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 identifiers.org 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 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.
