the new volume.
If one tried to load an XML file as a COPASI file (.cps) the program would crash.
Selecting the MCA results widget before the MCA calculation was performed would crash COPASI.
COPASI would ask to save a file if elementary mode or mass conservation calculations were required.
If the initial time of a trajectory would not be t=0, COPASI would forget what the value was and reset it to t=0.
Reaction names could be lost if a parameter value was also changed but then not committed. No the name change is not lost.
If a metabolite name was changed in the metabolite widget, the reaction list would not be updated to reflect this metabolite name change. Now this works correctly.
If changes in a slider caused a new simulation to be run, the steady-state or time course results widgets would not be updated with the new results.