COPASI 4.30 (Build 240)

Version 4.30.240

Release Date: February 24, 20201

New Features since COPASI 4.29 (Build 228)

• Graphical User Interface (CopasiUI)
  • Added intensive reaction flux to the steady-state results relevant for small compartments.
• Simulation Engine
  • Added Just In Time compilation of all user defined mathematical expression to assembler code significantly improving COPASI's performance.
• Language Bindings
  • It is now possible to capture data generated from tasks directly without using a temporary file.

Bug Fixes since COPASI 4.29 (Build 228)

• Graphical User Interface (CopasiUI)
  • Loading a model parameter set with a name already in the model is no longer silently ignored. Instead a new unique name is generated.
  • Fixed dragging an dropping of report items which may cause a crash in certain situations.
  • Improved layout of parameter estimation result widgets to better display Eigenvalues of the Fisher Information Matrix.
  • Fixed problem where the deletion of a just created parameter set could cause a crash.
  • Fixed update of local reaction parameters in the parameter overview, which was not correctly refreshed.
  • Fixed problem updating the separator when editing a report definition.
  • Improved display of Elementary Flux Mode results where some table rows were not correctly adjusted.
  • Improved object selection for Time Course Sensitivity task to include only and all relevant objects.
  • Fixed loading of XHTML comments including entities like π (π).
  • Updated MIRIAM resources to correctly handle identifiers using https://.
• Simulation Engine
  • Temporary Files for user with special characters in the name is now correctly handled.
  • Fixed issue with Hybrid LSODA integration method which was not correctly initialized on its initial use.
  • Fixed an issue where it was not possible to read extremely old COPASI files using user defined functions with recent versions.
  • Fixed file permissions for COPASI files which in some situation under Linux did not respect umask settings.
  • Fixed report output of Elementary Flux Mode task.
  • Fixed tracking of wall clock and CPU time in the Sensitivities Task.
• Standards
  • SED-ML export of plots may have used non-unique IDs for a variable if that variable occurred in multiple curves.
  • SBML import no longer crashes if an event without a name and an id is encountered.
  • SBML unit import and export preserve the user specified volume unit instead of converting to liter.
  • SBML improved import of reactions with undefined stoichiometry which could crash COPASI.
• Language Bindings
  • Fixed problem where bindings terminated if the environment variable HOME was not set.
  • Language bindings no longer crash when calling getStringValue from a non existing variable.
  • It is now possible to create parameters of type Common Name (CN) in language bindings.