Sat . 19 Apr 2019

Spatiotemporal Epidemiological Modeler

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The Spatiotemporal Epidemiological Modeler STEM is a free software 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 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 These plug-ins contain global data including geographic data, population data, demographics, and basic models of disease 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 transportation, such as connections by roads 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 can be assembled with a drag and drop interface New disease vectors can simply 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 also exchange these models and scenarios as reusable components and thereby build on each other's work As an 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

External links

  • Original version of STEM from IBM Alphaworks
  • STEM Current version updated weekly from the Eclipse Foundation
  • Compartmental models in epidemiology
  • Epidemic model
  • STEM Wiki
  • STEM Newsgroup
  • English Language STEM Tutorial
  • Graphical Model Designer STEM Tutorial

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