7/31/2019 Spatiotemporal Epidemiological Modeler
1/1
Spatiotemporal Epidemiological Modeler
The Spatiotemporal Epidemiological Modeler (STEM) is a free
software available through the EclipseFoundation. Originally
developed by IBM Research, STEM is a framework and development
tooldesigned to help scientists create and use spatial and temporal
models of infectious disease. STEM uses acomponent software
architecture based on the OSGi standard. The Eclipse Equinox
platform is areference implementation of that standard. By using a
component software architecture, all of thecomponents or elements
required for a disease model, including the code and the data are
available assoftware building blocks that can be independently
exchanged, extended, reused, or replaced. Thesebuilding blocks or
plug-ins are called eclipse "plug-ins" or "extensions". STEM
plug-ins containdenominator data for administrative regions of
interest. The regions are indexed by standard (ISO3166)codes.
STEM currently includes a large number of plug-ins for the 244
countries and dependent areas defined bythe Geographic Coding
Standard maintained by the International Organization for
Standardization. Theseplug-ins contain global data including
geographic data, population data, demographics, and basic modelsof
disease. The disease models distributed with STEM include
epidemiological compartment models.
Other plug-ins describe relationships between regions including
nearest-neighbor or adjacencyrelationships as well as information
about transportation, such as connections by roads and a model of
airtransportation.
Relationships between regions can then be included in models of
how a disease spreads from place toplace. To accomplish this, STEM
represents the world as a "graph". The nodes in the graph
correspond toplaces or regions, and the edges in the graph describe
relationships or connections between regions. Boththe nodes and the
ed ges can be labeled or decorated with a variety of denominator
data and models.This graphical representation is implemented using
the Eclipse Modeling Framework (EMF). Since amodel can be built up
using separate subgraphs, STEM enables model composition.
Predefined subgraphsdefining different countries can be assembled
with a drag and drop interface. New disease vectors cansimply be
added to existing models by augmenting the model with a new set of
edges. The architecture
also supports collaboration as users can not only create new
models and compose new scenarios but alsoexchange these models and
scenarios as reusable components and thereby build on each other's
work. Asan open source project, users are encouraged to create
their own plug-ins (both data and models) and, if appropriate, to
contribute their work back to the project.
Source: http://www.eclipse.org/stem/
