Steady-State Analysis

To run a Steady-State analysis in COPASI, go to the Tasks → Steady-State branch in the object tree.

In the dialog for the Steady-State task, you can adjust several settings that impact how the steady-state analysis is performed. For example, you may select whether COPASI should calculate the Jacobian matrix and/or perform a stability analysis by checking the relevant checkboxes.

The Executable checkbox determines whether the command-line version CopasiSE will perform this task when running the associated file.

Within the Method Parameter table, you can configure specific settings that affect the method COPASI uses to calculate the steady state. For detailed information on these, refer to the relevant method documentation.

To start the calculation, click the Run button at the bottom of the screen. When the calculation finishes, COPASI will switch to the Result widget.

The Result widget for Steady-State analysis is organized into several tabs, each displaying a specific set of results:

• The first tab displays information about the species at steady state.
• The second tab shows data for the compartments.
• The third tab presents the model quantities.
• The fourth tab lists the reactions and their fluxes. You can choose between concentration-based fluxes and particle-based fluxes using the drop-down menu above the tab. You may change this display at any time.
• The fifth tab (shown only if Jacobian calculation was requested) shows the Jacobian matrix for the full system, including its eigenvalues.
• The sixth tab (also shown only if Jacobian calculation was requested) contains the Jacobian matrix for the reduced system, along with eigenvalues.
• The seventh tab displays the stability analysis results if a stability analysis was performed.
• The last tab provides a protocol listing the steps COPASI took while attempting to compute the steady state.

Each tab helps you review the various result categories generated during the analysis.

To generate output from the Steady-State Task, you need to create an output definition as described in the Output section, or you can use the default report called Steady-State. The default report provides a summary stating whether a steady state was found, along with the concentration, concentration rate, particle number, particle number rate, and transition time for all species, as well as the flux for all reactions. If you requested them, the Jacobian matrix and its eigenvalues are also included in the report.

For custom output, the easiest approach is to use the Output Assistant, accessed via the Output Assistant button. For details on how to use it, see the Output Assistant section.

To save the output to a file, you need to connect the output definition to a file. Click the Report button to open a dialog that allows you to link the report from a specific task to a location on your computer. First, select a report suitable for the Steady-State task from the drop- down menu at the top of the dialog. Then, specify the file where the report should be saved by clicking the Browse button and selecting the destination. By default, COPASI will create a new file or overwrite an existing file with the same name. If you prefer to add the output to the end of an existing file, select the checkbox labeled Append at the bottom of the dialog.

Once your selections are complete, click Confirm. The next time you run the Steady-State task, COPASI will write the output to the file you specified.