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Change History | COPASI (4.0 Build 17 RC 1)

COPASI (4.0 Build 17 RC 1)

Release Candidate 1 (Build 17)

Release Date: February 15, 2006

New Features

  • 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 #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.