Spatiotemporal Epidemiological Modeler
Encyclopedia
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 transport
ation, such as connections
by road
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
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.
Free software
Free software, software libre or libre software is software that can be used, studied, and modified without restriction, and which can be copied and redistributed in modified or unmodified form either without restriction, or with restrictions that only ensure that further recipients can also do...
available through the Eclipse Foundation
Eclipse Foundation
The Eclipse Foundation is a not-for-profit, member supported corporation that hosts the open-source Eclipse Projects and helps cultivate both an open source community and an ecosystem of complementary products and services...
. Originally developed by IBM Research
IBM Research
IBM Research, a division of IBM, is a research and advanced development organization and currently consists of eight locations throughout the world and hundreds of projects....
, STEM is a framework and development tool designed to help scientists create and use spatial
Space
Space is the boundless, three-dimensional extent in which objects and events occur and have relative position and direction. Physical space is often conceived in three linear dimensions, although modern physicists usually consider it, with time, to be part of a boundless four-dimensional continuum...
and temporal
Time
Time is a part of the measuring system used to sequence events, to compare the durations of events and the intervals between them, and to quantify rates of change such as the motions of objects....
models of infectious disease. STEM uses a component software architecture
Component-based software engineering
Component-based software engineering is a branch of software engineering that emphasizes the separation of concerns in respect of the wide-ranging functionality available throughout a given software system...
based on the OSGi
OSGi
The Open Services Gateway initiative framework is a module system and service platform for the Java programming language that implements a complete and dynamic component model, something that does not exist in standalone Java/VM environments...
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
Denominator data
-Definition:In epidemiology, data or facts about a population is called denominator data. Denominator data is independent of any specific disease or condition. Disease specific data includes the incidence of disease in a population, the susceptibility of the population to a specific condition, the...
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
International Organization for Standardization
The International Organization for Standardization , widely known as ISO, is an international standard-setting body composed of representatives from various national standards organizations. Founded on February 23, 1947, the organization promulgates worldwide proprietary, industrial and commercial...
. These plug-ins contain global data including geographic data
Geographic data
Geographic data is about much more than electronic pictures of maps.The geographic data that describes our world allows for city planning, flood prediction and relief, emergency service routing, environmental assessments, wind pattern monitoring and many other applications.Geographic data is...
, population data
Census
A census is the procedure of systematically acquiring and recording information about the members of a given population. It is a regularly occurring and official count of a particular population. The term is used mostly in connection with national population and housing censuses; other common...
, demographics
Demographics
Demographics are the most recent statistical characteristics of a population. These types of data are used widely in sociology , public policy, and marketing. Commonly examined demographics include gender, race, age, disabilities, mobility, home ownership, employment status, and even location...
, and basic models of disease
Compartmental models in epidemiology
In order to model the progress of an epidemic in a large population, comprising many different individuals in various fields, the population diversity must be reduced to a few key characteristics which are relevant to the infection under consideration...
. The disease models distributed with STEM include epidemiological compartment models
Compartmental models in epidemiology
In order to model the progress of an epidemic in a large population, comprising many different individuals in various fields, the population diversity must be reduced to a few key characteristics which are relevant to the infection under consideration...
. Other plug-ins describe relationships between regions including nearest-neighbor or adjacency
Adjacent
Adjacent is an adjective meaning contiguous, adjoining or abuttingIn geometry, adjacent is when sides meet to make an angle.In graph theory adjacent nodes in a graph are linked by an edge....
relationships as well as information about transport
Transport
Transport or transportation is the movement of people, cattle, animals and goods from one location to another. Modes of transport include air, rail, road, water, cable, pipeline, and space. The field can be divided into infrastructure, vehicles, and operations...
ation, such as connections
Connectedness
In mathematics, connectedness is used to refer to various properties meaning, in some sense, "all one piece". When a mathematical object has such a property, we say it is connected; otherwise it is disconnected...
by road
Road
A road is a thoroughfare, route, or way on land between two places, which typically has been paved or otherwise improved to allow travel by some conveyance, including a horse, cart, or motor vehicle. Roads consist of one, or sometimes two, roadways each with one or more lanes and also any...
s and a model of air transportation
Aviation
Aviation is the design, development, production, operation, and use of aircraft, especially heavier-than-air aircraft. Aviation is derived from avis, the Latin word for bird.-History:...
.
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"
Graph (mathematics)
In mathematics, a graph is an abstract representation of a set of objects where some pairs of the objects are connected by links. The interconnected objects are represented by mathematical abstractions called vertices, and the links that connect some pairs of vertices are called edges...
. The nodes
Vertex (graph theory)
In graph theory, a vertex or node is the fundamental unit out of which graphs are formed: an undirected graph consists of a set of vertices and a set of edges , while a directed graph consists of a set of vertices and a set of arcs...
in the graph correspond to places or regions, and the edges
Edge (geometry)
In geometry, an edge is a one-dimensional line segment joining two adjacent zero-dimensional vertices in a polygon. Thus applied, an edge is a connector for a one-dimensional line segment and two zero-dimensional objects....
in the graph describe relationships or connections between regions. Both the nodes and the edges can be labeled or “decorated”
Graph labeling
In the mathematical discipline of graph theory, a graph labeling is the assignment of labels, traditionally represented by integers, to the edges or vertices, or both, of a graph....
with a variety of denominator data and models. This graphical representation is implemented using the Eclipse Modeling Framework
Eclipse Modeling Framework
Eclipse Modeling Framework is an Eclipse-based modeling framework and code generation facility for building tools and other applications based on a structured data model...
(EMF). Since a model can be built up using separate subgraphs, STEM enables model composition
Object composition
In computer science, object composition is a way to combine simple objects or data types into more complex ones...
. Predefined subgraphs defining different countries
Country
A country is a region legally identified as a distinct entity in political geography. A country may be an independent sovereign state or one that is occupied by another state, as a non-sovereign or formerly sovereign political division, or a geographic region associated with a previously...
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
Collaboration
Collaboration is working together to achieve a goal. It is a recursive process where two or more people or organizations work together to realize shared goals, — for example, an intriguing endeavor that is creative in nature—by sharing...
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
- http://www.alphaworks.ibm.com/tech/stem Original version of STEM from IBM Alphaworks.
- STEM Current version (updated weekly) from the Eclipse FoundationEclipse FoundationThe Eclipse Foundation is a not-for-profit, member supported corporation that hosts the open-source Eclipse Projects and helps cultivate both an open source community and an ecosystem of complementary products and services...
. - Compartmental models in epidemiologyCompartmental models in epidemiologyIn order to model the progress of an epidemic in a large population, comprising many different individuals in various fields, the population diversity must be reduced to a few key characteristics which are relevant to the infection under consideration...
. - STEM Wiki at Eclipsepedia.
- STEM Newsgroup.
- English Language STEM Tutorial on You Tube(TM).
- Spanish Language STEM Tutorial on You Tube(TM).