Previous Page Parent Page Next Page TOC
Change History | COPASI 4.17 (Build 135)

COPASI 4.17 (Build 135)

Version 4.17.135

Release Date: November 21, 2016

New Features since COPASI 4.16 (Build 104)

  • Graphical User Interface (CopasiUI)
    • Support for user defined units.
    • Extended unit selection options for time, volume and quantity of the model. These extended options include user defined units.
    • Unit support for Global Quantities.
    • Undo and redo support for all model changes.
    • Improved user interface to method parameters.
    • Selection of matrix and vector elements by name in addition to the index for plots, reports, and in mathematical expressions.
    • Support for contour plots.
    • Sorting off all analysis result tables is now enabled where appropriate.
    • The MCA results contain now information whether the summation theorems are violated or not allowing the user to easily evaluate the numerical accuracy of the result.
    • It is now possible to the select the units of the rate low for a reaction as either amount per time or concentration per time. If concentration per time is selected and the reaction participates in multiple compartments the scaling compartment can be selected.
  • Simulation Engine
    • Added support for arbitrary events to the Stochastic Direct Method.
    • New hybrid simulation algorithm: (Hybrid RK-45) which supports arbitrary discrete events and user defined ODEs. Additionally, the user can specify which reaction are treated continuously and which are treated discretely. This algorithm passes the SBML semantic test suite and stochastic suite.
    • It is now possible to report or plot only the internal steps taken by the integration algorithm in the trajectory task.
  • SBML
    • Full support for SBML Level 3.1 event semantics
    • Import and export of unit definitions.
    • SBOTerms are no imported and displayed as part of the MIRIAM annotation. On export a the first SBOTerm of the MIRIAM annotation is used if the SBML entity does not have the SBOTerm set.

Bug Fixes since COPASI 4.16 (Build 104)

  • Graphical User Interface (CopasiUI)
    • Fixed problem that prevented stopping of the automatic layout for large networks.
    • Fixed issue with unintuitive cursor movement in when editing tables.
    • The list of MIRIAM resources is now sorted case insensitive in the drop-down list.
    • Fixed layout of species widget to utilize all available space for the list of reactions
    • Fixed encoding of special character such as an apostrophe in the notes.
    • Removed erroneous error message which could occur when a COPASI file with a layout was saved.
    • Fixed an issue where COPASI would close unexpectedly when switching to a task after opening a new file.
    • Fixed issue where accessing the elementary flux mode results after opening a new model could lead to COPASI closing unexpectedly.
    • The layout support now UTF8 character in species, compartment and reaction names.
    • Updating the MIRIAM resources is no possible even if you require to go through a proxy server which requires authentication. The required information can provided in the preference dialog.
    • Improved moving of reactions in layouts.
    • When deleting a function all functions which are depending on it will now also be deleted upon confirmation by the user.
    • Fixed occasional crash in the GUI which occurred when opening a new model and immediately (before the load completes) selecting another item in the browser pane.
    • Fixed issue on newer Linux distributions where icons on buttons where no longer displayed due library conflicts when using the binary packages provided for download.
    • Fixed issue where the objective function was not correctly updated when a entity referenced in it was renamed.
  • Simulation Engine
    • Improved the check for positivity of species values for small compartment sizes.
    • Fixed an issue where in certain situations involving events with constant assignments were not reevaluated after the constant value was changed during parameter estimation.
    • The default report for parameter estimation includes now all the information provided in the GUI.
    • Fixed issue where the calculation of the Jacobian would created error messages on the command-line if the Jacoabian contained NaN values.
    • If update model is specified and an analysis tasks fails where the result contains NaN values then the model values are no longer updated instead the original state is preserved.
    • Loading of the initial time for non autonomous models has been restored.
  • SBML
    • Fixed problem where in certain situation duplicate SBML Ids were created.
    • Fixed a problem where functions where not correctly exported if they made use of another function which had spaces in the name.
    • Fixed issues where the import of CellDesigner layouts embedded in the SBML file would fail.
    • Fixed export of layout names.
    • Fixed issue where reaction kinetics were incomplete when the same model was imported a second time in the same session.
  • SED-ML
    • SED-ML export works now correctly when species or compartment names contained spaces.
  • Source package
    • The source package build now correctly when libsbml and libsedml are compiled with the use of namespaces.