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Change History | COPASI (4.0 Build 14 test version)

COPASI (4.0 Build 14 test version)

COPASI (4.0 Build 14 test version)

Release Date: August 30, 2005

New Features

  • 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.
  • Slider behavior was enhanced.