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Change History | COPASI 4.9.45 (development)

COPASI 4.9.45 (development)

Version 4.9.45 (Development)

Release Date: January 20, 2013

New Features since 4.8 (Build 35)

  • Graphical User Interface (CopasiUI)
    • The start values and parameter boundaries are now displayed in optimization and parameter estimation results. Boundaries are additionally colored red if the result is very close.
    • If an unknown MIRIAM resource is found the user receives a message with instruction on how to update the MIRIAM resource database.
    • It is now possible to specify the line style and width of curves in a plot.
    • Improved GUI for defining plots
    • "Window" menu for easier access to plot windows
    • Logarithmic axis scaling can now be easily toggled on the plot windows
    • Improved default plots for parameter estimation results
    • Added User Interface for Linear Noise Approximation Task
    • Added User Interface for Cross Section Task
    • Added the capability to add validation data to the parameter estimation task.
    • The location of the last open or save file dialog is no remembered between sessions.
    • SBML documents can now be imported by dragging the file onto CopasiUI.
    • MIRIAM annotation which uses resources are now supported.
    • The web page describing a MIRIAM resource can now be openend in a Web browser by double clicking the entry in the GUI.
    • Method parameters are now remembered while working with one file. This allows easy switching between methods without the need to reenter the customized parameters.
    • Added capability to create an layout the current reaction network.
  • Simulation Engine
    • Added property DisplayName to all objects which allows to create more meaningful column headers in reports.
    • Added Linear Noise Approximation Task
    • Added Cross Section Task (for Poincar√ɬ© type cross sections and bifurcation diagrams)
    • Added min() and max() functions to be used in mathematical expressions.
    • Added indicator functions for finding bifurcation points to the steady state task
    • Added value scaling for parameter estimation
  • SBML
    • Added support for exporting rates of compartments, species and global quantities
    • Export and Import of Level 3 Layout and Render information
    • support for exporting min, max, uniform and normal functions
  • Language Bindings
    • It is now possible to add tool specific annotation in XML format to many entities of the model (compartment, species, reaction, etc.)

Bug Fixes since COPASI 4.8 (Build 35)

  • Graphical User Interface (CopasiUI)
    • The name of an object (compartment, species, reaction etc.) appears now on all widgets associated with it.
    • Boolean expressions entered in places where numerical results are expected are automatically converted to evaluate to 1.0 (true) or 0.0 (false)
    • Fixed crash when moving the last item in a report up.
    • Fixed update button in the steady-state result widget which occasionally could lead to incorrect model updates.
    • On Mac OS double clicking a COPASI file will now correctly open the file.
    • Fixed crash when deleting all reports at once.
    • Fixed problem with sliders where no all dependent initial values were updated before a new simulation was performed.
    • Improved Latex export of names containing underscores and spaces.
    • The tool Convert to Irreversible has been significantly improved to correctly handle modifiers and to avoid duplicate function creation.
    • The tool Convert to Irreversible deals now correctly with situations where the a reaction flux of a reversible reaction is referenced in other expressions.
  • Simulation Engine
    • Some messages were incorrectly labeled as warning messages but caused CopasiSE to stop. These messages are now correctly labeled as errors.
    • Improved handling of start values for optimization and parameter estimation in the CopasiML file.
    • Fixed rare problem in event trigger detection which could lead to firing the same event multiple times without advancing the simulation time.
    • Improved load of CopasiML files with large mathematical expressions.
    • The suppress output feature in the trajectory task now also suppresses output during events.
    • If continue from current state is selected in the scan task the user is warned if initial values are changed which do not have any effect on the current state.
    • The error message created when parsing an invalid expression or function contains now the name of the object so that is easier to determine the location of the problem.
    • Fixed rare problem in event execution due to invalid initialization of the trigger status before integration.
  • SBML
    • Fixed possible crash loading Level 3 files which uses undefined unit ids as model attributes.
    • Improved import performance of files with large MathML expressions
  • Language Bindings
    • It is now possible to set the SBML Id of the model.
    • Fixed possible crash when writing out incomplete models to CopasiML.
    • Fixed crash when accessing a non existing task by name.
    • Report definitions can now be retrieved by name.