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COPASI Changelog

What's new in COPASI 4.42 Build 284

Dec 2, 2023
  • New Features:
  • Simulation Engine:
  • Scan task: implemented support iterating through parameter sets.
  • Optimization & Parameter Estimation: It is now possible to run current solution statistics before adding any optimization parameters.
  • Bug Fixes:
  • Graphical User Interface (CopasiUI)
  • Fixed issue were results of tasks were not properly displayed after the first run of the task.
  • Fixed scan task to correctly show parameter estimation results.

New in COPASI 4.40 Build 283 (Nov 22, 2023)

  • New Features:
  • Simulation Engine
  • Species particle numbers are no supported as event targets.
  • Optimization & Parameter Estimation: It is now possible to run current solution statistics before adding any optimization parameters.
  • Bug Fixes:
  • Graphical User Interface (CopasiUI):
  • Reduced COPASI's start up time.
  • Fixed display of message boxes under Qt 6.5.
  • Improved functionality and stability of the plotting engines QWT & QCustomPlot
  • The output assistant suppresses now any check boxes which are not applicable to the current task.
  • Improved display of SBML imported units.
  • Fixed rare crash occurring when lading a new file while displaying a global quantity.
  • Simulation Engine:
  • Utilize balanced Abstract Syntax Tree to avoid stack overflows.
  • Fixed loading of COPASI files containing parameter estimation created with COPASI 4.0 (Build 18).
  • The COPASI Version is now correctly displayed in reports.
  • Fixed an error message for trajectory method RK45 which was referring to LSODA.
  • Standards:
  • SBML Import: Corrected function parameter classification which effected the UI parameter overview.
  • SBML Import: Avoid redundant division by log(10) when importing logarithm with base 10.
  • SBML Import (layout): Allow import of empty curves.
  • SED-ML Import: Improved import of SED-ML files with multiple task lists, falling back to SBML when all fail.
  • SED-ML Import: Create a warning message when referenced the SBML model is remote resource (unsupported).
  • API & Language Bindings:
  • Added utility function CFunctionDB::purgeUnusedUserDefinedFunctions().
  • Added editing of constraints in optimization and parameter estimation tasks.

New in COPASI 4.40 Build 278 (Jun 1, 2023)

  • New Features:
  • The is a bug fix release and does not include new features
  • Bug Fixes:
  • Graphical User Interface (CopasiUI):
  • Fixed issue where loading a parameter estimation protocol in which the values had been sorted externally lead to incorrect parameter mapping.
  • Show both modification and creation time entities in local time.
  • Fixed plot for parameter estimation results for steady state experiments to properly map the independent data.
  • The parameter estimation result now includes a counter for failed constraints.
  • Fixed crash when deleting all global quantities.
  • Simulation Engine:
  • Fixed temporary directory for export of Combine and Shiny archives to address security restrictions on MacOS X.
  • Stochastic simulation methods now correctly report whether they support events and thus whether they can be used for the simulation of model with events.
  • Standards:
  • SBML import: Fixed issue where it was not possible to change the delay of an imported event.
  • SBML import: Fixed crash caused by particular unit definitions during importing.
  • SBML import: Fixed import of reaction kinetics which occasionally lost the parameter mapping.
  • SBML import: Handle references to missing modifier species in reactions gracefully.
  • SBML export: Reduced warnings about Model History not being exported to only check the model itself and not all model components.

New in COPASI 4.39 Build 272 (Feb 1, 2023)

  • New Features since COPASI 4.38 (Build 268):
  • Graphical User Interface (CopasiUI)
  • Implement the creation of expressions for sum, sum of squares, sum of absolute, and product for a selected class of objects in expression widgets.
  • Simulation Engine
  • Added irreversible uni-molecular and bimolecular Arrhenius kinetic functions to the build in functions.
  • Bug Fixes since COPASI 4.38 (Build 268):
  • Graphical User Interface (CopasiUI)
  • Fix possible crash when clicking the revert button in the parameter estimation task.
  • Improved plotting of parameter estimation results for steady-state experiments.
  • Simulation Engine
  • Fixed possible crash when running optimization or parameter fitting using the optimization method Praxis.

New in COPASI 4.38 Build 268 (Dec 1, 2022)

  • Graphical User Interface (CopasiUI):
  • Improved import von Combine Archives containing multiple SED-ML files and task.
  • Improved display of the Fischer Information Matrix (FIM) and it's analysis supporting unscaled and scaled results in different tabs.
  • Fixed editing of function parameters under Mac OS Big-sur and Monterrey caused by switch to Qt 6.
  • Fixed editing of the weight in the experimental data for parameter fitting when using multiple experiments.
  • Simulation Engine:
  • Optimization and Parameter Fitting deal now properly with invalid start values for the optimization parameters.
  • Standards:
  • Support export to SBML of mathematical expression containing initial values.
  • When exporting to SBML all COPASI annotations are now prefixed.
  • Fixed SBML import of units using multipliers different from 1 to encode scaled units.
  • Improved Combine archive export by adding the master flag to SED-ML files.
  • Fixed Combine archive export of old COPASI files created with COPASI prior to COPASI 4.6 (Build 32).
  • Implemented SED-ML import of scan tasks using functional ranges.

New in COPASI 4.36 Build 260 (May 16, 2022)

  • Graphical User Interface (CopasiUI):
  • Fixed an issue where the mapping of substrates could not be changed in the reaction widget when the compartment name included spaces.
  • Simulation Engine:
  • Updated XML parsing to use the latest Expat library to prevent a billion laughs attack.
  • Standards:
  • SBML: Removed spurious error message when importing compartment volumes.
  • SBML: Fixed import and export of atto, zepto, yocto, exa, zetto, and yotta scale.
  • SBML: Fixed round trip problem with dimensionless quantity unit.
  • SEDML: Fixed export of plot colors, markers; added labels for items without SBMLId; assured that output start time is ≥ initial time; and added support for parameter estimation plots.
  • MIRIAM: Added support for the new 'compact' representation of identifiers.org URLs

New in COPASI 4.35 Build 258 (Mar 16, 2022)

  • Graphical User Interface (CopasiUI):
  • Fixed problem merging models using global quantities in mathematical expressions.
  • Fixed problem changing a reaction parameter pointing to a global quantity back to a fixed value.
  • Fixed problem when plotting multiple experimental data when the numbers of data points differed in the data sets.
  • Fixed crash when entering an invalid math expression of the form: a = b
  • Improved support of dark themes.
  • Simulation Engine:
  • Fixed encoding of expression using a function which name includes a backslash .
  • Fixed problem running running optimization using a scan, sensitivities, or cross section task to calculate the objective function.
  • Fixed calculation event delays which uses an expression only containing fixed objects.
  • Improved steady state rate criterion to correctly handle constant rates for variables with large values.
  • Fixed restoring the model state after a failed steady state calculation
  • Standards:
  • SEDML: Fixed export of time course of non autonomous models with an initial time different from 0.
  • SBML: Fixed crash occurring when consecutively importing models using functions with the same name and expression but different parameter type.
  • SBML: Fixed import of models including species with an invalid SBML id (e.g. 2.8.1.8).
  • Language Bindings:
  • Fixed crash occurring when converting compiling an initial expression which is derived from an invalid expression.

New in COPASI 4.34 Build 251 (Aug 13, 2021)

  • Bug Fixes since COPASI 4.33 (Build 246)
  • Graphical User Interface (CopasiUI):
  • In any file save dialog the base name of the currently loaded model is the default instead of untitled.
  • Improved the display of complex units.
  • Improved layout of the Lyapunov exponent results to provide more space for the exponent table.
  • Prevent crash when entering a reaction with species whose name is a valid number.
  • The statistics and the fitting plots are again correctly calculated and displayed for a stopped parameter tasks.
  • Simulation Engine:
  • The Avogadro constant has been updated to it's final value: 6.02214076 x 10^23
  • Standards:
  • SBML: Fixed problems importing and exporting mathematical expressions using Avogadro's number.
  • SBML: Fixed import of mathematical expression using functions without any arguments.
  • SBML: Fixed occasional crash when importing the same SBML file twice in a row.
  • Language Bindings:
  • Fixed crash occurring when deleting several species at once, i.e., without compiling the model after each delete.
  • Fixed crash when deleting a function which is still in use in the model.
  • Fixed crash when creating an expression with numbers in the German format like 1,2.

New in COPASI 4.33 Build 246 (Jun 18, 2021)

  • Bug Fixes:
  • Simulation Engine:
  • Fixed problem for models with species of type ODE, for which no simulation or analysis was possible.

New in COPASI 4.32 Build 245 (Jun 16, 2021)

  • New Features:
  • Installation:
  • The Linux installation support parallel installation of COPASI versions.associations.
  • Language Bindings:
  • Exposed SED-ML exporter.

New in COPASI 4.31 Build 243 (May 10, 2021)

  • New Features:
  • Installation:
  • The Linux installation has been changed to a self extracting interactive archive which also creates a desktop file and registers file and URL associations.
  • Language Bindings:
  • Exposed the MIRIAM annotation in the language bindings.

New in COPASI 4.30 Build 240 (Feb 25, 2021)

  • 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.

New in COPASI 4.29 Build 228 (Aug 11, 2020)

  • New Features since COPASI 4.28 (Build 226):
  • Graphical User Interface (CopasiUI)
  • Time course fluxes are now shown in the layout when playing back a time course.
  • The number of reactions a species is involved in is now shown in the species table.
  • Bug Fixes since COPASI 4.28 (Build 226):
  • Graphical User Interface (CopasiUI)
  • The layout setting dialog is now using the display names in stead of the CN.
  • Updated introduction wizard images.
  • Added a tool bar menu to modify the layout effects for playing a time course.
  • Fixed coloring of scan task components which had been lost in the last release.
  • Fixed crash occurring when an object which is used in an expression is deleted by the user.
  • Fixed crash in the Qt Math-ML widget which occasionally caused a crash.
  • Fixed a crash which occasionally occurred after viewing the annotation tab.
  • Fixed crash occasionally occurring when entering the time scale separation analysis result.
  • Improved advance editing of expressions by recognizing reaction fluxes based on the display name.
  • Fixed saving data of plots containing multiple curves.
  • Fixed parameter overview which did o show all entities when one of the groups was empty.
  • Fixed report of scan of steady-states which did not correctly show the current scan parameters.
  • Standards
  • Improved SBML unit import to reproduce the exact same units as given on export.
  • Fixed SBML import of entities which had a name consisting of only white spaces by using the SBML id instead.
  • Fixed crash when opening an invalid combine archive.

New in COPASI 4.28 Build 226 (Jun 12, 2020)

  • New Features:
  • Graphical User Interface (CopasiUI):
  • Performance improvements while switching to tables of species and reactions or the parameter overview for large models through deferred loading.
  • Simulation Engine:
  • Added additional convergence criterion to the steady state calculation. The user can chose between distance, rate, or both (default).
  • Language Bindings:
  • The model analyzing tool is now available.
  • Bug Fixes:
  • Graphical User Interface (CopasiUI):
  • Fixed problem where changing species concentrations in the parameter overview was not updated in the model.
  • The working directory is now correctly updated when saving a file to a different location.
  • Avoid race condition during model load or import through drag and drop which occasionally caused a crash.
  • Added option to disable automatic resizing of table columns to decrease time to display.
  • Fixed header display in the parameter table of the optimization and parameter estimation tasks.
  • Fixed issue where the display of MIRIAM annotation could cause a crash after a new models is loaded.
  • Fixed undo of MIRIAM annotation for species. reactions, compartments, etc.
  • Fixed crash when switching a species, compartment, or global quantity with a noise term assigned to no longer be of simulation type ODE.
  • Fixed crash caused by saving of existing plots after another model has been loaded into COPASI.
  • Simulation Engine:
  • Avoid incorrect error messages about recursive dependencies.
  • Fixed issue where incorrect COPASI files could cause a crash due to missing attributes of type enum.
  • Fixed issue where occasionally the parameters of the time series sensitivities task where not correctly read back from the COPASI file.
  • Fixed problem where an error during parameter scan would cause the subsequent scan parameter to no be correctly updated and thus leading incorrect results.
  • SBML:
  • Fixed problem exporting the Avogadro constant.
  • Improved handling of malformed MIRIAM annotations which could COPASI to hang on import.
  • SED-ML:
  • Fixed issue exporting plots of species without an SBML name.

New in COPASI 4.27 Build 217 (Sep 14, 2019)

  • A new release of COPASI has been made available. Please visit our free download page to retrieve this latest development release. Please note this version is released under the Artistic License 2.0, which is an OSI approved license. This license allows non-commercial and commercial use free of charge. This release has several new features:
  • Graphical User Interface (CopasiUI)
  • Fixed missing application icon on Mac OS X.
  • In rare occasions it was possible that the COPASI file was corrupted when simultaneously checking for new updates and saving a file.
  • Simulation Engine
  • Fixed a problem where COPASI incorrectly reported a steady-state due to a singular Jacobian.
  • Fixed a problem where a scan task caused an exception due to incomplete specification.

New in COPASI 4.26 Build 213 (Jul 31, 2019)

  • New Features since COPASI 4.25 (Build 207)
  • Graphical User Interface (CopasiUI)
  • Added feature to open files directly from a web page which use the link format: 'copasi://'.
  • It is to possible to specify a user selected list of time point for output in the trajectory tasks.
  • It is now possible to enable automated checks for updates of COPASI as you are used to in many other applications.
  • We added a tool to remove SBML Ids from the COPASI file which are used to facilitate referencing the original SBML Id on export. When an object was renamed the original SBML Id is preserved which is desired in most cases. However there are circumstances where this behavior is not desired. Removing the SBML Ids leads to newly created Id based on the names in COPASI.
  • A COPASI file downloaded using the 'Open URL' method has the targets of reports removed so that a malicious user cannot automatically create harmful content.
  • Command-line (CopasiSE)
  • Added option to export ant import different parameterizations of the model through simple ini file.
  • Bug Fixes since COPASI 4.25 (Build 207)
  • Graphical User Interface (CopasiUI)
  • Fixed a problem where saving a COPASI file to a different location lost the experimental data in the parameter estimation task.
  • Fixed erroneous message and editing problems for models where the volume of a compartment is dependent on a contained species' concentration.
  • Fixed an issue where tab navigation in the trajectory task widget lead to confusing behavior when synchronizing the interval size and number.
  • Fixed a sorting problem in the trajectory task result table which was sorting lexicographically instead numerically.
  • Fixed a crash in the reaction widget which could occur when the reaction parameter were previously deleted.
  • Fixed issues with entering numbers in the scan parameter fields when the local decimal separator is not a '.' (dot).
  • Fixed exporting of model parameter sets to exclude non numeric values.
  • Fixed a crash occurring occasionally after editing changing the preferences.
  • Fixed editing number in scientific notation in the slider dialog.
  • Fixed problem with species containing species when editing the chemical equation.
  • Simulation Engine
  • Improved steady state detection which was overly conservative when estimating the progress for a singular systems Jacobian.

New in COPASI 4.25 Build 207 (Mar 16, 2019)

  • 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.

New in COPASI 4.24 Build 197 (Jul 31, 2018)

  • Graphical User Interface (CopasiUI)
  • Implemented a new 3d bar graph view of matrixes allowing for better selection of interesting values. The new view also avoids OpenGL issues due to incomplete graphic card support of the OS.
  • Improved issue display in the object browser which did not recognize missing expressions for entities of type ODE and occasionally marked missing initial expressions when not required.
  • Improved display of advanced method parameters. If advanced parameter usage is indicated in the preferences they will be shown last. If it is not selected non advanced parameters which are not at their value will be shown to inform the user.
  • SBML
  • Models which explicitely reference Avogadro's number can now be exported to SBML.

New in COPASI 4.23 Build 184 (Apr 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.

New in COPASI 4.22 Build 170 (Nov 12, 2017)

  • New Features:
  • Graphical User Interface (CopasiUI)
  • Reaction diagrams can now be exported in SVG format.
  • Bug Fixes:
  • Graphical User Interface (CopasiUI):
  • Rendering of diagrams including hidden text has been corrected.
  • The interface for displaying multi-dimensional (≥ 3) arrays has been fixed.
  • The total amount and particle number of moieties is now correctly updated in the mass conservation results. The moieties were correctly calculated and used during simulation and analysis. This was just a display issue.
  • Fixed problem when attempting to plot elements of the sensitivity result matrices.
  • Improved tab navigation in the scan task interface.
  • Simulation Engine:
  • The interpretation of mathematical expressions has been fixed to correctly determine whether function variables are Boolean or not. Thus fixing rare crashes when importing SBML.
  • SBML:
  • The detection of mass action kinetics has been fixed to correctly handle reversible mass action like kinetics having only one rate constant.
  • Fixed import of SBML species references without defined stoichiometry by updating to a patched libSBML.

New in COPASI 4.21 Build 166 (Oct 10, 2017)

  • Graphical User Interface (CopasiUI):
  • Improved editing of report definitions allowing drag and drop of items.
  • Simulation Engine:
  • Improved performance of calculation significantly leading to calculation time being less than 50% compared to COPASI 4.20 (Build 158) and less than 80% of COPASI 4.16 (Build 104).

New in COPASI 4.20 Build 158 (Aug 1, 2017)

  • NEW:
  • Graphical User Interface (CopasiUI):
  • It is now possible to export the rendered mathematical expressions to a PDF document.
  • The application window remembers the size of the window and the with of the left browser pane to avoid frequent adjustment by the user.
  • Plots can now be activated and deactivated in the plot itself.
  • When an experimental data file is not found at the expected location COPASI allows now specify a new location by opening a file open dialog.
  • Simulation Engine:
  • The Avogadro symbol can now be used in user defined functions.
  • FIXES:
  • Graphical User Interface (CopasiUI):
  • Changing the quantity unit is now reflected in plots for which data new data is generated after the change.
  • Name changes in newly created plots and report are now properly propagated.
  • Fixed a problem which prevented the changing of the rate law for reactions.
  • Fixed a problem which prevented setting the initial state to the current state of the model through by pressing the S -> IS button.
  • Fixed problem which caused reactions to loose parameter mapping for species when the species had been renamed.
  • The scaling compartment is now correctly displayed in the ODEs.
  • Stead-State analysis result are no longer editable by the user.
  • The units of model can now be entered directly by the user instead of being limited by the selection available in the combo boxes.
  • Fixed crash when changing a rate law while sliders associated with reaction parameters were displayed.
  • Saving a model right after entering an initial assignment for a species without committing the changes lead to an inconsistency when loading the file. The assignment was correctly loaded however the outdated initial value was not recalculated.
  • Improved the undo/redo functionality to better record and apply the changes done by the user.
  • Improved graphics quality and Mac-OS with retina display.
  • Prevented crash when attempting to set the start value of parameters in the optimization and parameter estimation task based on current solution values occurring when no current solution was found.
  • Simulation Engine:
  • Prevent crash occurring when attempting to access result matrix elements which are not existing.
  • When loading a COPASI while with a broken parameter mapping for species in a reaction COPASI recovers automatically.
  • Prevented crash of models with discontinuities that where triggered by the condition during time course execution.
  • Fixed an issues in the parameter estimation task where constraints where in some cases constraints where not correctly evaluated.
  • Fixed a problem where empty reactions could cause a crash during undo.
  • Improved restart after a discrete event did not change the model state to prevent detecting the same event twice.
  • Fixed scaling problem of MCA result caused by the addition of the summation theorem error check column.
  • Prevent problem where in some situations during stochastic simulations with discrete events COPASI did no longer proceed.
  • Fixed a problem where an event assignment changing an infinite value to a finite value was not propagated to the integrator.
  • Improved stability of the time scaling separation analysis.
  • SBML:
  • Fix problem which prevented opening an SBML file through the open dialog or drag and drop.
  • Fixed an issue where SBML export and subsequent SBML import changed the model behavior of reactions whose modifiers where in different compartment than substrates and products.
  • Corrected the export of the scaling compartment in the case where the user choose non-default behavior for a multi-compartment reaction.
  • Constraints are now correctly listed in the default report for parameter estimation.
  • SED-ML:
  • Fixed export of reactions which had parenthesis in the reaction name.
  • Improved import and export of time course description to properly handle output start times different from the initial time.
  • Improved export of plots so that they can be unique associated with an analysis task.
  • ODE Export:
  • Fixed problem where not all local rection parameters where exported.

New in COPASI 4.19 (Build 140) (Apr 8, 2017)

  • Release Date: January 12, 2017
  • New Features since COPASI 4.18 (Build 136):
  • Graphical User Interface (CopasiUI)
  • Added matrix results of the Linear Noise Analysis tasks to the results available for selection.
  • Simulation Engine
  • Added option to limit the internal step size of the LSODA integration method which is needed in very rare cases to assure that events or discontinuities are properly detected.
  • Bug Fixes since COPASI 4.18 (Build 136):
  • Graphical User Interface (CopasiUI)
  • Fixed stability issues related to the new features introduced in COPASI 4.17 (Build 135)
  • Improved unit display in the GUI in particular for dimensionless units.
  • Simulation Engine
  • Fixed performance degradation related to the new features introduced in COPASI 4.17 (Build 135)
  • SBML
  • Fixed issues in the unit import of global quantities.

New in COPASI 4.16 Build 104 (Jun 15, 2016)

  • New Features:
  • Graphical User Interface:
  • The copy to next feature in the Experimental data description dialog is now able to handle the situation were the target experiment has less columns than the copied one.
  • Simulation Engine:
  • The Gamma distribution and the Poisson distribution are now accessible in mathematical expressions and exported to SBML.
  • SBML:
  • COPASI now exports the SBML L1V1 legacy format.
  • Bug Fixes:
  • Graphical User Interface:
  • The tool "Create Events For Time-series Experiment" does now handle ignored columns correctly.
  • Fix issue where deleting a reaction and running a parameter estimation afterward could cause the initial values to be corrupted.
  • Fixed problem in the tool "Convert to irreversible" which could lead to crashes if a reaction parameter of a reversible reaction was referenced out side the reaction.
  • Fixed handling of HTML entities like — in notes.
  • Improved performance of the "Update MIRIAM" tool.
  • Warning about unknown MIRIAM resources are now only issued when the resource is accessed.
  • All available tasks are now selectable as sub-tasks for the Optimization task.
  • Fixed issue where copying a compartment could lead to a crash in COPASI.
  • Simulation Engine:
  • Fixed problem in the Linear Noise Approximation task which occasionally lead to crashes in COPASI.
  • Fixed issue in the Parameter Estimation Task where the un-normalized weight would not be calculated correctly.
  • The recently introduced Persistent Trigger flag for events was not correctly read from files causing the default value to be used.
  • Numerical instability issues in the Metabolic Control Analysis task result in a warning reported to the user.
  • Removed erroneous error messages caused by a premature function compile during when loading a file.
  • Fixed issue were HTML notes not save correctly when the user added the name space manually to the top level element.
  • Renaming an object triggers now an immediate update of the infix of all mathematical expression where the object is referenced.
  • Improved handling of experimental data files for parameter estimation which are not in the same directory as the the COPASI file.
  • Fixed issue where incorrect numerical values for parameter bounds in Optimization or Parameter Estimation would lead to an occasional crash.
  • SBML:
  • The import of SBML files previously exported from COPASI does no longer create any warnings.
  • COPASI handles the export of log10 correctly.
  • The import of n-ary relational operators is now correctly handled.
  • Improved handling of incorrect SBML documents on import.
  • Fixed issue where COPASI could crash when loading and SBML file, which contains the same model name as the currently loaded model in COPASI.
  • Source package:
  • The python example files are now also compatible with Python 3.x
  • Fixed problems compiling COPASI for the arm architecture.

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:
  • 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 (Apr 23, 2014)

  • New Features:
  • 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
  • Bug Fixes:
  • Graphical User Interface (CopasiUI)
  • COPASI now uses a decimal point even in countries where it is common to use a comma.
  • The results of optimization and parameter estimation display not the correct start values even if update model is selected.
  • The slider dialog shows now the currently active task and has been overall improved.
  • Reversible reaction in network diagrams are now displayed with 2 arrows.
  • Improved the C export of the ODEs and assignments.
  • Fixed crash occurring when the parameter estimation task was selected for models which had parameters defined acting on deleted experiments. Such models could only be created with 3rd party tools.
  • Fixed issues editing reactions parameters for models which have multiple compartments of which at least contained spaces in the name.
  • Improved display of expressions in the table widget for compartments, species, etc.
  • It is no longer possible to close the progress dialog by hitting the escape key which left the user interface in a disabled state.
  • Simulation Engine
  • Fixed a problem when simulating delayed events when the delayed execution coincided with an output time of the integration.
  • Fixed a crash which could occur at the end of a scan task when out put during sub task has been selected.
  • SBML
  • Annotation for kinetic laws is now preserved during an import/export cycle.
  • Export of the Avogadro constant has been implemented.

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

  • Bug Fixes:
  • 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.

New in COPASI 4.11 Build 64 (Oct 26, 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 (Oct 26, 2013)

  • New Features:
  • Graphical User Interface (CopasiUI):
  • Impproved the cross section task interface to be more intuitive.
  • SBML:
  • Enabled export of models which use initial values of species, compartments or global quantities in mathematical expression.
  • Bug Fixes:
  • Graphical User Interface (CopasiUI):
  • Fixed problem causing a crash in the slider dialog when the tool "Convert to irreversible" was used.
  • Improved performance of large list of sliders on Windows 8.
  • Simulation Engine:
  • Fixed problem when loading CopasiML files which contained nested groups.
  • Fixed crash when exporting a model which contained an event without any assignments.
  • Fixed the calculation of the standard deviation and RMS in the parameter task fir the case where the experimental data contained missing values.
  • The subtask of the sensitivity is now always performed with the update model flag set to false.
  • Fixed problem in the result display of the time scale separation task which could lead to a crash if the task itself failed.
  • Fixed problem in the calculation of the Fisher information matrix which ignored the weights in the objective functions.
  • Fixed stochastic simulation to stop if a propensity evaluates to NaN.
  • Fixed problem in the parameter estimation task when validation data was present.
  • SBML:
  • Fixed SBML import of function definitions specifying unused variables.
  • Improved import of functions reducing the number of duplicates and simultaneously preserving the name.
  • Improved import of irreversible reactions in which the product contributes to the kinetic law and is listed as a modifier.
  • Create a warning message if the model contains an invalid function definition and cannot be exported.
  • Language Bindings
  • Fixed various crashes in the Java binding caused by the retrieval of non existing objects.

New in COPASI 4.9 Build 45 (Oct 26, 2013)

  • New Features:
  • 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
  • Language Bindings
  • It is now possible to add tool specific annotation in XML format to many entities of the model (compartment, species, reaction, etc.)
  • Bug Fixes:
  • Graphical User Interface (CopasiUI):
  • The name of an object (compartment, species, reaction etc.) appears now on all widgets associated with it.
  • Boolean expressions entered in places where numerical results are expected are automatically converted to evaluate to 1.0 (true) or 0.0 (false)
  • Fixed crash when moving the last item in a report up.
  • Fixed update button in the steady-state result widget which occasionally could lead to incorrect model updates.
  • On Mac OS double clicking a COPASI file will now correctly open the file.
  • Fixed crash when deleting all reports at once.
  • Fixed problem with sliders where no all dependent initial values were updated before a new simulation was performed.
  • Improved Latex export of names containing underscores and spaces.
  • The tool Convert to Irreversible has been significantly improved to correctly handle modifiers and to avoid duplicate function creation.
  • The tool Convert to Irreversible deals now correctly with situations where the a reaction flux of a reversible reaction is referenced in other expressions.
  • Simulation Engine:
  • Some messages were incorrectly labeled as warning messages but caused CopasiSE to stop. These messages are now correctly labeled as errors.
  • Improved handling of start values for optimization and parameter estimation in the CopasiML file.
  • Fixed rare problem in event trigger detection which could lead to firing the same event multiple times without advancing the simulation time.
  • Improved load of CopasiML files with large mathematical expressions.
  • The suppress output feature in the trajectory task now also suppresses output during events.
  • If continue from current state is selected in the scan task the user is warned if initial values are changed which do not have any effect on the current state.
  • The error message created when parsing an invalid expression or function contains now the name of the object so that is easier to determine the location of the problem.
  • Fixed rare problem in event execution due to invalid initialization of the trigger status before integration.
  • SBML:
  • Fixed possible crash loading Level 3 files which uses undefined unit ids as model attributes.
  • Improved import performance of files with large MathML expressions
  • Language Bindings
  • It is now possible to set the SBML Id of the model.
  • Fixed possible crash when writing out incomplete models to CopasiML.
  • Fixed crash when accessing a non existing task by name.
  • Report definitions can now be retrieved by name.

New in COPASI 4.8 Build 35 (Oct 26, 2013)

  • New Features:
  • Graphical User Interface (CopasiUI):
  • Added plots and reports for parameter scans to the output assistant.
  • Only applicable plots and reports are shown in the output assistant by default.
  • Simulation Engine:
  • Time Scale Separation Analysis can now handle multi compartment models.
  • The Time Scale Separation Analysis can now be applied to the full as well as the reduced model.
  • It is now possible to calculate the sensitivities of Eigen values.
  • Add kinetic function Bi (irreversible) to the builtin functions.
  • Bug Fixes:
  • Graphical User Interface (CopasiUI):
  • Fixed crash in the species table when clicking the comportment cell for a newly created model.
  • Fixed editing problem in the species table when creating a new species in a multi compartment model.
  • All sub windows are no closed automatically.
  • Fixed reaction interface to handle reactions with non integer stoichiometries correctly.
  • Fixed crash when creating a new model and canceling the save of the modified open model.
  • Fixed crash caused by sliders of a previous model in a single COPASI session.
  • Modifying sliders in a model triggers the save model dialog when closing COPASI.
  • Fixed crash caused by notes when creating a new model in an existing COPASI session and inserting a reaction in the reaction table.
  • Enabled resizing of columns in the EFM results.
  • Fixed problem caused by an ampersand '&' in an object name in the ODE display.
  • Enabled the Save button int the Time Scale Separation Analysis result.
  • Sliders for species are now always displayed in the current selected frame work (concentration or particle number).
  • The update model button in the optimization and parameter estimation results be have now similar to the update model check box in the task.
  • Simulation Engine:
  • Improved event detection during cascading events.
  • The deterministic integration is now only restarted after events if the ODEs have changed discontinuously improving performance and avoiding restart failures.
  • Improved the modulo operator '%' to handle zero as the second argument.
  • Fixed Time Scale Separation Analysis methods ILDM and ILDM modified to return the same results as in Build-32
  • Prevent crash caused by invalid reactions in a CopasiML file.
  • Fixed unreported numeric overflow in the Ï„-Leap and Adaptive SSA/Ï„-Leap methods.
  • Fixed Gibson and Bruck method to correctly handle output of non integer particle number as initial values.
  • Improved error message for invalid parameter intervals in optimization and parameter estimation.
  • SBML:
  • Fixed problem exporting empty reaction L3V1.
  • Corrected unit export for L3V1.
  • Language Bindings
  • Improved handling of spaces in function names.
  • Fixed crash in CModelEntity::setExpression.

New in COPASI 4.7 Build 34 (Oct 26, 2013)

  • New Features:
  • This release features new 64 bit packages for all supported platforms.
  • Graphical User Interface (CopasiUI):
  • Enhanced parsing of mathematical expression to allow the comparison operator =, and == as well as the Boolean operators || and &&.
  • Allowed calculation results to be selected as constraints for optimization and parameter estimation.
  • Improved display of mass conservation results. The moieties are now displayed in amount if the user is in the concentration framework.
  • Added Update Model button to the optimization result widget
  • Simulation Engine:
  • The calculation of statistics is no optional for optimization and parameter estimation tasks.
  • Start values can no be randomized automatically for optimization and parameter estimation tasks.
  • SBML:
  • Added support for constant conversion factors in Level 3.
  • Bug Fixes:
  • Graphical User Interface (CopasiUI):
  • Fixed crash when editing notes and switching the view mode.
  • Fixed display of rate law interpretation in the model.
  • The model name no longer appears in the left navigation tree.
  • Fixed write access to the example directory so that users are able to execute them.
  • Fixed opening of files which included non-ascii characters in the name through double click under Windows
  • Allowed calculation results to be selected as constraints for optimization and parameter estimation.
  • Deleting functions now prompts the user if the function is used within the model.
  • Improved editing behavior in tables for compartments, species, global, quantities and reactions.
  • Boolean values in tables are now represented by check boxes.
  • Preserved line breaks and indents in notes when free text and not XHTL is used.
  • Fixed problem editing particle numbers when in the particle number framework.
  • All numerical values are now displayed and edited with 10 significant digits.
  • Prevent crashes caused by incomplete specification of kinetic parameters or modifiers.
  • Fixed editing of event assignments to trigger update the internal dependencies.
  • Fixed erroneous empty error messages at the end the steady state calculation.
  • Improved MathML and rendering of build in functions like sin, cos, ceil(), and floor().
  • Fixed deletion of multiple objects which could cause a crash in COPASI.
  • Improved handling of MIRIAM resource Ids, leading and trailing spaces are now stripped automatically.
  • Simulation Engine:
  • Fixed crash in hybrid stochastic simulation method occurring for some models
  • Fixed event detection to correctly deal with saddle points which have value 0.
  • Fixed output of time course for models with events which did not distinguish between equality and inequality when an event occurred at the end of an integration intervall.
  • Fixed occasional problem when calculating the steady-state for models with moieties for which the dependent species amount is 0.
  • Improves sensitivities task to handle failed subtasks gracefully. COPASI will report a warning when more than 20% of the subtasks fail.
  • Fixed parameter estimation to work correctly with model or experimental data containing changes to the volume.
  • Improved handling of experimental data files not located in the same directory as the COPASI file.
  • SBML:
  • Fixed SBML export of initial assignment for species for which the hasOnlySubstance flag is set.
  • Fixed import of piecewise defined functions which are missing an otherwise construct.
  • Fixed export of render extension information.
  • Improved import of models containing initial assignments for species which in rare circumstances where not executed.
  • Fixed import of the Avogadro constant in Level 3.

New in COPASI 4.6 Build 33 (Oct 26, 2013)

  • New Features:
  • Graphical User Interface (CopasiUI):
  • Notes in text or XHTML format are now available for compartments, species, reactions, global quantities, events, and kinetic functions.
  • Support links in XHTML notes.
  • Support of render informations in graphical model layouts.
  • Simulation Engine:
  • Enhanced EFM algorithm performance by applying a new selection criterion before each internal step.
  • Added an stochastic algorithm (Adaptive SSA/Tau-Leap) which dynamically partitions the model into parts simulated by the direct algorithm and the Tau-Leap algorithm.
  • SBML:
  • Import SBML Level 3 Version 1.
  • Added SBML notes support for compartments, species, reactions, global quantities, events, and kinetic functions.
  • Added MIRIAM annotation support for events.
  • Support for the SBML Render Extension.
  • Bug Fixes:
  • Graphical User Interface (CopasiUI):
  • The selected items in the navigation tree do now correspond to the object displayed in the main widget.
  • Fixed a crash caused by not marking any of the check boxes before, during, and after in the plot definition widget.
  • Fixed progress report for the scan task which was not updated during the execution.
  • Fixed crash which could occur in a model with circular calculation dependencies which additionally used sliders.
  • The delete buttons in the tables are now only active when one or more objects are selected.
  • In the steady-state result widget the button to update the model is now working.
  • Fixed crash which occasionally occurred when saving the ODEs in TeX format.
  • Fixed crash caused by saving a model where reports referenced in tasks have been deleted by the user.
  • Enabled scrolling for the rendered mathematical expressions.
  • Simulation Engine:
  • Fixed problem in Stochastic Gibson Bruck algorithm which could make COPASI unresponsive.
  • Fixed problem in the MCA task which did not execute the selected sub task when the model was created with a previous version of COPASI.
  • Fixed crash which occasionally occurred when exporting the ODEs to C.

New in COPASI 4.6 Build 32 (Oct 26, 2013)

  • New Features:
  • 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
  • Bug Fixes:
  • Graphical User Interface (CopasiUI):
  • Added support for saving sensitivity results.
  • Fixed the display of the method parameter table for tasks.
  • Removed empty lines in the rendering of the ODEs.
  • Fixed crash which may occur when deleting an event assignment.
  • Fixed crash which may occur after the execution of the Lyapunov task.
  • Simulation Engine:
  • The initial time of non-autonomous models is now loaded correctly.
  • The information whether the MCA task shall calculate a steady-state may have been lost when loading a COPASi file.
  • If the data file and its description differ in the parameter estimation task COPASI shows now the appropriate error messages instead of crashing.
  • Fixed problem calculating the sensitivities of a steady-state towards a fixed global quantity.
  • SBML:
  • Fixed a crash when exporting to SBML which may occur after renaming of any model object.
  • Fixed a crash when attempting to exporta model containing piecewise defined functions to L1V2?.
  • Fixed error messages of SBML export to report the user selected level and version.
  • Fixed problem exporting invalid XHTML notes which were missing a meta tag defining the used style type.