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(STEM Documentation)
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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 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.
+
== '''STEM Community Phone Call''' ==
  
=== STEM Documentation ===
+
The STEM community runs a [[Join the STEM Community|monthly phone call]] anyone is free to join. The agenda for the call is posted on stem-dev.org every month early in the week of the call for you to view.
 +
The special series of [[Community Ebola Modeling Phone Call]]s has been merged back with our regular [[Join the STEM Community|monthly phone call]].
 +
You can still see all the Ebola content [[Join the STEM Community#Ebola Community Efforts|here]]
  
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== '''STEM Documentation''' ==
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<!--outer table-->|
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{| style="width:50%" ; border="1" ; cellpadding="5" ; style="background: #f1f5fc;"
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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.
|-style="background: #cceeff;"
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!
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{| style="width: 90%" border="1" cellpadding="5" cellspacing="0" align="center"
=== Introductory Resources  ===&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
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|+ 
 +
|-
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! style="width: 45%; background: #cceeff;" |
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=== Introductory Resources  ===
 +
! colspan="2" style="width: 45%; background: #cceeff;" |
 +
=== Tutorials ===
 
|-
 
|-
 
|  
 
|  
 +
<!-- upper left (INTRODUCTORY RESOURCES GO HERE) -->
 +
*[[Installation Guide]]
 
*[http://www.eclipse.org/stem/ The STEM Website]  
 
*[http://www.eclipse.org/stem/ The STEM Website]  
 
*[[About STEM]]  
 
*[[About STEM]]  
 
*[[Whats New in STEM|What's New in STEM]]  
 
*[[Whats New in STEM|What's New in STEM]]  
 
*STEM Tutorials on YouTube<sup>TM</sup>
 
*STEM Tutorials on YouTube<sup>TM</sup>
 
+
#[http://www.youtube.com/watch?v=MtQlS7g7Qnw STEM Model Generator (new!!)] ''requires STEM V2.0 milestone''
 
#Full length video [http://www.youtube.com/watch?v=LfiibQX4IFE In English]  
 
#Full length video [http://www.youtube.com/watch?v=LfiibQX4IFE In English]  
 
#Full length video [http://www.youtube.com/watch?v=AFYXvazKkms In Hebrew]  
 
#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=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)]
 +
#Avian Influenza
 +
##Only [https://youtu.be/tI0Ogy-8O10 Poultry-Human Transmission]
 +
##Including  [https://youtu.be/0YJ6FxdhFm8 Human-Human Transmission]
  
*[http://www.eclipse.org/stem/talksOnline.php Scientific Talks Online]  
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*[http://www.eclipse.org/stem/talksOnline.php Scientific Talks Online] &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 
*[[STEM FAQ|STEM FAQ]]  
 
*[[STEM FAQ|STEM FAQ]]  
 
*[[Publications and Presentations on STEM]]  
 
*[[Publications and Presentations on STEM]]  
 +
*[[Citing STEM]]
 
*[[Join the STEM Community|How to Join the STEM Community]]  
 
*[[Join the STEM Community|How to Join the STEM Community]]  
 
*[[The STEM Development Team]]  
 
*[[The STEM Development Team]]  
 
*[[Join the STEM Community|Weekly phone call]]
 
*[[Join the STEM Community|Weekly phone call]]
 
==== Getting Started ====
 
 
*[[STEM Installation Guide|Installing the STEM Application]]
 
*[[STEM Addons|Installing Additional Features]]
 
*[[Sample Projects available for Download|Sample Projects (Downloadable Scenarios)]]
 
 
<br>
 
<br>
 
<br>
 
 
|}
 
<!--outer table start-->|
 
{| style="width:50%" ; border="1" ; cellpadding="5" ; style="background: #f1f5fc;"
 
|-style="background: #cceeff;"
 
!
 
 
=== Tutorials ===
 
|-
 
 
|  
 
|  
*[[Creating a STEM Scenario]]  
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<!-- upper right (TUTORIALS) -->
*[[How_scenarios_are_structured|How Scenarios are Structured]]
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*'''[[Creating a STEM Scenario]]''' '''step by step'''
*[[Initializing Disease Compartments|Initializing Diseases ''(Infectors, Inoculators, and Initializers)'']]
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*'''[[How_scenarios_are_structured| Scenario Structure: Tutorial with Templates]]'''
*[[Triggering interventions|'''Triggering Interventions''']]  
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#[[How_scenarios_are_structured#Template_for_a_Basic_Scenario_with_a_Human_Disease|Model with Human-Human Transmission]]
 +
#[[How_scenarios_are_structured#Template_for_a_Food_Borne_Disease_Scenario|Model of Food Borne disease]]
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*'''[[Initializing Disease Compartments|Initializing Diseases ''(Infectors, Inoculators, and Initializers)'']]'''
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*'''[[STEM Import Discrete Transportation Events|Import Discrete Transportation Events]]'''
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*'''[[Triggering interventions|Triggering Interventions]]'''
 
#[[Triggering interventions#Social Distancing Example|Social Distancing Example]]
 
#[[Triggering interventions#Social Distancing Example|Social Distancing Example]]
 
#[[Triggering interventions#Vaccination Example|Vaccination Example]]
 
#[[Triggering interventions#Vaccination Example|Vaccination Example]]
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#[[Triggering interventions#Air Transportation Example|Air Transportation Example]]
 
#[[Triggering interventions#Air Transportation Example|Air Transportation Example]]
  
* '''Using Population Models'''
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*'''Using Population Models'''
 
# [[Initializing a Population]]  
 
# [[Initializing a Population]]  
 
#[[Using Structured Populations in STEM|Using Structured Populations in STEM]]  
 
#[[Using Structured Populations in STEM|Using Structured Populations in STEM]]  
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#[[Batch Mode (Running Experiments)|Running Experiments in Batch Mode]]  
 
#[[Batch Mode (Running Experiments)|Running Experiments in Batch Mode]]  
 
#[[Running an Automated Experiment]]  
 
#[[Running an Automated Experiment]]  
#[[STEM Headless|Running STEM Headless]]
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#[[STEM Headless|Running STEM Headless]] ''(STEM on Server)''
 
#[[Importing Data from Files]]  
 
#[[Importing Data from Files]]  
 
#[[STEM Loggers|Simulation Data Logging]]
 
#[[STEM Loggers|Simulation Data Logging]]
 +
#[[Visualizing STEM Simulations with Google Earth]]
  
*[[Importing and Exporting Projects]]
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*'''''(new)'' Automated Model Creation'''
*[[Analysis|Some Built in Tools for Analysis]]
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#[[STEM Model Creator]] for users (''beta'')
*[[Context-Sensitive Help]]
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|-
 
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|}
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{| style="width:48%" ; border="0" ; cellpadding="5" ; style="background: #f1f5fc;"
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|-style="background: #cceeff;"
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!
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=== Advanced Guides ===
 
=== Advanced Guides ===
 +
! colspan="2" style="background: #cceeff;" |
 +
=== Epidemiological Modeling ===
 
|-
 
|-
|  
+
|
====Developers====
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<!-- middle left (ADVANCED GUIDES GOES HERE) -->
 
*[[Welcome STEM Developers]]
 
*[[Welcome STEM Developers]]
 
*[[STEM Eclipse Setup|Setting up a STEM Development Environment]]
 
*[[STEM Eclipse Setup|Setting up a STEM Development Environment]]
*[[STEM Design Document]]
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*[[STEM Design Document]] ''(updated 4/29/2016)''
 
*[[STEM National Language Support | National Language Support]]
 
*[[STEM National Language Support | National Language Support]]
 
+
*[http://www.eclipse.org/projects/project.php?id=technology.stem Project Stats]
 
*[[Building the STEM RCP Application|Building the STEM RCP Application]]
 
*[[Building the STEM RCP Application|Building the STEM RCP Application]]
 +
*[[STEM Create EMF Project|Example: Create a STEM JSON Logger (a new EMF Project)]]
 
*[[Running STEM from the Development Environment]]
 
*[[Running STEM from the Development Environment]]
 +
*[[STEM Headless|Running STEM Headless]] ''(STEM on Server)''
 
*[[Creating a Customized Color Provider|Customizing Colors]]
 
*[[Creating a Customized Color Provider|Customizing Colors]]
 
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*[[STEM Performance Tips |General tips when writing performance critical code]]
====Working with Graphs====
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*Working with Graphs
 
#[[Composing a Graph]]
 
#[[Composing a Graph]]
#[[Creating a new Graph|Creating a Custom Graph]]
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#[[Creating a new Graph|Creating a Custom Graph]] (''new'') ''seasonal migration''
 
#[[Visualizing and Editing Graphs]] ''with the STEM Graph Editor  ''&nbsp;&nbsp;
 
#[[Visualizing and Editing Graphs]] ''with the STEM Graph Editor  ''&nbsp;&nbsp;
 
#[[Importing a Pajek Graph|Importing a Graph from a Pajek File]]
 
#[[Importing a Pajek Graph|Importing a Graph from a Pajek File]]
 
#[[Importing an Esri Shapefile|Importing a Graph from an Esri Shapefile]]
 
#[[Importing an Esri Shapefile|Importing a Graph from an Esri Shapefile]]
 
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*[[STEM_Solvers|Available STEM Solvers]]
====Modeling new Diseases====
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**STEM Native Solvers
#[[Creating a new Disease Model Plug-in|Creating a New Disease Model Plug-in Using EMF]]  
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**Apache Common Math Solvers
#[[Creating a new disease label|Creating a New Disease Label]]
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**Stochastic Solver
 
+
|
==== Epidemiological Modeling ====
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<!-- middle right (EPIDEMIOLOGICAL MODELING GOES HERE)-->
 
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*[[Sample Projects available for Download|Sample Projects (Downloadable Scenarios)]]
*[[Introduction to Compartment Models|Compartment Models]]  
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* ''(new!!)'' [[Epidemiological Parameters]]
*[[Available Models|Disease and Population Models]]
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*[[Introduction to Compartment Models|Intro to Compartment Models]]  
 +
*[[STEM Disease Models|Disease Models (basic to advanced)]]
 +
*[[STEM Population Models|Population Models]]
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#[[STEM_Population_Models#Standard_Population_Model|Standard Populations]]
 +
#[[STEM_Population_Models#Advanced_Models|Insect Vectors]]
 +
#[[STEM_Population_Models#Seasonal_Migratory_Population_Model|Migratory Birds]]
 +
#[[STEM_Population_Models#Multipopulation_Models|Demographic Models (and Aging)]]
 +
*[[STEM Food and Food Borne Disease|Food Borne Disease Models]]
 +
#[[Sample_Projects_available_for_Download#1._Beef_Production|Beef Production Example]]
 +
#[[Sample_Projects_available_for_Download#2._A_scenario_for_modelling_the_transmission_of_Salmonella_to_pigs.2C_pork_and_humans|Salmonella in Pork Example]]
 +
#[[How_scenarios_are_structured#Template_for_a_Food_Borne_Disease_Scenario|How to Structure a Food Borne Disease Scenario]]
 
*[[Transportation Models|Transportation Models]]
 
*[[Transportation Models|Transportation Models]]
 
*[[Air Travel Model|Air Travel Model]]
 
*[[Air Travel Model|Air Travel Model]]
*[[STEM_Solvers|Solvers]]
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*'''Modeling New Diseases'''
 +
#[[STEM Model Creator|Using the '''''New!!''''' STEM Model Creator tool]] (''beta'')
 +
#[[STEM Model Generator]] tool (for Developers)
 +
#[[STEM_Model_Generator/Install|Model Generator Installation]]
 +
#[[Creating a new Disease Model Plug-in|Manual Model Plug-in generation]]
 +
#[[Creating a new disease label|Manual Disease Label creation]]
  
|}
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|-
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{| style="width:48%" ; border="0" ; cellpadding="5" ; style="background: #f1f5fc;"
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|-style="background: #cceeff;"
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!
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=== Release Planning ===
 
=== Release Planning ===
 +
! colspan="2" style="background: #ffdead;" |
 +
=== Disclaimer ===
 
|-
 
|-
 
|  
 
|  
''please also see our [http://www.eclipse.org/stem website]'' and [[Whats New in STEM|What's New in STEM]]  
+
<!-- bottom left (RELEASE PLANNING GOES HERE) -->
<br>
+
''Please also see our [http://www.eclipse.org/stem website]'' and [[Whats New in STEM|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''
  
====V1.3.1====
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* V2.0.3 Now Available (Feb. 2015)
 +
** Bug Fixes
 +
** Updated Admin 0 borders added
 +
** New models
 +
** Updated Google Earth(tm) Interface
  
Plan Features: (''Tentative Date 4/15/2012'')
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* Release Engineering
* Bug Fixes to 1.3.0
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** STEM releases are created by the team of STEM committers and uploaded to Eclipse on a regular basis.
* STEM EMF update to version 2.7.2
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** Documentation for the process may be found on the [[STEM Releng]] page.
* Generalized model replay mechanism
+
|
* Shape File Importer: Improvements to GUI
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<!-- bottom right (DISCLAIMER GOES HERE) -->
* Population Transformer: food mediated disease
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* Graph Editor: improved features
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* New Population re-scaler
+
  
====...future====
 
* Running Distributed STEM
 
* parameter sensitivity analysis
 
* mcmc optimizer
 
* Simple creation of new Disease and Population models
 
* Pajek-file Importer:
 
** Enable import of discrete transportation events
 
** Enable integration between user graphs and existing STEM graphs &nbsp;&nbsp;
 
* Scenario ''"compile"'' proof of concept
 
* Ability to Delete Items inside a Graph from Designer Perspective
 
* Tools for generating new disease plugins
 
  
 
<br>
 
<br>
 
+
Click on the header for this section to view the [[Disclaimer]].
 +
|-
 +
| colspan="3" align="center" |
 
|}
 
|}
<!--outer table-->|}
 
 
==[[Disclaimer]]==
 
 
<br>
 
  
 
[[Category:Eclipse Technology Project]]
 
[[Category:Eclipse Technology Project]]

Revision as of 21:28, 29 April 2016

STEM TOP BAR.gif

STEM Community Phone Call

The STEM community runs a monthly phone call anyone is free to join. The agenda for the call is posted on stem-dev.org every month early in the week of the call for you to view. 
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 (STEM on Server)
  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.



Click on the header for this section to view the Disclaimer.

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