Metabolites are now called Species, in line with the terminology used in SBML.
The scope of local reaction parameters is now limited to the reaction which defines them. This is in line with the SBML specifications.
Graphical User Interface (CopasiUI)
Improved display and reporting of mass conservation analysis results.
Command Line (CopasiSE)
Added a mass conservation analysis task has been added to the command line version.
Added option --nologo, which suppresses COPASI version and license statement.
Added option --validate, which only validates the input files (CopasiML, Gepasi, or SBML).
SBML
Import SBML Level 1 Version 1, 2 and Level 2 Version 1 - 3.
Export SBML Level 1 Version 2 and Level 2 Version 1 - 3.
Added support for initial assignments.
Bug Fixes
Results
A bug that produced incorrect stochastic simulation results in models with changing volumes has been fixed.
Fixed problem calculating Jacobian and MCA for SBML models whose reaction kinetics were defined without explicit dependence on species (ie through expressions that involved these species).
Fixed numerical problem in stochastic simulations, which could interrupt the integration.
Improved numerical differentiation, which would lead to incorrect results for changing compartment volumes close to zero.
Graphical User Interface (CopasiUI)
Fixed occasional access violation when closing COPASI under Windows.
Fixed problem where changes to local parameter in the reaction display were occasionally ignored.
Models with circular dependencies can now be saved.
The histograms have now the correct bin size for the bin at zero.
The time series displayed in the time course and optimization result does no show the values for the individual task instead of the result of the last executed task.
Changes to the mapping of the kinetic function parameters in the reaction display are now preserved when the reaction is committed.
Changes to the initial particle number of species are now preserved.
The MathML saved in the ODE display is now a valid XML document.
Fixed the scaling of plots, which failed when the first value to be displayed was missing or invalid.
Fixed problem editing initial values when disabling an initial assignment.
Fixed occasional crash when enabling an initial assignment.
Added a column for initial assignments to the tables of compartments, species, and model quantities.
Saving extremely large time series in memory will no longer lead to a crash. Instead an error message will be displayed.
The time series shows now the correct species concentration for models with changing compartment volumes.
Fixed occasional crash occurring when constraints are used in optimization or parameter estimation.
The object selection for constraints show now additionally transient values.
Results are now cleared when a new model is created or loaded avoiding confusion and occasional crashes.
The quantity conversion factor can now be used in initial assignments and has been added to the object selection.
Disabled editing the initial concentration for metabolites where this would lead to circular dependencies due assignment rules for the containing compartment.
Command Line (CopasiSE)
Error messages are now printed to std::error when CopasiSE fails.
The --verbose options prints now all internal messages whether they are errors or not to std::out.
SBML
Fixed problem importing compartments without the volume attribute set from SBML level 1.
Export of models using COPASI's uniform and normal distribution functions will create now proper error messages
Species with the hasOnlySubstanceUnits flag set to true are now handled correctly in kinetic laws.
Fixed problem where every second SBML export failed.
Improved export of models with changing compartment volumes.
Fixed import and export of piecewise defined mathematical expressions.
ODE Export
The C code export of models using COPASI's uniform and normal distribution functions expects the user to provide these functions instead of failing the export.
