Difference between revisions of "STEM Model Generator"

Revision as of 14:44, 5 September 2012

About

Holder page for model generator

Installation

Important note:  the STEM Model Generator is currently intended for use in the Eclipse SDK only.  It is not intended for installation or use within the STEM application.

• Follow the steps of the STEM/Eclipse Setup to prepare your development environment
• Add the STEM Model Generator Update Site into Eclipse
  1. Launch your Eclipse SDK
  2. Select the Help menu and choose Install New Software

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  3. When the Available Software dialog opens, click Add
  4. In Add Repository dialog, enter the following values:

     Name: STEM Developer Tools

     Location: http://download.eclipse.org/stem/update-site/prerelease/

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  5. Click OK

• Install the STEM Model Generator
  1. From the Available Software dialog, select STEM Developer Tools from the drop down
  2. Choose the STEM Model Generator Feature from the list of available software

     Note: You may have to uncheck Group items by category

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  3. Click Next
  4. On the Install Details page, verify STEM Model Generator Feature is listed

     Note: If you did not install the Eclipse Modeling Framework (EMF) previously, it will be installed automatically

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  5. Click Next
  6. On the Review Licenses page, review the licenses of the required software
     • If you accept all the license terms, select I accept the terms of the license agreements and click Finish
     • If you do NOT accept the terms, click Cancel
  7. The installer will now download and install the software. This process may take 5-10 minutes.
  8. If prompted with a Security Warning that you're about to install unsigned content, click OK

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  9. When the install finishes, you will be prompted to restart Eclipse
     • If all your changes are saved, click Restart Now
     • Otherwise, click Not Now, save any changes, and restart Eclipse

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• After Eclipse restarts, the STEM Model Generator is ready for use

Create a new STEM Computational Model Project

Launch the STEM Model Generator Wizard

1. Open the Eclipse SDK
2. Open the File menu, New, and choose Other

   You can also do Control-N (Command-N on Mac OS X)

3. In the list of Wizards, expand the STEM category and select New STEM Model Project
4. Click Next
5. Choose Create and configure a new STEM Model Package

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6. Click Next

Configure the Model Package

The model package is the container for all models in a given package. A model package generates an Eclipse plug-in project.

Parameter Name	Data Type	Example Value
Package Name	String (Java Identifier)	CattleSalmonellosis
Package Prefix	String (Java Package Identifier)	com.example.diseasemodels

The Package Name and Package Prefix are combined to create the resulting Eclipse plug-in/project identifier. For example, the model package with values above will generate an Eclipse plug-in/project with ID com.example.diseasemodels.cattlesalmonellosis.

Add/Edit a Computational Model

When you're ready to add a computational model to the package, from the Model Package page, click Add Model.

If you want to edit an existing computational model, choose it from the Contained Models list and click Edit Model.

This will launch the Computational Model Wizard.

Configure Model Properties

Model properties are the most basic settings of a STEM Computational Model. Properties include the model's name, the model's type, and which parent model it extends and inherits parameters and compartments from. All are required.

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Property	Type	Example	Description
Model Name	String (Java Identifier)	CattleSalmonella	The model's name.  This value will be the Java class name of the generated model. Should contain alphanumeric characters, no spaces, and cannot begin with a number.
Model Type	String from list	DiseaseModel	The underlying model type. If you're implementing a Disease Model, select DiseaseModel. A Population Model, select PopulationModel. This value is used to find appropriate parent models.
Parent model	Computational Model	SIR	The computational model this new model will extend. If you're not sure, select the textbook model that most closely resembles the compartment model you're implementing (SI, SIR, SEIR)

When you're finished, click Next to configure the Model Parameters

Configure Model Parameters

Model parameters - also called rate parameters - represent user-defined variables that are passed into the computational model. The values can represent many things, but are often variables to the differential equations that make up the model. Users are asked to provide values for these parameters when a new Disease/Population/etc is created in STEM. Examples include Transmission Rate, Immunity Loss Rate, etc.

By default, a model inherits parameters from its ancestor models. These are show in light gray italics. You cannot edit or remove parameters inherited from another model.

To add a new model parameter, click Add Parameter. To edit an existing parameter, select one from the list and click Edit Parameter.

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When you click Add or Edit Parameter, the Model Parameter Editor window opens. Use the form provided to set the properties for the model parameter.

Property	Required?	Type	Example	Description
Name	Yes	String (Java Identifier)	transmissionRate2	The parameter's name. This is the name of the Java member variable in the resulting computational model. This required property is a Java identifier and should contain alphanumeric characters, no spaces, and cannot begin with a number.
Display Name	Yes	String	Transmission Rate 2	The display name of the parameter.  This should be a short, user-friendly description of the parameter.
Data Type	Yes	EClassifier	double	The data type of the parameter.  This will be the Java type of the resulting member variable.  Tip: For models with multiple populations, select a ValueList or ValueMatrix data type.
Default Value	Yes**	Type-specific	0.0	The default value of the parameter if a value is not provided by the user.  A default value often accompanies the parameter in literature. **This field is required for numeric data types (like double, integer, float, etc).
Constraints	No	Constraint	minValue	Parameter constraints are used to restrict the allowed parameter values. See below for more details about Parameter Constraints.
Units	No	String	PM/TP	User interface message that explains what units are expected for this parameter
Help Message	No	String		User interface message that further explains the purpose or other details about this parameter.
Missing Message	No	String		User interface message that displays when no value is entered for this parameter.
Invalid Message	No	String		User interface message that displays when an invalid value (e.g. violates the constraints) is entered for this parameter.

Parameter Constraints

Parameter constraints are used to restrict the allowed values for a model parameter. A parameter can have multiple constraints. Each constraint is evaluated independently and must be fulfilled for a value to be accepted.

To Add a constraint, click Add . To edit an existing constraint, select one from the constraint list and click Edit.

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Use the Constraint Editor to select the Constraint Type and enter a Constraint Value.

Available Constraints

Constraint Type	Example Constraint Value	Description
minValue	0.0	The minimum numeric value allowed for the parameter
maxValue	1.0	The maximum numeric value allowed for the parameter
More constraint types coming soon...

Configure Model Compartments

Run the Code Generator

Edit an existing computational model

The STEM Metamodel

Use an existing EMF Ecore/GenModel with the Model Generator