Revision as of 17:58, 25 August 2010

Sample Projects Available For Download

The STEM home page ([[1]]) contains several example projects users can import and run with STEM. STEM is designed to allow collaboration and sharing of work by simply importing and exporting projects from your workspace. For information on how to import a project please see: Importing and Exporting Projects

The Square Lattice demo described below requires STEM version dated July 1, 2010 or later The SuperContinentExample project requires GlobalGeography to exist in the STEM workspace before it any of the examples can run.

Some of the example projects you can download are very large as they contain continents or even groups of continents. Before you try to run any of these large scenarios you must make sure you allocate enough system memory for STEM. If you don't do this the application may hang or crash with a "Heap Space" error. To allocate enough memory in Windows, create a shortcut for launching STEM. You may place this anywhere (e.g., on your desktop or on the quicklaunch bar).

Right click on the shortcut. Select "Properties" You should see a field in the Properties Dialogue labeled Target: to the right in the text field you will see something like

C:\stem_builds\stem\STEM.exe -vmargs -Xms812M -Xmx812M

To launch STEM with more memory you must add "virtual machine arguments" to the target line. For example, Target:

C:\stem_builds\stem\STEM.exe -vmargs -Xms896M -Xmx896M

Should work for the demo projects available.

On MAC OS X, using the finder, navigate to where the STEM application is located, right click and select "Show Package Content". Navigate to Contents->MacOS and open the STEM.ini file in an editor. Change the -Xms and the -Xmx lines to increase the memory, e.g. -Xms896M -Xmx 896M or more depending on how much memory is available.

Multi-Population Example

Figure 1. Square lattice world where the anopheles and human population is evenly distributed on each lattice square

Figure2: Square lattice world where there is a human village located in the center square

The Multi-Population disease model example shows a very much simplified Malaria model spreading across a 3x3 square lattice world

Square Lattice Example

Figure 1. Square Lattice Example

The Square Lattice Example shows how a square lattice, migration edges, and initial population gradient can be used to model the interaction between an infected and uninfected population. It also demonstrates the hierarchy required to set up a SquareLatticeScenario.scenario: disease models must contain population models, and population models must contain initialized graphs, etc.

As illustrated in the figures that follow, the Square Lattice Example shows how to use migration edges to create two population gradients that cause a population to spread out over space and time. Only one of two populations is initially infected with a disease so you can see both the spread of disease within the original population as well as the eventual transmission from the infected population to the susceptible group when they meet. To accomplish this, the example uses both a standard population model and a Population Initializer (see Figure 1 below and the Tutorial on Using Structured Populations). The population initializer places an initial number of individuals at two separate locations at time zero. Migration edges exist (with equal migration rates) in both directions between all sites but, because there is a population gradient, the population spreads out or diffuses across the lattice.

Note that the components that appear when you click on SquareLatticeScenario.scenario (Figure 1, right) are hierarchical. The two population initializers are placed within the innermost option, HumanPopulation1.standard. The standard population object (HumanPopulation.standard) depends on the existence of the initialized graph and, therefore, is placed in the outer HumanPopulationModel. Both of these submodels are components or bundles that can be reused across many scenarios. Finally, the disease itself (Flu.standard) is a human disease that depends on a contained human model so it is placed in the outermost model of the hierarchy (FluLatticeModel). This too is a reusable component.

The Infector for the disease (FluInfector.standard) depends on a model of what is already known about the disease. An infector changes the state of a model by moving individuals from the susceptible state to the infectious state (given the presence of the indicated disease). As such, an infector is really part of the scenario - the topmost level in the hierarchy that contains ALL models.

In the figures below, you can see the initial population spread by migration edges. In the same simulation at runtime you can select the disease as the property to display and watch the disease spread.

Figures 2a-c. Spread of the Human Population by Migration Edges

The figures above show the spread of the population itself by migration edges. The population is seeded in the center (10x10) and in a node just left of center. The center population is much larger than the smaller seed to the left (the intensity is saturated). Only the population to the left is infected initially. Open the infector and the population initializer in the property editor to see the initial values. As the infected population on the left spreads, it eventually makes contact with and infects the main population spreading from the center.

Figures 3a-c. Spread of the Disease

The figures above show the same simulation but display the fraction of people infected as a function of time. Note that the intensity does not reflect the NUMBER of infections (only the fraction). When the infected population on the left reaches the much larger fully susceptible (but not yet infected) population spreading from the right, the intensity actually goes down as the fraction of people infected drops (initially) at the point of contact (see the middle image above). Eventually (right) the main population also becomes infected.

Mexico/USA H1N1 Scenario

Global Geographic Models Only

The Global Geographic Models project contains no runnable scenarios. Rather, is contains a set of pre-composed models for large regions of the world intended to be built upon in developing your own scenarios. These models, shown int he figure below, include a model for global air transportation, and a set of continent and super-continent models for geographic regions and people. After you download them, please expand them to see the inner components.

Super-Continent Examples

The Super-Continent Scenarios provide an examples of how to construct scenarios using the Global Model examples described above. These scenarios show how to model large regions such as the Americas, Europe+Africa, and Europe+Asia. The figure below expands the Eur-Africa Scenario. Note that the Inner Eur-Africa Model contains a model for Europe, a model for Africa, together with the connection between Spain and Morocco.