COPASI

COPASI: Biochemical System Simulator

COPASI is a software application for simulation and analysis of biochemical networks and their dynamics.

COPASI is a stand-alone program that supports models in the SBML standard and can simulate their behavior using ODEs, SDEs, or Gillespie's stochastic simulation algorithm. Arbitrary discrete events can be included in such simulations. COPASI provides a set analysis methods and parameter estimation, a list of all features can be found here.

Most recent News

Release

COPASI 4.42 (Build 284) Released

Stefan Hoops: 2023-12-01 01:00:00 +0000

The COPASI team announces the immediate availability of the stable release COPASI 4.42 (Build 284).

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.

Release Date: December 1, 2023

We have chosen to quickly release a fix for a UI problem which resulted in not displaying the results of any task after the first run. Especially for lengthy tasks this seriously impacted the usability of the software.

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.

More information can be found in the changelog.

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COPASI

COPASI's presence on social media

Pedro Mendes: 2023-11-28 20:20:00 +0000

COPASI’s presence on social media

For many years we have operated an account on Twitter/X: @COPASI_software, but we have now stopped using it.

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Release

COPASI 4.41 (Build 283) Released

Stefan Hoops: 2023-11-21 01:00:00 +0000

The COPASI team announces the immediate availability of the stable release COPASI 4.41 (Build 283).

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.

Release Date: November 21, 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

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Release

COPASI 4.40 (Build 278) Released

Stefan Hoops: 2023-05-31 01:00:00 +0000

The COPASI team announces the immediate availability of the stable release COPASI 4.40 (Build 278).

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.

Release Date: May 31, 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.

More information can be found in the changelog.

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Release

COPASI 4.39 (Build 272) Released

Stefan Hoops: 2023-01-31 01:00:00 +0000

The COPASI team announces the immediate availability of the stable release COPASI 4.39 (Build 272).

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.

Release Date: January 31, 2023

New Features

  • 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 build in functions.

Bug Fixes

  • 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.

More information can be found in the changelog.

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