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Change History | COPASI 4.16 (Build 104)

COPASI 4.16 (Build 104)

Version 4.16.104

Release Date: August 19, 2015

New Features since COPASI 4.15 (Build 95)

  • Graphical User Interface (CopasiUI)
    • The copy to next feature in the Experimental data description dialog is now able to handle the situation were the target experiment has less columns than the copied one.
  • Simulation Engine
    • The Gamma distribution and the Poisson distribution are now accessible in mathematical expressions and exported to SBML.
  • SBML
    • COPASI now exports the SBML L1V1 legacy format.

Bug Fixes since COPASI 4.15 (Build 95)

  • Graphical User Interface (CopasiUI)
    • The tool "Create Events For Time-series Experiment" does now handle ignored columns correctly.
    • Fix issue where deleting a reaction and running a parameter estimation afterward could cause the initial values to be corrupted.
    • Fixed problem in the tool "Convert to irreversible" which could lead to crashes if a reaction parameter of a reversible reaction was referenced out side the reaction.
    • Fixed handling of HTML entities like — in notes.
    • Improved performance of the "Update MIRIAM" tool.
    • Warning about unknown MIRIAM resources are now only issued when the resource is accessed.
    • All available tasks are now selectable as sub-tasks for the Optimization task.
    • Fixed issue where copying a compartment could lead to a crash in COPASI.
  • Simulation Engine
    • Fixed problem in the Linear Noise Approximation task which occasionally lead to crashes in COPASI.
    • Fixed issue in the Parameter Estimation Task where the un-normalized weight would not be calculated correctly.
    • The recently introduced Persistent Trigger flag for events was not correctly read from files causing the default value to be used.
    • Numerical instability issues in the Metabolic Control Analysis task result in a warning reported to the user.
    • Removed erroneous error messages caused by a premature function compile during when loading a file.
    • Fixed issue were HTML notes not save correctly when the user added the name space manually to the top level element.
    • Renaming an object triggers now an immediate update of the infix of all mathematical expression where the object is referenced.
    • Improved handling of experimental data files for parameter estimation which are not in the same directory as the the COPASI file.
    • Fixed issue where incorrect numerical values for parameter bounds in Optimization or Parameter Estimation would lead to an occasional crash.
  • SBML
    • The import of SBML files previously exported from COPASI does no longer create any warnings.
    • COPASI handles the export of log10 correctly.
    • The import of n-ary relational operators is now correctly handled.
    • Improved handling of incorrect SBML documents on import.
    • Fixed issue where COPASI could crash when loading and SBML file, which contains the same model name as the currently loaded model in COPASI.
  • Source package
    • The python example files are now also compatible with Python 3.x
    • Fixed problems compiling COPASI for the arm architecture.