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basiCO: A simplified python interface to COPASI
CoRC: the COPASI R Connector
Piecewise parameter fitting
| COPASI (4.0 Build 17 RC 1)
COPASI (4.0 Build 17 RC 1)
Release Candidate 1 (Build 17)
Release Date: February 15, 2006
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.
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
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
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.
preventing circular dependencies
in function calls has been implemented.
Householder decomposition method
described by Herbert Sauro, et al. is now used for moiety calculation. This results in better performance and accuracy.
Hooke & Jeeves
method has been added for optimization and parameter estimation.
It is now possible to
pause the excecution
of a task in CopasiUI.
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.