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Change History | COPASI 4.23 (Build 184)

COPASI 4.23 (Build 184)

Version 4.23.184

Release Date: April 18, 2018

New Features since COPASI 4.22 (Build 170)

  • Graphical User Interface (CopasiUI)
    • Model Merging: COPASI allows to add a second model and to merge its content with the existing one.
    • Compartment dimensionality may now be specified as: volume, area, length, or dimensionless.
    • Problems (Errors, Warnings) of the model are no marked in the object browser at the problematic entity.
    • Enhanced Unit Support for kinetic parameters.
    • Import and export of Combine Archive is now supported.
    • The full and reduced Jacobian of the current model state are now shown under Model/Mathematical/Matrices.
    • Enable copying table and annotated matrix items to the clipboard.
    • A warning is now raised when loading an invalid model (i.e: one that does not compile) and the problematic entity is marked in the browser pane.
    • Added ability to add COPASI version, current date/time, first name, last name, email and organization as well as line breaks to a reports.
    • Allow for the selection of matrices in Object Browser expert mode.
    • Plots can be associated with tasks similar to the existing report association
    • The direct dependencies, i.e, the objects which are directly effected by changes or removal of an entity are now displayed on all modeling entities.
  • Simulation Engine
    • COPASI supports Stochastic Differential Equations (SDEs). It is possible to add noise to reactions and entities (compartments, species, and global quantities) determined by ODEs.

Bug Fixes since COPASI 4.22 (Build 170)

  • Graphical User Interface (CopasiUI)
    • Improved interface for parameter sets and parameter overview
    • Fixed display of units containing space in the symbol.
    • Fixed issue where derived units where not correctly displayed in the global quantities widget.
    • Common Names edited directly in the report definition are now resolved.
    • Preserve assigned layout name after export and re-import.
    • Fixed issue where some window types (sliders, etc.) remained in the open window menu, after they were closed.
    • Fixed issue where fit result eigenvalues took up way to much space in the display.
    • Suppress inconsequential errors when reloading a file with defined functions.
    • Fixed improper multiplier exponentiation in unit display.
    • The steady-state result was incorrectly displayed in the GUI in the previous release. However, reports, plots, and the model show the correct state.
    • Ensure the "unsaved model" warning dialog appears after reactions are added, when not saving prior to loading/creating a new model, or closing.
    • Fixed crash where a specific sequence of GUI events caused a reaction expression to be invalid.
    • Fixed issue where changing multiple compartment volumes through the compartments table in succession lead to inconsistent updates of species concentrations and particle numbers.
    • Fixed crash which might occur when deleting global quantity.
    • The precision of real numbers displayed in the GUI is now configurable and consistent.
    • Fixed issue where species concentrations or numbers appeared to change, after moving to a new compartment.
    • Correct (transpose) the display of the Fisher Information Matrix eigenvectors to match the eigenvalues.
    • Fixed default filename ending for saving plots.
    • Undefined units are now suppressed on plot axis instead of showing '?'.
    • Fixed deletion of sliders where occasionally the wrong slider was deleted.
  • Simulation Engine
    • Random functions are now always recalculated when used in any expression, even if the expression is otherwise constant.
    • The elements of the column 'Summation Error' in the MCA results are now accessible in reports and plots.
    • During a scan of optimization the results where not correctly reported or displayed for the following algorithms: Particle Swarm, Praxes, GASR, and SRES.
    • Fixed crash in parameter estimation with cross-validation in the case that a fitted parameter was not found.
    • Fixed crash when using experimental data that was mapped to no longer existing model elements.
    • Fixed crash that might occur of deleting a global used in a reaction.
  • SBML
    • Import of SBML files which have an unneeded BOM (byte order mark) is now supported.
    • Fixed export of rate of global quantities.
    • Fixed import of MIRIAM annotations which could occasionally result in the process not finishing.
    • During import, don't raise an error when when more than one annotation from a particular namespace is encountered.
    • Fixed issue where data and math objects were not re-mapped during resize.