Added capability to load and save model parameter sets from files.
Moiety results are now displayed according to the framework, i.e. in amount units or particle numbers.
Added default report moiety task
Advanced rarely used method parameters are no hidden if they are at default setting. The user can
change this behavior through the preference dialog.
Combine archive are can now be opened via drag and drop like all other supported formats.
Added additional plot type supporting banded graphs.
Added the capability to open files directly from an URL under the file menu.
Added Lyapunov exponents to the selectable result in the object selection widget.
Command-line (CopasiSE)
Added option to convert the model reactions to irreversible
Added option to specify the task to be executed
Added option to override the report file name to be used.
Language Bindings
The sed-ml and combine archive functionalities are now exposed in the language bindings.
Bug Fixes since COPASI 4.24 (Build 197)
Graphical User Interface (CopasiUI)
Improved layout model check display to show filter capabilites without scrolling.
The linear noise approximations task has now steady-state analysis enable by default.
Experiment settings for parameter estimation can now be copied to several experiments in one step.
Fix crashed which occasionally happened when deleting events.
Fixed several instability issues encountered when merging the same model multiple times.
Fixed issue with raising secondary windows (plots) on Mac OS
Fixed crash when selecting an incomplete parameter set for display.
Fixed problem updating the MIRIAM resources.
Fixed the 'edit rate law' button in the reaction widget to again switch to selected function.
Fixed handling of names which are only comprised of digits.
Fixed layout of optimization parameter estimation tasks to give mor space to the optimization parameters.
Fixed initial display of concentration value when adding a missing species to a parameter set.
Fixed crash when selecting a result matrix for plotting.
Fixed race condition in the slider dialog which could lead to losing slider definitions.
The backward integration strategy is disabled now disabled by default for steady-state tasks.
Default slider ranges changed to 10 times the current value and logarithmic scaling.
The progress dialog is now re-sizable.
Fixed issue where COPASI hang during unit validation in rare cases.
Ignore NaN values in count of values when scaling histogram.
Simulation Engine
Added verbose log messages to all optimization methods. These verbosity can be set through an advanced
method parameter.
Increased default internal step limit 100,000 in the LSODA deterministic integration method.
Improved detection whether the model is autonomous for edge cases where the ODE system was not
time dependent but some assignments not used in the calculation were.
Fixed stability issues with the SDE solver (RI5)
Fixed issue in the hybrid RK54 integration method leading to exceeding the internal step size.
Fixed issue in the generation of result distributions in the hybrid RK54 method when the stochastic
system was very fast, i.e., advanced in very small steps.
SBML
Fixed import of multi-compartment reaction where the compartments have the spatial dimension 0.
Allow import of models with broken function definitions. The broken function is ignored and
the user is warned about the missing function only if it is used within the model.
Fixed SBML error message (78) about differences between the substance units used and the global
default substance unit which is no longer required.
Fixed export of render information which used the numeric value NaN for unspecified attributes.
Dependencies
Updated libCombine to fix invalid manifests
SED-ML
Fixed import of files using change-attribute to modify the referenced model.
Language Bindings
It is no possible to add a second model to an already loaded model, i.e., model merging is supported.
