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Modeling Using the SimBiology Graphical User Interface

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About the Model Used in This Tutorial Creating a Model Saving Your Work as a SimBiology Project File Adding Reactions to a Model Simulating a Model

About the Model Used in This Tutorial

This section shows how to mathematically model a simple gene-regulation pathway using the SimBiology desktop. The example uses the model described in Gene Regulation Model and shows you how to build this model using a spreadsheet-style interface in the SimBiology desktop.

If you prefer to interact with diagrammatic representations of pathways, see Modeling Using the SimBiology Diagram.

Alternatively, you can use M-code and the MATLAB command-line interface (see Modeling Using the Command-Line Interface). A comparison of these methods will help you understand the model objects that MATLAB creates behind the SimBiology desktop, and how to access and edit a model through the MATLAB Command Window.

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Creating a Model

A SimBiology model is a collection of objects that are structured hierarchically. At least one model object is needed to contain all the other objects.

1. In the MATLAB Command Window, type:

   simbiology

   The SimBiology desktop opens.

2. Select File > New Project. The New Project Wizard opens.

3. Skip the Add Data step for this example and select Add Model.

4. In the Add Model pane, from the Select a model to add list, select Create a new blank model. This selection creates a Model Session containing one compartment (at least one compartment is required for all models). You will later add model components such as species, reactions, rules, and events to the model.

   

5. In the Model Name box, type the name for your model.

   cell

6. Click Next.

7. In the Choose Analysis pane, leave the default selection (Simulate model) selected for the analysis tasks to add to the model and click Finish.

   A new project with the selected specifications opens.

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Saving Your Work as a SimBiology Project File

Project is the file format that the SimBiology software uses to save one or more model sessions. The file extension is .sbproj. Projects let you save custom settings, notes, and data associated with your models. For more information on projects, see Data Formats and Projects.

Save your work as a project now so that you can access this file later.

1. Select File > Save Project as to open the Save SimBiology Project dialog box.

2. Browse to the folder in which you want to save your projects, and enter a name for the project file, such as:

     gene_regulation.sbproj

3. Click Save.

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Adding Reactions to a Model

SimBiology models are defined by connected reactions representing transformation, binding, and transport.

1. In the Project Explorer, expandSimBiology Model and click Reactions to open the Reactions pane.

2. In the Enter Reaction box, enter the reactants and products, separated by a hyphen and right angle bracket. For example, enter the following simple reaction for transcription:

   DNA -> DNA + mRNA

3. Click Add.

   A red indicator appears to the right of the table (and in the Project Explorer). Move the pointer over the indicator for the reaction to get more information about the reason for the indicator. In this case, the indicator shows that the reaction rate is as yet undefined. Beginning in step 5, you will learn how to define the reaction rate.

4. Double-click the Name cell, enter a name for the reaction and press Enter. For example, enter the following:

   Transcription

5. From the KineticLaw list, select MassAction. Your screen should resemble this one.

   

   Note   Species names are automatically populated for Mass Action. In this example notice that MassAction Species lists DNA.

6. In the Map between KineticLaw Parameters and Parameter Names section, locate the Forward Rate Parameter row, double-click the Parameter Name cell, type k1 and press Enter.

   The SimBiology desktop updates ReactionRate for the reaction to show k1*DNA.

   Your reaction table should resemble the following.

   

   The indicator is green, showing that the reaction rate is now defined. The red indicator in the Project Explorer also disappears.

7. Double-click the Value cell and enter a new value.

   0.2

8. From the ValueUnits list, select the units for this parameter. The rate constant k1 is a first order constant with units 1/second.

   Your parameters table should resemble the following.

   

    About Scope

   Notice that the Scope box for the parameter lists the reaction, indicating that the parameter is only available for reference at the level of the reaction.

   If you set the scope of a parameter to the model (Model Name), you can use this parameter in rules, other reactions, and events. All the parameters for this example are scoped to their respective kinetic laws.

   Scoping lets you overload parameters, that is you can have parameters with the same name at the kinetic law and at the model level. Because the desktop searches up from the kinetic law to the model level, when a parameter is overloaded, a reaction uses the parameter and parameter value in its kinetic law; however rules and events use the parameter value at the model level.

   A reaction uses a parameter at the model level only if a corresponding parameter is not defined at the kinetic law level for the reaction.

9. In the Map between KineticLaw Species and Species Names section, locate the MassAction Species row (DNA), double-click the InitialAmount cell, type 50 and press Enter.

10. From the InitialAmountUnits list, select molecule.

    The Scope of the species indicates the compartment that the species is within, and this is still unnamed. The next steps show you how to name the compartment.

11. In the Project Explorer, click Compartments to open the Compartments pane.

    In the SimBiology desktop, models contain a compartment by default. The process of adding a reaction automatically adds the reaction species to a compartment in the model. If there are multiple compartments in the model, you must specify the reactants and products using qualified names (compartmentName.speciesName). For example, nucleus.DNA denotes the species DNA in the compartment nucleus.

12. This example contains only one compartment. Rename the compartment by doing the following:

    In the Name cell, double-click and type a name such as contents for the compartment and press Enter. The compartment table updates with the new entry.

13. From the Capacity Units list select liter.

    Leave other compartment properties such as Owner and Capacity in the default settings, for the purposes of this example.

14. In the Project Explorer, expand Compartments and click contents Species. The species you entered in the reaction are automatically added to the species table.

    The default value for a species is 0.0.

15. In the row containing mRNA, from the InitialAmountUnits list, select molecule. Leave the InititalAmounts value at 0.0.

16. Enter the remaining reactions. For a list of reactions and parameters, see Model Reactions.

    Notice that the ValueUnits for the second-order rate constant k3 is not a default unit in the list. However, molecule and second are default units and you can enter this unit directly by typing the following:

    1/(molecule*second)

    Your reaction, species, and parameter panes should resemble the following ones.

    

    

    

    For more detailed information about the reactions in this model, see Gene Regulation Model.

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Simulating a Model

After you enter the reactions for your model, you can simulate its dynamic behavior and plot the results.

• Click (Run).

  The simulation uses the default configuration settings, runs to completion, and then plots the results in a figure window. You can annotate your plot in the figure window. The following figure shows you an annotated version of the plot:

  

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Gene Regulation Model

Modeling Using the SimBiology Diagram

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