Desktop Example - Applying Changes to Parameter Value Using a Variant

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Desktop Example — Applying Changes to Parameter Value Using a Variant

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Overview Prerequisites Applying Alternate Values Using Variants Simulation Results for the Model of the Mutant Strain

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Overview

Prerequisites

Applying Alternate Values Using Variants

Simulation Results for the Model of the Mutant Strain

Overview

For a description of variants, see Storing and Applying Alternate Model Values Using Variants.

About the Example Model

This example uses the model from Modeling a G Protein Cycle in the SimBiology Model Reference documentation.

This table shows the reactions used to model the G protein cycle and the corresponding rate parameters (rate constants) for each reaction. For reversible reactions, the forward rate parameter is listed first.

No.	Name	Reaction	Rate Parameters
1	Receptor-ligand interaction	`L + R <-> RL`	`kRL`,`kRLm`
2	Heterotrimeric G protein formation	`Gd + Gbg -> G`	`kG1`
3	G protein activation	`RL + G -> Ga + Gbg + RL`	`kGa`
4	Receptor synthesis and degradation	`R <-> null`	`kRdo`, `kRs`
5	Receptor-ligand degradation	`RL -> null`	`kRD1`
6	G protein inactivation	`Ga -> Gd`	`kGd`

About the Variant Created in This Example

This example shows you how to apply a variant representing a parameter value for G protein cycle in a mutant strain to a model representing the wild-type strain. Thus, when the model is simulated without applying the variant, you see results for the wild-type, and when the model is simulated with the variant you see results for the mutant.

The value of the parameter kGd is 0.11 for the wild-type and 0.04 for the mutant. To represent the mutant, the alternate value of the parameter kGd is stored as 0.004 in a variant and applied during simulation.

Prerequisites

Opening and Saving the Example Model

Load the example project by typing the following at the command line:
```
sbioloadproject gprotein
```
The model is stored in a variable called m1.
Open the SimBiology desktop with the model loaded by typing:
```
simbiology(m1)
```
The desktop opens with Model Session-Heterotrimeric_G_Protein_wt.
Select File > Save Project As. The Save SimBiology Project dialog box opens.
Specify a name (for example, gprotein_ex) and location for your project, and click Save.

Applying Alternate Values Using Variants

In the Project Explorer, under Model Session-Heterotrimeric_G_Protein_wt, expand Model Variable Settings, and click Variants to open the Variants pane.
For this example, ignore the preexisting variant that appears in the table.
In the Enter Name box, type a name for the variant, and then click Add or press Enter. For example:
```
  mut_value_ex
```
Add content to the variant:
1. In the Settings tab, click (Add table row). The table updates with a row containing information about a model component.
2. From the Type list, select parameter. The Property list updates to show the property available for changing.
3. In the Name cell, type the name of the component.
```
Gprotein Inactivation.kGd
```
  The parameter kGd is at the kinetic law level, and not the model level. Thus, you must specify the parameter in the format ReactionName.ParameterName.
4. In the Value cell, type a value to apply using the variant.
```
0.004
```

Simulation Results for the Model of the Mutant Strain

To simulate the model of the mutant strain, apply the variant and simulate as follows:

If the Simulation pane is not already open, in the Project Explorer , in Model Session-Heterotrimeric_G_Protein_wt, under Model Tasks, select Simulation to open the pane.
Before simulating, set options to remove species L during plotting because large amounts of L are present in the model and this affects the scaling of the plot.
Click the Plots tab.
Under Arguments, click . The Select Values for y dialog box opens.
Clear the check box for L (unnamed.L) and click OK.
Click the Simulation Settings tab.
In the Variants table, select the Use in Task check box for mut_value_ex.
Click (Run). Your plot should resemble the following figure.
In the Data pane for the latest simulation, click Save to open the Save Data dialog box.
Specify a name for your data, and then click Save.
```
mut_model_run1
```
The desktop adds the saved data under the Simulation task in the Project Explorer.