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Change History | COPASI 4.28 (Build 226)

COPASI 4.28 (Build 226)

Version 4.28.226

Release Date: June 12, 2020

New Features since COPASI 4.27 (Build 217)

  • Graphical User Interface (CopasiUI)
    • Performance improvements while switching to tables of species and reactions or the parameter overview for large models through deferred loading.
    • Added line numbers to table of items in the report definition widget.
    • It is now possible to add/merge SBML models to the currently loaded model.
    • It is no possible to change the order of plot items and thus controlling the order in the legend.
  • Simulation Engine
    • Added additional convergence criterion to the steady state calculation. The user can chose between distance, rate, or both (default).
    • Added advanced parameter to the Levenberg Marquardt method adjusting the step increase/decrease strategy.
  • Language Bindings
    • The model analyzing tool is now available.

Bug Fixes since COPASI 4.27 (Build 217)

  • Graphical User Interface (CopasiUI)
    • Fixed problem where changing species concentrations in the parameter overview was not updated in the model.
    • The working directory is now correctly updated when saving a file to a different location.
    • Avoid race condition during model load or import through drag and drop which occasionally caused a crash.
    • Added option to disable automatic resizing of table columns to decrease time to display.
    • Fixed header display in the parameter table of the optimization and parameter estimation tasks.
    • Fixed issue where the display of MIRIAM annotation could cause a crash after a new models is loaded.
    • Fixed undo of MIRIAM annotation for species. reactions, compartments, etc.
    • Fixed crash when switching a species, compartment, or global quantity with a noise term assigned to no longer be of simulation type ODE.
    • Fixed crash caused by saving of existing plots after another model has been loaded into COPASI.
    • Fixed editing of multiple plot item simultaneously.
    • Fixed edition of the event flag persistent.
    • Changing the kinetic law unit type in the reaction widget was not recognized in computational model until the next model compile.
    • Model volume changes were not correctly reflected in the compartment details widget.
    • Fixed uncaught error when editing the comment in a report definition.
    • Fixed occasional crash when deleting sliders which refer to no longer existing elements.
    • Fixed sorting of tables by numeric values including NaN.
    • Improved display of steady state results.
    • Fixed problem adjusting the initial time for non autonomous models.
    • Fixed occasional issue when applying a parameter set containing non local reaction parameters.
    • Fixed crash when deleting all events simultaneously.
    • Saving the sensitivity results contains now also the summary table.
  • Simulation Engine
    • Avoid incorrect error messages about recursive dependencies.
    • Fixed issue where incorrect COPASI files could cause a crash due to missing attributes of type enum.
    • Fixed issue where occasionally the parameters of the time series sensitivities task where not correctly read back from the COPASI file.
    • Fixed problem where an error during parameter scan would cause the subsequent scan parameter to no be correctly updated and thus leading incorrect results.
    • Added Root Mean Square (RMS) and Standard Deviation to the values selectable for plots and reports.
  • SBML
    • Fixed problem exporting the Avogadro constant.
    • Improved handling of malformed MIRIAM annotations which could COPASI to hang on import.
  • SED-ML
    • Fixed issue exporting plots of species without an SBML name.