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Difference between revisions of "STEM FAQ"

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==What is the STEM project release schedule?==
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[[Image:STEM TOP BAR.gif|800px]]
  
Release 0.3.0a was released on September 13th, 2008 (Windows only), replacing release 0.3.0 from September 9th, 2008.
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{| align="right"
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|-
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| __TOC__
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|}
  
Release 0.2.1 became svailable December 17th, 2007, updating release 0.2.0 dated June 8th, 2007.  
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'''[http://wiki.eclipse.org/STEM Back]'''
  
These include the current STEM source code and downloadable executables for Windows, Linux and Mac OS X.
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== Where should I start?  ==
 +
To learn about how to use STEM, please read the [[STEM#STEM_Documentation | Tutorials]]
  
==What platforms are supported?==
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The most important tutorial is probably the one that teaches about [[Creating a STEM Scenario]]
  
In theory, STEM will run on any platform supported by Eclipse.  The current downloads are for RCP versions of Windows, Linux, and Mac OSX.  Note that Java 1.6 is required for MacOS.
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To learn about the design of STEM, please read the [[STEM Design Document]]
  
If a downloadable RCP version is not available for your platform, you must download the STEM source from CVS and run from the source.
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== 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? ==
  
==What features are new in release 0.3.0a?==
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Please see [[What's New in STEM]]
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<br>
  
* 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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== What are other features are available in STEM? ==
  
* 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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*A full implementation of the STEM graph based simulation engine for [http://www.google.com/search?hl=en&q=spatiotemporal%20 spatiotemporal] modeling
  
* Various improvements to the visualizations including display of the graph edges
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*Geographic visualization of the spread of disease using internally implemented graphics
 +
*Geographic visualization of the spread of disease using [http://earth.google.com/ Google Earth]
 +
*"Wizards" to create Projects, Graphs, Models, Scenarios, Sequencers, and Diseases
 +
*Visual editors to edit Graphs, Models, Scenarios, Sequencers, and Diseases
  
* A new Analysis Perspective
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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
  
 +
*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]
  
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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*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 wide variety of mathematical models of infectious disease
 +
*Lots more. We are adding features all the time
  
 +
== What features are planned for future releases? ==
  
'''Model Parameter Estimation View'''
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For the latest release and plan information, please visit the [http://www.eclipse.org/projects/project-plan.php?projectid=technology.stem STEM Project Plan Page]
  
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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== Can STEM be used for more than just disease modeling? ==
  
beta, the disease transmission rate
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In principle, 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. Today we are focused on supporting a framework for modeling diseases. In order to model diseases one must also model populations, transportation, etc. So STEM is really a way to build models on top of other models. Some models, like models of insect vectors, may depend on global data including things like climate factors. All this "denominator" data is available as STEM plugins. Some users have build higher level economic models on top of disease models in STEM.
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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== Where can I find some tutorials on STEM? ==
  
'''Dynamical Systems View (Lyapunov Analysis)'''
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*[[STEM#STEM_Documentation | Tutorials for Developers]]
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*STEM Tutorials on YouTube<sup>TM</sup>
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#Full length video [http://www.youtube.com/watch?v=LfiibQX4IFE In English]
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#Full length video [http://www.youtube.com/watch?v=AFYXvazKkms In Hebrew]
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#Full length video [http://www.youtube.com/watch?v=NM5X8-MaiKo In Japanese]
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#Full length video [http://www.youtube.com/watch?v=3S5DbjCHsx4 In Spanish]
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#[http://www.youtube.com/watch?v=OoiFLemepw4 5 min Video (English)]
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*[http://www.eclipse.org/stem/talksOnline.php Scientific Talks Online]
  
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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== Where can I learn about the design of STEM? ==
  
 +
[[STEM Design Document]]
  
'''Cross Model Comparison (RMS compare)'''
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== Are there publications where I can read more about STEM ? ==
  
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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[http://wiki.eclipse.org/STEM#Publications_and_Presentations_on_STEM Publications and Presentations on STEM]
  
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== How can I contribute to STEM ? ==
'''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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Please see [[Join the STEM Community|How to Join the STEM Community]]
  
==What are other features are available in STEM?==
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You may also contact the [[The STEM Development Team| STEM developers]]
  
* A full implementation of the STEM graph based simulation engine for [http://www.google.com/search?hl=en&q=spatiotemporal%20 spatiotemporal] modeling
+
New Contributors to STEM are always welcome. This includes not only researchers interested in disease modeling but also experts in GIS data or any other data that might be important in understanding or modeling the spread of infectious disease. We also welcome input from users and contributions to our documentation.
  
* Geographic visualization of the spread of disease using internally implemented graphics
+
To contribute to STEM, please use the standard Eclipse process. Open a "bug" in our bugzilla (https://bugs.eclipse.org/bugs/)
* Geographic visualization of the spread of disease using [http://earth.google.com/ Google Earth]
+
A bug can be more than just a new defect - it can also be a new feature or other contribution.
* "Wizards" to create Projects, Graphs, Models, Scenarios, Sequencers, and Diseases
+
You can attach your contribution as a "patch" to your bug (http://wiki.eclipse.org/index.php/Bug_Reporting_FAQ)
* Visual editors to edit Graphs, Models, Scenarios, Sequencers, and Diseases
+
Please also feel free to e-mail the STEM development team, many of whom are Eclipse Committers [http://wiki.eclipse.org/index.php/STEM#The_STEM_Development_Team The STEM Development Team]. For those interested in joining the project, we also have a weekly phone call and a newsgroup, etc.
  
* 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
+
== Where can I get more help ? ==
  
* 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]
+
Please start by reading the extensive documentation on our [http://wiki.eclipse.org/index.php/STEM wiki] and our [http://www.eclipse.org/stem/ website]. The STEM community also has a weekly conference call.  
 
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The call is held most Thursdays at 12PM ET (9AM PDT).
* An extensive set of predefined "Graph" fragments that can be reused in user Models
+
For more information, or if you wish to join, please send mailto:judyvdouglas@verizon.net
* 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 [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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* New experimental disease models
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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
+
 
+
==Can STEM be used for more than just disease modeling?==
+
 
+
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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==What is the most novel extension to 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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==Can STEM be used for "situational awareness"?==
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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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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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Revision as of 13:47, 4 February 2013

STEM TOP BAR.gif

Back

Where should I start?

To learn about how to use STEM, please read the Tutorials

The most important tutorial is probably the one that teaches about Creating a STEM Scenario

To learn about the design of STEM, please read the STEM Design Document

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?

Please see What's New in STEM

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 wide variety of mathematical models of infectious disease
  • Lots more. We are adding features all the time

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. 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. In order to model diseases one must also model populations, transportation, etc. So STEM is really a way to build models on top of other models. Some models, like models of insect vectors, may depend on global data including things like climate factors. All this "denominator" data is available as STEM plugins. Some users have build higher level economic models on top of disease models in STEM.

Where can I find some tutorials on STEM?

  1. Full length video In English
  2. Full length video In Hebrew
  3. Full length video In Japanese
  4. Full length video In Spanish
  5. 5 min Video (English)

Where can I learn about the design of STEM?

STEM Design Document

Are there publications where I can read more about STEM ?

Publications and Presentations on STEM

How can I contribute to STEM ?

Please see How to Join the STEM Community

You may also contact the STEM developers

New Contributors to STEM are always welcome. This includes not only researchers interested in disease modeling but also experts in GIS data or any other data that might be important in understanding or modeling the spread of infectious disease. We also welcome input from users and contributions to our documentation.

To contribute to STEM, please use the standard Eclipse process. Open a "bug" in our bugzilla (https://bugs.eclipse.org/bugs/) A bug can be more than just a new defect - it can also be a new feature or other contribution. You can attach your contribution as a "patch" to your bug (http://wiki.eclipse.org/index.php/Bug_Reporting_FAQ) Please also feel free to e-mail the STEM development team, many of whom are Eclipse Committers The STEM Development Team. For those interested in joining the project, we also have a weekly phone call and a newsgroup, etc.

Where can I get more help ?

Please start by reading the extensive documentation on our wiki and our website. The STEM community also has a weekly conference call. The call is held most Thursdays at 12PM ET (9AM PDT). For more information, or if you wish to join, please send mailto:judyvdouglas@verizon.net