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Change History | COPASI 4.20 (Build 158)

COPASI 4.20 (Build 158)

Version 4.20.158

Release Date: July 31, 2017

New Features since COPASI 4.19 (Build 140)

  • Graphical User Interface (CopasiUI)
    • It is now possible to export the rendered mathematical expressions to a PDF document.
    • The application window remembers the size of the window and the with of the left browser pane to avoid frequent adjustment by the user.
    • Plots can now be activated and deactivated in the plot itself.
    • When an experimental data file is not found at the expected location COPASI allows now specify a new location by opening a file open dialog.
  • Simulation Engine
    • The Avogadro symbol can now be used in user defined functions.

Bug Fixes since COPASI 4.19 (Build 140)

  • Graphical User Interface (CopasiUI)
    • Changing the quantity unit is now reflected in plots for which data new data is generated after the change.
    • Name changes in newly created plots and report are now properly propagated.
    • Fixed a problem which prevented the changing of the rate law for reactions.
    • Fixed a problem which prevented setting the initial state to the current state of the model through by pressing the S -> IS button.
    • Fixed problem which caused reactions to loose parameter mapping for species when the species had been renamed.
    • The scaling compartment is now correctly displayed in the ODEs.
    • Stead-State analysis result are no longer editable by the user.
    • The units of model can now be entered directly by the user instead of being limited by the selection available in the combo boxes.
    • Fixed crash when changing a rate law while sliders associated with reaction parameters were displayed.
    • Saving a model right after entering an initial assignment for a species without committing the changes lead to an inconsistency when loading the file. The assignment was correctly loaded however the outdated initial value was not recalculated.
    • Improved the undo/redo functionality to better record and apply the changes done by the user.
    • Improved graphics quality and Mac-OS with retina display.
    • Prevented crash when attempting to set the start value of parameters in the optimization and parameter estimation task based on current solution values occurring when no current solution was found.
  • Simulation Engine
    • Prevent crash occurring when attempting to access result matrix elements which are not existing.
    • When loading a COPASI while with a broken parameter mapping for species in a reaction COPASI recovers automatically.
    • Prevented crash of models with discontinuities that where triggered by the condition during time course execution.
    • Fixed an issues in the parameter estimation task where constraints where in some cases constraints where not correctly evaluated.
    • Fixed a problem where empty reactions could cause a crash during undo.
    • Improved restart after a discrete event did not change the model state to prevent detecting the same event twice.
    • Fixed scaling problem of MCA result caused by the addition of the summation theorem error check column.
    • Prevent problem where in some situations during stochastic simulations with discrete events COPASI did no longer proceed.
    • Fixed a problem where an event assignment changing an infinite value to a finite value was not propagated to the integrator.
    • Improved stability of the time scaling separation analysis.
  • SBML
    • Fix problem which prevented opening an SBML file through the open dialog or drag and drop.
    • Fixed an issue where SBML export and subsequent SBML import changed the model behavior of reactions whose modifiers where in different compartment than substrates and products.
    • Corrected the export of the scaling compartment in the case where the user choose non-default behavior for a multi-compartment reaction.
    • Constraints are now correctly listed in the default report for parameter estimation.
  • SED-ML
    • Fixed export of reactions which had parenthesis in the reaction name.
    • Improved import and export of time course description to properly handle output start times different from the initial time.
    • Improved export of plots so that they can be unique associated with an analysis task.
  • ODE Export
    • Fixed problem where not all local rection parameters where exported.