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Change History | COPASI 4.25 (Build 207)

COPASI 4.25 (Build 207)

Version 4.25.207

Release Date: March 15, 2019

New Features since COPASI 4.24 (Build 197)

  • Graphical User Interface (CopasiUI)
    • 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.