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Change History | COPASI (4.0 Build 13 test version)

COPASI (4.0 Build 13 test version)

COPASI (4.0 Build 13 test version)

Release Date: April 28, 2005

New Features

  • 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.

Bug Fixes

  • 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.