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COPASI Changelog

What's new in COPASI 4.15 Build 95

Mar 4, 2015
  • New Features:
  • Simulation Engine
  • Bug Fixes:
  • Graphical User Interface (CopasiUI)
  • Simulation Engine
  • SBML
  • Source package

New in COPASI 4.14 Build 89 (Oct 11, 2014)

  • NEW FEATURES:
  • Simulation Engine:
  • Added gamma distribution to the option for the sampling distributions for the scan task.
  • BUG FIXES:
  • Graphical User Interface (CopasiUI):
  • Fixed issue were slider reverted resulting optimization and fitting parameters.
  • Simulation Engine:
  • Fixed problem with the scatter search optimization algorithm which did no respond to stopping the task.
  • Fixed selection dialog for sensitivity object selection for the effect which showed model constants.
  • SBML:
  • Updated libsbml to 5.10.3 to avoid crashes during SBML import and export.
  • Fixed Immport of Avogadro constant which differ in different SBML versions.
  • Source package:
  • Improved instructions on how to build COPASI from source.

New in COPASI 4.13 Build 87 (Aug 16, 2014)

  • New Features:
  • Graphical User Interface (CopasiUI):
  • Copy feature implemented for reports and plots
  • Simulation Engine:
  • The parameter task can now save multiple parameter set for each fitted experiment.
  • Bug Fixes:
  • Graphical User Interface (CopasiUI):
  • In some situations it was not possible to assign kinetics with multiple modifiers to a reaction since the reaction did not list the modifiers. Now the reaction is updated once the modifiers are selected.
  • Improved graphical presentation of mathematical expression using if statements.
  • The selection dialog for dependent experimental data no longer shows constant objects.
  • Improved auto layout for models containing multiple compartments.
  • Fixed crash when duplicating compartments.
  • Fixed editing issue when creating new reference or relationship annotation which caused an additional insert.
  • Improved cut and paste functionality in the mathematical expression editor to properly recognize species with compartment information.
  • Simulation Engine:
  • The arguments for the log normal sampling (mean and standard deviation) are now correctly interpreted in the scan task, i.e., the log of the sampled parameter has the specified mean and standard deviation.
  • Corrected problem when loading models with non default Avogadro constants.
  • Fixed problem which could lead to saving outdated initial conditions and parameters after a task with update model enabled was executed.
  • The performance statistics for the optimization task are now correctly calculated, i.e., the CPU time is measured correctly.
  • During parameter estimation the time course task update model flag is no always set to false which is the expected behavior.
  • SBML:
  • Improved import of hierarchical composition models by creating more user friendly names.
  • Fixed problem exporting the model history annotation if it is only partially specified.
  • Language Bindings:
  • A crash in the language bindings used by 3rd party tools (CellDesigner) has been resolved.
  • Added methods which make it easier to update all dependent initial values once a values is changed.
  • Source package:
  • Fixed build under MacOS X which in some situations attempted to use lapack instead of the Accelerate framework.

New in COPASI 4.12 Build 81 (Jul 4, 2014)

  • Graphical User Interface (CopasiUI):
  • Model Parameter Sets
  • Import and Export of Kinetic Function databases.
  • Improved Network Diagrams
  • Copy functionality for model entities (compartment, species, reactions, functions, etc.)
  • Improved child window management under the window menu entry.
  • Histograms are now displaying consistently scaled bars (% of total number of recorded values)
  • Fixed problem where MIRIAM hyperlinks where not correctly generated for some old style resource identifiers.
  • Simulation Engine:
  • New optimization algorithm: Scatter Search
  • New MCA algorithm (Smallbone)
  • Continuation on simultaneous events
  • SED-ML:
  • Implemented SED-ML support
  • Source package:
  • CMake based build system

New in COPASI 4.11 Build 65 (Oct 26, 2013)

  • Graphical User Interface (CopasiUI):
  • Fixed crash when editing experimental data in the parameter estimation task. The crash occurred when deleting an experiment, which was specifically listed in an parameter as affected experiment.
  • SBML:
  • Fixed crash, which occasionally occurred when importing an SBML file created with CellDesigner? under Linux and Mac OS X

New in COPASI 4.11 Build 64 (Oct 2, 2013)

  • Bug Fixes:
  • Graphical User Interface (CopasiUI)
  • The Model Analysis tool does no longer treat function with unspecified reversibility as irreversible, which resulted in misleading error messages.
  • Fixed crash when double clicking the white space in the parameter overview widget.
  • Fixed problem updating the display of the weights of the individual column of the experimental data for parameter estimation occuring when some weights were set manually.
  • Fixed crash occurring when canceling the time scale separation task using the CSP method.
  • Fixed crash when attempting to display the bar chart of a 1x1 matrix.
  • Fixed crash occurring when loading a second model while the layout of the first is still visible.
  • Simulation Engine
  • Fixed saving of method parameters of the time scale separation method CSP.
  • SBML
  • Fixed problem importing functions for which the parameter names do not match the local reaction parameter names.
  • Improved recognision of identical functions.
  • Fixed export of notes to SBML level 2 which has very strict requirements on the XHTML.
  • Added warnings explaining the problems when exporting incomplete models, which cannot be exported correctly to SBML.
  • Fixed export of the object role when using the SBML render package in Level 3.
  • The exported coordinates of objects for the SBML level 3 layout package are enforced to be positive by moving the origin.
  • Improved import of reaction kinetics for reactions with computed stoichiometry.
  • Source package
  • Added missing file MIRIAMResources.xml.

New in COPASI 4.10 Build 55 (Sep 5, 2013)

  • Graphical User Interface (CopasiUI):
  • The start values and parameter boundaries are now displayed in optimization and parameter estimation results. Boundaries are additionally colored red if the result is very close.
  • If an unknown MIRIAM resource is found the user receives a message with instruction on how to update the MIRIAM resource database.
  • It is now possible to specify the line style and width of curves in a plot.
  • Improved GUI for defining plots
  • "Window" menu for easier access to plot windows
  • Logarithmic axis scaling can now be easily toggled on the plot windows
  • Improved default plots for parameter estimation results
  • Added User Interface for Linear Noise Approximation Task
  • Added User Interface for Cross Section Task
  • Added the capability to add validation data to the parameter estimation task.
  • The location of the last open or save file dialog is no remembered between sessions.
  • SBML documents can now be imported by dragging the file onto CopasiUI.
  • MIRIAM annotation which uses identifiers.org resources are now supported.
  • The web page describing a MIRIAM resource can now be openend in a Web browser by double clicking the entry in the GUI.
  • Method parameters are now remembered while working with one file. This allows easy switching between methods without the need to reenter the customized parameters.
  • Added capability to create an layout the current reaction network.
  • Simulation Engine:
  • Added property DisplayName to all objects which allows to create more meaningful column headers in reports.
  • Added Linear Noise Approximation Task
  • Added Cross Section Task (for Poincaré type cross sections and bifurcation diagrams)
  • Added min() and max() functions to be used in mathematical expressions.
  • Added indicator functions for finding bifurcation points to the steady state task
  • Added value scaling for parameter estimation
  • SBML:
  • Added support for exporting rates of compartments, species and global quantities
  • Export and Import of Level 3 Layout and Render information
  • support for exporting min, max, uniform and normal functions
  • Enabled export of models which use initial values of species, compartments or global quantities in mathematical expression.
  • Language Bindings:
  • It is now possible to add tool specific annotation in XML format to many entities of the model (compartment, species, reaction, etc.)

New in COPASI 4.6 Build 32 (Jul 23, 2010)

  • Graphical User Interface (CopasiUI):
  • Sorting and filtering in tables, which eases handling of large models.
  • Enhanced result representation of elementary flux mode analysis.
  • Improved SBW registration to handle multiple COPASI installations.
  • Simulation Engine:
  • Support of conditional events, which are discrete changes to the model.
  • 2 new stochastic simulation algorithms, which implements the direct Gillespie algorithm and Tau-Leap method.
  • Eigenvalues of the steady-state Jacobians are now available for further processing or output.
  • SBML:
  • Import and export of SBML Level 2 Version 4.
  • Full support for SBML event import/export
  • COPASI now passes all test of the SBML testsuite for all version of SBML up to L2V4 except for the tests including algebraic rules or 'fast' reactions

New in COPASI 4.4 Build 31 Dev (Mar 19, 2010)

  • New Features:
  • Support of conditional events, which are discrete changes to the model.
  • New stochastic simulation algorithm, which implements the direct Gillespie algorithm.
  • Sorting and filtering in tables, which eases handling of large models.
  • Enhanced result representation of elementary flux mode analysis.
  • Import and export of SBML Level 2 Version 4.
  • Full support for SBML event import/export
  • COPASI now passes all test of the SBML testsuite for all version of SBML up to L2V4 save for the tests including algebraic rules or 'fast' reactions
  • Bug Fixes:
  • Graphical User Interface (CopasiUI):
  • Using a slider before committing changes to a task no longer reverts the changes.
  • It is no possible to select multiple objects simultaneously when creating sliders.
  • Improved error message which occurred when the MIRIAM web service connection was interrupted during update.
  • Plot and layout windows can now be closed with the keyboard shortcut Ctrl+W (Cmd+W on Mac OS X).
  • Invalid mathematical expression no longer cause the GUI to crash.
  • Fixed handling of deprecated URIs in the MIRIAM annotation which may be present in older SBML or COPASI file.
  • Fixed display of random and normal distribution function in MathML and LaTeX.
  • The warning message that the calculation of a Steady-State is not meaningful during parameter estimation is now only shown if the Newton method is used and Steady-State data is provided.
  • Completed renaming from metabolites to species in the GUI.
  • Fixed progress dialog for a scan of of parameter estimations, which continued to grow for each parameter estimation completed.
  • Prevent closing of COPASI while as task is running which could lead to a crash report.
  • Fixed crash caused by the MIRIAM relation 'occursIn'.
  • Randomizing parameter start values takes now into consideration the latest updates to the boundaries. This problem occurred when switching between infinity and a finite value.
  • The scan task indicates now the overall progress correctly.
  • Simulation Engine:
  • Improved Steady-State criterion which estimates the distance of the current state from a Steady-State.
  • Scan of Steady-States? may have lead to incorrect results when COPASI was unable to find any Steady-State. In this case scan values after the unsuccessful attempt would have used incorrect parameters.
  • On Windows COPASI is now able to deal with file names starting with '\', i.e., are relative to the current drive.
  • EFM no longer fails for models which only have reversible reactions.
  • Fixed the Simulated Annealing optimization method which failed when a parameter started with value '0'.
  • Fixed Praxis optimization method which did not terminate for problems containing only 1 parameter.
  • Fixed the behavior of the Slider Dialog which would stay on top of all other Windows covering open and save dialogs.
  • In rare situations on Linux COPASI does not recognize the application font chosen by the user. This can now correct by selecting an application font in COPASI.
  • The MathML rendering will recognize now the application font setting of the user.
  • SBML:
  • In rare circumstance COPASI could have created two identical SIds leading to invalid SBML files.
  • COPASI identifies itself in an XML comment as the creator of the SBML file.
  • Implemented export of the modulo '%' operator which is available in COPASI's mathematical expressions.
  • COPASI supports now round trip of models containing the delay symbol.
  • If a model was directly loaded from an SBML file, the default level and version for the export are the same as in the original file. Otherwise export to SBML is now done as SBML Level 2 Version 4 per default.
  • additional bugfixes which would lead to incorrectly imported and/or exported SBML models in certain situations

New in COPASI 4.4 Build 29 Dev (Jan 8, 2009)

  • New Features:
  • There are no new features in this release. This is a bug fix release for COPASI 4.4 (Build 28)
  • Bug Fixes:
  • Graphical User Interface (CopasiUI)
  • Added missing reaction rates to the selection widget for mathematical expressions where appropriate.
  • Fixed crash caused by changing the assignment of modifiers in the kinetic law in the reaction widget.
  • Fixed rare crash occurring when leaving/committing the sensitivities task.
  • Fixed crash in the optimization task with MCA which occurred when the MCA task was not applicable to the model.
  • Fixed problem in selecting the result of the sensitivity task, which was not possible if the result of the sensitivity is just a single value instead of a vector or a matrix.

New in COPASI 4.4 Build 26 (Jan 7, 2009)

  • New Features:
  • There are no new features in this release.This is a bug fix release for COPASI 4.3 (Build 25)
  • Bug Fixes:
  • Graphical User Interface (CopasiUI):
  • Initial expression depending only on fixed numerical values are now properly updated.
  • Fixed problem which may lead to a crash when running the Mass Conservation task.
  • Fixed crash in the dialog for specifying the experimental data of the parameter estimation which occurred in rare cases.
  • Fixed problem where cut and paste of mathematical expressions for ODEs assignments and initial assignments could lead to spurious results after committing the data.
  • Simulation Engine:
  • Fixed possible crash in MCA calculation which may occur if the model contains species of type ODE or assignment.
  • SBML:
  • Fixed multiple use of the same SId in SBML exports. This problem only occurred when the model has been previously imported from SBML.
  • The constant flag is now set correctly if a species is changed from constant to determined by reactions in COPASI. This problem only occurred when the model has been previously imported from SBML.