sbmodelr - New modeling tool to create complex models

The COPASI team is happy to announce a new tool, called sbmodelr, which is intended to construct large models that are composed of repeating units. Essentially, you start with a base model and then tell sbmodelr to create a number of repeat units of that model, as well as which model entities interact between units.

sbmodelr is a python-based command line utility that reads a systems biology model, encoded in COPASI or SBML formats, to create a new model that is composed of several connected units that are replicates of the base model. These units may be organized as an arbitrarily connected network, a 2D rectangular grid, or a 3D cuboid array. Each unit contains a complete copy of the original model with all its species, reactions, compartments, events, and global quantities.

The COPASI team announces the immediate availability of the stable release COPASI 4.43 (Build 288).

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: July 08, 2024

Bug Fixes

• Command Line (CopasiSE)
  • No files are created or modified when the option –validate is given.
• Simulation Engine
  • Time Course Task: The methods RADAU5 now correctly supports the option Suppress Output Before …
  • Time Course Task: The hybrid methods Hybrid LSODA & Hybrid Runge-Kutta now supports automatic step size correctly.
  • Optimization and Parameter Estimation Tasks: The method Praxis now correctly terminates if the if solution is within the tolerance.
  • Parameter Estimation Task: The Method Evolution Strategy (SRES) now checks the functional constraints like other methods.
  • Metabolic Control Analysis and Linear Noise Approximation Tasks: The result now contains the Steady-State result.

More information can be found in the changelog.

The COPASI team announces the immediate availability of the stable release COPASI 4.43 (Build 288).

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: April 29, 2024

New Features

• Standards
  • SBML: Added support of SBML Level 3 Version 2

Bug Fixes

• Graphical User Interface (CopasiUI)
  • Event Overview: The assignments associated with an event are no properly displayed.
  • Optimization: Changing of the subtask is now preserved without running the optimization task.
  • Task and subtask names are now consistently handled in sensitivities, optimization, and scan.
  • Scan Task: Improved handling of output from subtask by allowing finer control over when output is captured.
• Simulation Engine
  • Fix calculations involving constant rates which were in certain situations (e.g. event assignments) not correctly updated.
• Language Bindings
  • In the case that multiple data models with the same name where loaded simultaneously, renaming an object in one data model does not longer effect references the other models.
  • Setting CCopasiParameter values directly will now result in a call to the parent group to assure proper synchronization of related parameters.

More information can be found in the changelog.

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

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.

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.