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(STEM Documentation)
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== '''Ebola Community Efforts''' ==
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== '''STEM Community Phone Call''' ==
  [[Community Ebola Modeling Phone Call]]  
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  '''[[Ebola Models]]'''
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  The STEM community runs a [[Join the STEM Community|monthly phone call]] anyone is free to join.
[https://wiki.eclipse.org/Ebola_How_To How to install the Ebola models]  
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  The special series of [[Community Ebola Modeling Phone Call]]s has been merged back with our regular [[Join the STEM Community|monthly phone call]].
  Literature [[Ebola References]]
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  You can still see all the Ebola content [[Join the STEM Community#Ebola Community Efforts|here]]
Data [[Ebola Reference Data]]
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''Please sign up for the'' [https://dev.eclipse.org/mailman/listinfo/stem-ebola stem-ebola mailing list]
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== '''STEM Documentation''' ==
 
== '''STEM Documentation''' ==
  
The '''Spatio-Temporal Epidemiological Modeler (STEM)''' is a tool designed to help scientists and public health officials create and use models of emerging infectious diseases. STEM uses mathematical models of diseases (based on differential equations) to simulate the development or evolution of a disease in space and time (e.g., avian flu or salmonella). These models could aid in understanding, and potentially preventing, the spread of such diseases. STEM also comes pre-configured with a vast amount of reference or denominator data for the entire world. By using and extending the data and models in STEM it is possible to rapidly prototype and test models for emerging infectious disease. STEM also provides tools to help you compare and validate your models. As an open source project, the ultimate goal of STEM is to support and encourage a community of scientists that not only use STEM as a tool but also contribute back to it. STEM is designed so that models and scenarios can be easily shared, extended, and built upon.
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The '''Spatio-Temporal Epidemiological Modeler (STEM)''' is a tool designed to help scientists and public health officials create and use models of emerging infectious diseases. STEM uses mathematical models of diseases (based on differential equations) to simulate the development or evolution of a disease in space and time (e.g., avian flu or salmonella). These models could aid in understanding, and potentially preventing, the spread of such diseases. STEM also comes pre-configured with a vast amount of reference or denominator data for the entire world. By using and extending the data and models in STEM it is possible to rapidly prototype and test models for emerging infectious disease. STEM also provides tools to help you compare and validate your models. As an open source project, the ultimate goal of STEM is to support and encourage a community of scientists who not only use STEM as a tool but also contribute back to it. STEM is designed so that models and scenarios can be easily shared, extended, and built upon.
  
 
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<!-- upper left (INTRODUCTORY RESOURCES GO HERE) -->
 
<!-- upper left (INTRODUCTORY RESOURCES GO HERE) -->
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*[[Installation Guide]]
 
*[http://www.eclipse.org/stem/ The STEM Website]  
 
*[http://www.eclipse.org/stem/ The STEM Website]  
 
*[[About STEM]]  
 
*[[About STEM]]  
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#Full length video [http://www.youtube.com/watch?v=3S5DbjCHsx4 In Spanish]  
 
#Full length video [http://www.youtube.com/watch?v=3S5DbjCHsx4 In Spanish]  
 
#[http://www.youtube.com/watch?v=OoiFLemepw4 5 min Video (English)]
 
#[http://www.youtube.com/watch?v=OoiFLemepw4 5 min Video (English)]
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#Avian Influenza
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##Only [https://youtu.be/tI0Ogy-8O10 Poultry-Human Transmission]
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##Including  [https://youtu.be/0YJ6FxdhFm8 Human-Human Transmission]
  
 
*[http://www.eclipse.org/stem/talksOnline.php Scientific Talks Online] &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 
*[http://www.eclipse.org/stem/talksOnline.php Scientific Talks Online] &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
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<!-- bottom left (RELEASE PLANNING GOES HERE) -->
 
<!-- bottom left (RELEASE PLANNING GOES HERE) -->
 
''Please also see our [http://www.eclipse.org/stem website]'' and [[Whats New in STEM|What's New in STEM]]  
 
''Please also see our [http://www.eclipse.org/stem website]'' and [[Whats New in STEM|What's New in STEM]]  
* Next Release To Come September 2015
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* V3.0.0 Milestone 1 is now Available
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* Based on and compatible with Eclipse 4.5.1 (Mars)
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* STEM V3.0.0M1 supports (J2SE) 8.0 JVM. ''In fact - it's required''
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* V2.0.3 Now Available (Feb. 2015)
 
* V2.0.3 Now Available (Feb. 2015)
 
** Bug Fixes
 
** Bug Fixes

Revision as of 12:25, 21 October 2015

STEM TOP BAR.gif

STEM Community Phone Call

The STEM community runs a monthly phone call anyone is free to join.
The special series of Community Ebola Modeling Phone Calls has been merged back with our regular monthly phone call.
You can still see all the Ebola content here

STEM Documentation

The Spatio-Temporal Epidemiological Modeler (STEM) is a tool designed to help scientists and public health officials create and use models of emerging infectious diseases. STEM uses mathematical models of diseases (based on differential equations) to simulate the development or evolution of a disease in space and time (e.g., avian flu or salmonella). These models could aid in understanding, and potentially preventing, the spread of such diseases. STEM also comes pre-configured with a vast amount of reference or denominator data for the entire world. By using and extending the data and models in STEM it is possible to rapidly prototype and test models for emerging infectious disease. STEM also provides tools to help you compare and validate your models. As an open source project, the ultimate goal of STEM is to support and encourage a community of scientists who not only use STEM as a tool but also contribute back to it. STEM is designed so that models and scenarios can be easily shared, extended, and built upon.

Introductory Resources

Tutorials

  1. STEM Model Generator (new!!) requires STEM V2.0 milestone
  2. Full length video In English
  3. Full length video In Hebrew
  4. Full length video In Japanese
  5. Full length video In Spanish
  6. 5 min Video (English)
  7. Avian Influenza
    1. Only Poultry-Human Transmission
    2. Including Human-Human Transmission
  1. Model with Human-Human Transmission
  2. Model of Food Borne disease
  1. Social Distancing Example
  2. Vaccination Example
  3. Evacuation Example
  4. Air Transportation Example
  • Using Population Models
  1. Initializing a Population
  2. Using Structured Populations in STEM
  3. Using Aging Populations in STEM
  • Running Simulations
  1. The STEM Map View
  2. Running Experiments in Batch Mode
  3. Running an Automated Experiment
  4. Running STEM Headless
  5. Importing Data from Files
  6. Simulation Data Logging
  7. Visualizing STEM Simulations with Google Earth
  • (new) Automated Model Creation
  1. STEM Model Creator for users (beta)

Advanced Guides

Epidemiological Modeling

  1. Composing a Graph
  2. Creating a Custom Graph (new) seasonal migration
  3. Visualizing and Editing Graphs with the STEM Graph Editor   
  4. Importing a Graph from a Pajek File
  5. Importing a Graph from an Esri Shapefile
  1. Standard Populations
  2. Insect Vectors
  3. Migratory Birds
  4. Demographic Models (and Aging)
  1. Beef Production Example
  2. Salmonella in Pork Example
  3. How to Structure a Food Borne Disease Scenario
  1. Using the New!! STEM Model Creator tool (beta)
  2. STEM Model Generator tool (for Developers)
  3. Model Generator Installation
  4. Manual Model Plug-in generation
  5. Manual Disease Label creation

Release Planning

Disclaimer

Please also see our website and What's New in STEM

  • V3.0.0 Milestone 1 is now Available
  • Based on and compatible with Eclipse 4.5.1 (Mars)
  • STEM V3.0.0M1 supports (J2SE) 8.0 JVM. In fact - it's required
  • V2.0.3 Now Available (Feb. 2015)
    • Bug Fixes
    • Updated Admin 0 borders added
    • New models
    • Updated Google Earth(tm) Interface
  • Release Engineering
    • STEM releases are created by the team of STEM committers and uploaded to Eclipse on a regular basis.
    • Documentation for the process may be found on the STEM Releng page.



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