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Verifying that the Model Has No Warnings or Errors

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Verifying the Model in the SimBiology Desktop Verifying the Model at the Command Line

The SimBiology desktop and MATLAB command line have functionality that helps you find and fix warnings that you might need to be aware of, and errors that would prevent you from simulating and analyzing your model.

You can check your model for errors and warnings at any time in your workflow of building or working with your model, this check includes dimensional analysis or unit conversion issues. For example, verify your model during construction to ensure that the model is always complete, or verify the model or configuration set after changing simulation settings or settings for dimensional analysis or unit conversion.

Analysis such as simulation, scanning, and parameter fitting also causes a model to be verified before the task runs. Repeatedly running a task using different variants or setting different values for the InitialAmount of species, the Capacity of compartments, and the Value of parameters, generates warnings only the first time. Use the verification functionality described in this section to display warnings again.

Verifying the Model in the SimBiology Desktop

While you are building your model in the SimBiology desktop, you can click at any time to generate a list of any errors and warnings in the model. The errors and warnings appear in the Errors and Warnings pane. The following is an example of the error generated when the reaction rate of a reaction is set to a parameter that you have not defined.

To see details of the error or warning, click to expand the pane showing the details.

Double-click the error row to move to the location of the error.

You can interrupt and stop the verification process by clicking Stop at any time during verification.

Troubleshooting Using Colored Indicators

Model component tables and the items in the Project Explorer have colored indicators that let you see if the specified properties are valid. The error or warning icons in the Project Explorer allow you to quickly assess which model components have errors or warnings associated with them.

You can turn off these indicators by selecting File > Preferences to open the SimBiology Preferences dialog box. Select Explorers to find this preference.

In the tables, move the mouse over the indicator to see more details about the warning or error. This table shows the indicators and their significance.

Colored Indicator	Description
Green	Components have valid properties.
Yellow	There are warnings in the associated rows.
Red	There are errors in the associated rows.

• Click Verify in the Toolbar to see if any errors are listed in the Errors and Warnings pane. You must fix any reported errors before you can simulate a model. Warnings may not need to be resolved before simulating, but might result in unexpected answers.

• Click the colored square, if present, in the Settings tab to open a dialog box with tips on how to fix the warning or error.

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Verifying the Model at the Command Line

Use the verify method to see a list of warnings and errors in your model. This method checks a model or a configuration set, depending on the argument you give to the method, and returns a list of warnings and errors encountered.

The functions sbiolastwarning and sbiolasterror return the last warning and last error encountered during verification.

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Desktop Example — Applying Changes to Parameter Value Using a Variant

Desktop Example — Using User-Defined Functions in Expressions

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