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SimBiology Desktop Help and Tools

While building models and configuring tasks, you can obtain information about modeling elements and tasks from context-sensitive help. The desktop identifies errors and warnings of a project using message indicators. In addition, you can check the status bar to find out if the desktop is running a task or performing actions in the background such as loading a project. As you construct models using building blocks, you can use graphical context menus to edit block properties. The desktop also provides various tools for model building, error checking, and searching.

Contextual Help

The desktop provides context-sensitive help with additional information about models and tasks. For instance, while building models, you can get more information about quantities and expressions and how to use them. Look for the information icon, , and hover over it to see the help. To open the help as a separate dialog, click Pin on the top right corner.

Message Indicators

As you build models and configure tasks, the desktop identifies errors and warnings with message indicators. The indicators are color-coded as follows.

  • Red – one or more errors (and warnings) were detected.

  • Orange – warnings, but no errors, were detected.

  • Green – no errors or warnings were detected.

Click a square indicator, such as , to iterate through errors or warnings. Hover over a dash indicator, such as , to see the specific error or warning message. Clicking a dash indicator highlights the relevant row in a table. The following figure shows the locations of indicators in the desktop.

Message Indicators in Diagram View

For details about the diagram view and other views of a model, see Model Views.

Message Indicators in Table View

For details about the table view and other views of a model, see Model Views.

Message Indicators in Task Editor

For details about the task editor, see Task Editor.

Contextual Icons

The desktop uses contextual icons to provide more information about quantities and blocks. For instance, in the Diagram view, an icon is displayed above a block if it has an error: . In the Table view, an icon is shown when a species is being dosed or a quantity is being updated by an assignment rule.

For more information, hover the mouse over an icon. The following table has the complete list of contextual icons and corresponding model views where they are displayed.

IconDescriptionDiagram ViewTable ViewEquations View

Block has an error.χχ

Block has a warning or is not being used in a model.χχ

Block is pinned to its current location in the Diagram view.χχ

Species amount, parameter value, or compartment volume is set to be constant. In other words, the ConstantAmount, ConstantValue, or ConstantCapacity property of the species, parameter, or compartment block is set to true.χχ

Species block has the BoundaryCondition property set to true.χχ

Species or event block is cloned.χχ

Reaction block has the Reversible property set to true.χχ

Reaction, rule, or event block has the Active property set to false, meaning it does not participate in the model simulation.χχ

,

Reaction-scoped parameter shadows (i.e., takes precedence over) a model-scoped parameter. The up arrow icon indicates the parameter that shadows. The down arrow icon indicates the parameter that is being shadowed.

Species amount, parameter value, or compartment volume (capacity) is defined by an assignment rule.

Species amount is being increased by one or more doses. You must select the desired dose(s) in a task to see the dosing effects.

Graphical Context Menus

While building models using blocks, you can configure block properties using graphical context menus. Select a block and then hover over the graphical icons for the context menu options.

Tools

The desktop provides the following tools to help you build and analyze models.

ToolPurpose

MATLAB Code Capture Tool

Displays the equivalent MATLAB code of the desktop actions.

Diagram Overview

Shows the graphical representation of an entire model. Use this to pan through a model and zoom in on a particular area.

Component Palette

Lists of modeling elements such as quantities. You can drag and drop these elements to a task when configuring it.

Task Data Comparison

Compare results from fit tasks. For instance, you may want to run a fit task multiple times using different optimization methods and compare the final results using this tool. To compare results, first open the tool. Then run a fit task, and save the task result. Then make changes to the task and rerun it. The tool displays the parameter estimation quality measures, such as log-likelihood, AIC, and BIC, for the last run and each saved result.

Usages

Shows all expressions and tasks that reference a parameter, species, compartment, variant, dose, kinetic law, unit, unit prefix, or plot type. Use the context menu of the corresponding entry in a table to show the usages.

Errors and Warnings

Displays the error and warnings of a model. To populate the list, select Verify on the Model tab. When you run a task, SimBiology automatically checks if there are any errors or warnings. Double-click an error or warning to go to where it occurs.

Search Results

Shows all instances of word or phrase in a model, kinetic law library, unit and unit prefix library. To search, type in the search box above the toolstrip.

Tip

To search for any keyword or phrase on any open panel, click the Search button on the Home or Model toolstrip. You can define specific search criteria. For instance, you can specifically search for any parameters whose names start with 'k1'.

Tip

You can dock each tool to the desktop or undock as a separate dialog via the action menu button on the top right corner of the tool. When docked, you can drag and reposition the tool anywhere within the desktop.

Related Topics

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