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

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.

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).

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.

COPASI 4.38 (Build 268) Released

Stefan Hoops: 2022-11-30 01:00:00 +0000

The COPASI team announces the immediate availability of the stable release COPASI 4.38 (Build 268).

Release Date: November 30, 2022

Bug Fixes

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.

More information can be found in the changelog.

COPASI 4.37 (Build 264) Released

Stefan Hoops: 2022-10-05 01:00:00 +0000

The COPASI team announces the immediate availability of the stable release COPASI 4.37 (Build 264).

Release Date: October 5, 2022

New Features

Graphical User Interface (CopasiUI)
- Import dialogs for COMBINE archives or SED-ML files with importable entities like SBML models, SED-ML files, or SED-ML tasks.
Command Line (CopasiSE)
- Support for handling COMBINE archives or SED-ML files with importable entities like SBML models, SED-ML files, or SED-ML tasks.
Installation
- Installation package for Mac OS Big Sur and later on Intel platform
Language Bindings
- Java bindings for Mac OSC package on Arm platform
Standards
- Enhanced interfacing with COMBINE archives and SED-ML files in CopasiUI and CopasiSE

More information can be found in the changelog.

COPASI 4.36 (Build 260) Released

Stefan Hoops: 2022-05-16 01:00:00 +0000

The COPASI team announces the immediate availability of the stable release COPASI 4.36 (Build 260).

Release Date: May 16, 2022

More information can be found in the changelog.

All News