The Spatiotemporal Epidemiological Modeler (STEM) is

free software Free software, libre software, libreware sometimes known as freedom-respecting software is computer software distributed open-source license, under terms that allow users to run the software for any purpose as well as to study, change, distribut ...

available through the Eclipse Foundation. Originally developed by IBM Research, STEM is a framework and development tool designed to help scientists create and use spatial and temporal models of infectious disease. STEM uses a component software architecture based on the OSGi standard. The Eclipse

Equinox A solar equinox is a moment in time when the Sun appears directly above the equator, rather than to its north or south. On the day of the equinox, the Sun appears to rise directly east and set directly west. This occurs twice each year, arou ...

platform is a reference implementation of that standard. By using a component software architecture, all of the components or elements required for a disease model, including the code and the data are available as software building blocks that can be independently exchanged, extended, reused, or replaced. These building blocks or plug-ins are called eclipse "plug-ins" or "extensions". STEM plug-ins contain denominator 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 by the Geographic Coding Standard maintained by the

International Organization for Standardization The International Organization for Standardization (ISO ; ; ) is an independent, non-governmental, international standard development organization composed of representatives from the national standards organizations of member countries. M ...

. These plug-ins contain global data including geographic data, population data,

demographics Demography () is the statistical study of human populations: their size, composition (e.g., ethnic group, age), and how they change through the interplay of fertility (births), mortality (deaths), and migration. Demographic analysis examin ...

, and basic models of

disease A disease is a particular abnormal condition that adversely affects the structure or function (biology), function of all or part of an organism and is not immediately due to any external injury. Diseases are often known to be medical condi ...

. The disease models distributed with STEM include epidemiological compartment models. Other plug-ins describe relationships between regions including nearest-neighbor or adjacency relationships as well as information about

transport Transport (in British English) or transportation (in American English) is the intentional Motion, movement of humans, animals, and cargo, goods from one location to another. Mode of transport, Modes of transport include aviation, air, land tr ...

ation, such as connections by

road A road is a thoroughfare used primarily for movement of traffic. Roads differ from streets, whose primary use is local access. They also differ from stroads, which combine the features of streets and roads. Most modern roads are paved. Th ...

s and a model of air transportation. Relationships between regions can then be included in models of how a disease spreads from place to place. To accomplish this, STEM represents the world as a "graph". The nodes in the graph correspond to places or regions, and the edges in the graph describe relationships or connections between regions. Both the nodes and the edges 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 a model can be built up using separate subgraphs, STEM enables model composition. Predefined subgraphs defining different

countries A country is a distinct part of the Earth, world, such as a state (polity), state, nation, or other polity, political entity. When referring to a specific polity, the term "country" may refer to a sovereign state, List of states with limited r ...

can be assembled with a drag and drop interface. New

disease vectors In epidemiology, a disease vector is any living agent that carries and transmits an infectious pathogen such as a parasite or microbe, to another living organism. Agents regarded as vectors are mostly blood-sucking ( hematophagous) arthropods such ...

can simply be added to existing models by augmenting the model with a new set of edges. The architecture also supports

collaboration Collaboration (from Latin ''com-'' "with" + ''laborare'' "to labor", "to work") is the process of two or more people, entities or organizations working together to complete a task or achieve a goal. Collaboration is similar to cooperation. The ...

as users can not only create new models and compose new scenarios but also exchange these models and scenarios as reusable components and thereby build on each other's work. As an

open source Open source is source code that is made freely available for possible modification and redistribution. Products include permission to use and view the source code, design documents, or content of the product. The open source model is a decentrali ...

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.

References

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External links

* /www.eclipse.org/stem/ STEM Free science software Free health care software Epidemiology Public health and biosurveillance software IBM software Space and time