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Difference between revisions of "STEM FAQ"

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[[Image:STEM_SPLASH_TOPs.jpg|800px]]
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[[Image:STEM SPLASH TOPs.jpg|800px]]  
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{| align="right"
 
{| align="right"
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  | __TOC__
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| __TOC__
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== What is the STEM project release schedule? ==
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== What is the STEM project release schedule? ==
  
 
STEM V1.0 was officially released on Feb. 18, 2010, all platforms  
 
STEM V1.0 was officially released on Feb. 18, 2010, all platforms  
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*Incubation Release 0.2.1 became available December 17th, 2007, updating release 0.2.0 dated June 8th, 2007.
 
*Incubation Release 0.2.1 became available December 17th, 2007, updating release 0.2.0 dated June 8th, 2007.
  
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All releasese include the current STEM source code and downloadable executables for Windows, Linux and Mac OS X.
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All releasese include the current STEM source code and downloadable executables for Windows, Linux and Mac OS X.  
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== What platforms are supported? ==
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STEM will run on any platform supported by Eclipse. Downloads are available for RCP versions of Windows, Linux, and Mac OSX. Java 1.6 and the latest is required. The STEM development environment requires the latest version of Eclipse.If a downloadable RCP version is not available for your platform, you must download the STEM source from Eclipse and run from the source.
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==What features are new in release 0.5.0?==
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==What features are new in release 0.4.0?==
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==What features are new in release 0.3.0a?==
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* Experiments.  An Experiment is a combination of a Scenario and a set of Modifiers.  A Modifier is a definition of how to systematically change the value of some element of a Scenario in a specific manner. The intent is to be able to specify how to create a sequence of derivative Scenarios from the base Scenario referenced by the Experiment.  These derivative Scenarios are created by applying the Modifiers to the base Scenario.  An Experiment can be executed like Scenario creating a Batch which then spawns off separate Simulations from each of the derivative Scenarios.  Currently, the Simulations in a Batch are run sequentially. Parallel execution is planned for a future release.
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* A preliminary implementation of Triggers (Predicate & Action).  A Trigger is a combination of a Boolean Predicate and an Action.  At each cycle in the simulation, if the Boolean expression is True, then the Action is "triggered".  An action is a "Modifier" and can change arbitrary components of a running simulation including things like the values of labels in the graph (e.g., to close an airport) or the parameters of a disease model.  Currently, the predicates are limited to testing the absolute or elapsed time value.  This limitation will be removed in a future release.
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* Various improvements to the visualizations including display of the graph edges
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* A new Analysis Perspective
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The Analysis and Validation Perspective is a new STEM Perspective that supports a variety of analysis, fitting, and comparison functions across multiple simulations and data sets.
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'''Model Parameter Estimation View'''
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Given a set of data (SI, SIR, or SEIR) as a function of time, this perspective provides an estimation of the model parameters for a standard compartment model of the corresponding type. The view provides estimates for:
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beta, the disease transmission rate
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alpha, the recovery rate
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epsilon, the incubation rate
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gamma,the immunity loss rate
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'''Dynamical Systems View (Lyapunov Analysis)'''
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== What platforms are supported?  ==
  
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This view displays the rate of separation in phase space (I vs. S) of the trajectories representing two different data sets or disease models. The rate of separation is then plotted vs time in a second chart. The rate of spread of any infectious disease defines a dynamical system. The Lyapunov exponent of any dynamical system describes the rate of separation of infinitesimally close trajectories in phase space.  
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STEM will run on any platform supported by Eclipse. Downloads are available for RCP versions of Windows, Linux, and Mac OSX. Java 1.6 and the latest is required. The STEM development environment requires the latest version of Eclipse.If a downloadable RCP version is not available for your platform, you must download the STEM source from Eclipse and run from the source.  
  
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== What features are new? ==
  
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'''Cross Model Comparison (RMS compare)'''
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http://wiki.eclipse.org/index.php/STEM#What.27s_New<br>
  
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Given a data set and the results of a model (or two model generated data sets), the Root Mean Square (RMS) comparison function shows the RMS difference between the two as a function of time.
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== What are other features are available in STEM? ==
  
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*A full implementation of the STEM graph based simulation engine for [http://www.google.com/search?hl=en&q=spatiotemporal%20 spatiotemporal] modeling
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'''The Epidemic View'''
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This view displays the aggregated data (e.g., S,E,I,R, births, and deaths) as a function of time. It also creates a summary file integrating over the data from all locations in a previously run scenario. It also shows the incidence or "newly infectious count" for the aggregated data.
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*Geographic visualization of the spread of disease using internally implemented graphics
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*Geographic visualization of the spread of disease using [http://earth.google.com/ Google Earth]
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*"Wizards" to create Projects, Graphs, Models, Scenarios, Sequencers, and Diseases
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*Visual editors to edit Graphs, Models, Scenarios, Sequencers, and Diseases
  
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==What are other features are available in STEM?==
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*A complete data set that defines all of the countries specified by the [http://en.wikipedia.org/wiki/ISO_3166 ISO-3166 standard] includes area land mass and recent human population data
  
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* A full implementation of the STEM graph based simulation engine for [http://www.google.com/search?hl=en&q=spatiotemporal%20 spatiotemporal] modeling
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*A complete Lat/Long data set in [http://en.wikipedia.org/wiki/Geography_Markup_Language Geography Markup Language] (GML) format for all countries defined by the [http://en.wikipedia.org/wiki/ISO_3166 ISO-3166 standard]
  
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* Geographic visualization of the spread of disease using internally implemented graphics
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*An extensive set of predefined "Graph" fragments that can be reused in user Models
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* Geographic visualization of the spread of disease using [http://earth.google.com/ Google Earth]
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*An extensive set of predefined "Models", one for each country, that can be reused in user Models and Scenarios
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* "Wizards" to create Projects, Graphs, Models, Scenarios, Sequencers, and Diseases
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*A set of predefined "Scenarios" that illustrate disease spread models around the Earth
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* Visual editors to edit Graphs, Models, Scenarios, Sequencers, and Diseases
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*A predefined SEIR disease model for the [http://en.wikipedia.org/wiki/Spanish_flu Spanish Flu]  
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*Deterministic implementations of SI, SIR and SEIR disease models.
  
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* A complete data set that defines all of the countries specified by the [http://en.wikipedia.org/wiki/ISO_3166 ISO-3166 standard] includes area land mass and recent human population data
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== What features are planned for future releases? ==
  
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* A complete Lat/Long data set in [http://en.wikipedia.org/wiki/Geography_Markup_Language Geography Markup Language] (GML) format for all countries defined by the [http://en.wikipedia.org/wiki/ISO_3166 ISO-3166 standard]
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For the latest release and plan information, please visit the STEM Project Plan Page
  
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* An extensive set of predefined "Graph" fragments that can be reused in user Models
 
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* An extensive set of predefined "Models", one for each country, that can be reused in user Models and Scenarios
 
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* A set of predefined "Scenarios" that illustrate disease spread models around the Earth
 
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* A predefined SEIR disease model for the [http://en.wikipedia.org/wiki/Spanish_flu Spanish Flu]
 
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* Deterministic implementations of SI, SIR and SEIR disease models.
 
  
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==What features are planned for future releases?==
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== Can STEM be used for more than just disease modeling? ==
  
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* New experimental disease models
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In principle, yes (but only in principle). The core components of STEM implement a graph based spatiotemporal simulation engine. The components that extend it to disease modeling are in separate plug-ins and integrate themselves using Eclipse extension points. Today we are focused on supporting a framework for modeling diseases.
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* Enhanced editor functionality (better Drag'n Drop)
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* Improvements in the interface (menu, layout, wizards, etc.)
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* Improved documentation
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* Improved build environment
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* Lots of bug fixes
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==Can STEM be used for more than just disease modeling?==
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== Where can I find some tutorials on STEM? ==
  
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Yes.  The core components of STEM implement a graph based spatiotemporal simulation engine.  The components that extend it to disease modeling are in separate plug-ins and integrate themselves using Eclipse extension points.
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[Tutorials_for_Developers]
  
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==What is the most novel extension to STEM?==
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== Where can I learn about the design of STEM? ==
  
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The idea of creating a "pandemic game" out of STEM has been discussed by its developers for some time.  The basic idea would be to have "players" use their copies of STEM to connect to a central server with a single shared model.  The players would make (or not make) decisions based upon their geographic assignment and these would be communicated to the server which would then update and propagate the changes to the model to the distributed player machines.
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[Tutorials_for_Developers]
  
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==Can STEM be used for "situational awareness"?==
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http://wiki.eclipse.org/STEM#Publications_and_Presentations_on_STEM
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[Publications_and_Presentations_on_STEM]
  
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Yes.  Basically, you can run a simulation in "real-time" with a Decorator that interfaces to the outside world.  That Decorator can access data from outside of the simulation (e.g., from a database or a web service) and then "inject" it into the canonical graph that holds the state of the simulation.
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== Are there publications where I can read more about STEM ? ==
  
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It should be possible to extend STEM to use an existing simulation to initialize other simulations so that users could monitor the world and then spawn off different identically initialized Scenarios that simulate different options given the current world state.
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http://wiki.eclipse.org/STEM#Publications_and_Presentations_on_STEM
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[Publications_and_Presentations_on_STEM]

Revision as of 14:03, 8 June 2010

STEM SPLASH TOPs.jpg

What is the STEM project release schedule?

STEM V1.0 was officially released on Feb. 18, 2010, all platforms

For the latest release and plan information, please visit the STEM Project Plan Page

Older Releases

  • Incubation Release 0.5.0 was released on June 14th, 2009, all platforms
  • Incubation Release 0.4.0 was released on January 28th, 2009, all platforms
  • Incubation Release 0.3.0a was released on September 13th, 2008 (Windows only), replacing release 0.3.0 from September 9th, 2008.
  • Incubation Release 0.2.1 became available December 17th, 2007, updating release 0.2.0 dated June 8th, 2007.

All releasese include the current STEM source code and downloadable executables for Windows, Linux and Mac OS X.

What platforms are supported?

STEM will run on any platform supported by Eclipse. Downloads are available for RCP versions of Windows, Linux, and Mac OSX. Java 1.6 and the latest is required. The STEM development environment requires the latest version of Eclipse.If a downloadable RCP version is not available for your platform, you must download the STEM source from Eclipse and run from the source.

What features are new?

http://wiki.eclipse.org/index.php/STEM#What.27s_New

What are other features are available in STEM?

  • A full implementation of the STEM graph based simulation engine for spatiotemporal modeling
  • Geographic visualization of the spread of disease using internally implemented graphics
  • Geographic visualization of the spread of disease using Google Earth
  • "Wizards" to create Projects, Graphs, Models, Scenarios, Sequencers, and Diseases
  • Visual editors to edit Graphs, Models, Scenarios, Sequencers, and Diseases
  • A complete data set that defines all of the countries specified by the ISO-3166 standard includes area land mass and recent human population data
  • An extensive set of predefined "Graph" fragments that can be reused in user Models
  • An extensive set of predefined "Models", one for each country, that can be reused in user Models and Scenarios
  • A set of predefined "Scenarios" that illustrate disease spread models around the Earth
  • A predefined SEIR disease model for the Spanish Flu
  • Deterministic implementations of SI, SIR and SEIR disease models.

What features are planned for future releases?

For the latest release and plan information, please visit the STEM Project Plan Page


Can STEM be used for more than just disease modeling?

In principle, yes (but only in principle). The core components of STEM implement a graph based spatiotemporal simulation engine. The components that extend it to disease modeling are in separate plug-ins and integrate themselves using Eclipse extension points. Today we are focused on supporting a framework for modeling diseases.

Where can I find some tutorials on STEM?

[Tutorials_for_Developers]

Where can I learn about the design of STEM?

[Tutorials_for_Developers]

http://wiki.eclipse.org/STEM#Publications_and_Presentations_on_STEM [Publications_and_Presentations_on_STEM]

Are there publications where I can read more about STEM ?

http://wiki.eclipse.org/STEM#Publications_and_Presentations_on_STEM [Publications_and_Presentations_on_STEM]

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