A Parameter Estimation task has been added. This allows the user to simultaneously fit the model to data of steady state and time course experiments.
We have added the display of optimization results to the GUI.
Global parameters are available for reaction kinetics, allowing the modification of several kinetic parameters at once.
The plotting capabilities have been enhanced by adding logarithmically scaled plots.
The file dialog has been enhanced by adding navigation buttons as short cuts to home and example directories. In addition All Files (*.*) has been added everywhere to the file type selection.
Sliders are now functional in the Metabolic Control Analysis task.
HTML markup may now be entered in the model description. Please use the "Show Markup" button to access this functionality.
The user can now define explicitly time dependent models. This achieved by allowing time as a variable in the kinetic functions and adding the initial and current time to the model.
A test preventing circular dependencies in function calls has been implemented.
The Householder decomposition method described by Herbert Sauro, et al. is now used for moiety calculation. This results in better performance and accuracy.
The Hooke & Jeeves method has been added for optimization and parameter estimation.
It is now possible to pause the excecution of a task in CopasiUI.
Bug Fixes
A problem importing functions from SBML has been corrected.
The crash caused by importing biomodels.net #43 has been fixed.
A problem with the default absolute tolerance in the deterministic (LSODA) method has been fixed. The result is better performance and less failures caused by exceeding the internal step limit.
Moieties have been added to the object browser to allow access for calculations and reporting.
The input for the compartment volume is now verified to prevent invalid particle numbers and concentrations for metabolites.
Inconsistencies in the display of a metabolite's status have been corrected.
Updates of particle numbers in the single metabolite widget are now handled correctly.
A crash in the slider dialog after changing reaction kinetics has been fixed.
A problem preventing the saving of the result from a time course in the result widget is fixed.
String objects no longer clutter the object browser.
The display of kinetic functions with a plus or minus sign (not operator) imported from SBML has been fixed.
The crash when the model contained unused species is fixed.
The list of the optimization parameters now automatically scrolls to the parameter last added.
The button label in some save file dialog has been corrected from "Open" to "Save".
COPASI switches now to the result display only after a successful task execution.
A problem with the target files for reports and experiment data files in the COPASI file format has been fixed by changing to relative paths.
A crash when changing the compartment for a new metabolite in the multiple metabolite display has been fixed.
