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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.  
+
== '''Ebola Community Efforts''' ==
 +
[[Community Ebola Modeling Phone Call]]
 +
'''[[Ebola Models]]'''
 +
[https://wiki.eclipse.org/Ebola_How_To How to install the Ebola models]
 +
Literature [[Ebola References]]
 +
Data [[Ebola Reference Data]]
 +
''Please sign up for the'' [https://dev.eclipse.org/mailman/listinfo/stem-ebola stem-ebola mailing list]
  
 
== '''STEM Documentation''' ==
 
== '''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.
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|- style="background: #cceeff"
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|-
!
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! style="width: 45%; background: #cceeff;" |  
 
=== Introductory Resources  ===
 
=== Introductory Resources  ===
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! colspan="2" style="width: 45%; background: #cceeff;" |
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=== Tutorials ===
 
|-
 
|-
 
|  
 
|  
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<!-- upper left (INTRODUCTORY RESOURCES GO HERE) -->
 
*[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>
 
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#[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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*[[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)]]
 
*[[Importing and Exporting Projects]]
 
*[[Analysis|Some Built in Tools for Analysis]]
 
*[[Context-Sensitive Help]]
 
*[[STEM Model Creator|Using the '''''New!!''''' STEM Model Creator tool]] (''beta'')
 
 
 
|}
 
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{| style="width: 100%; height: 100%; background: #f1f5fc" ; border="0" ; cellpadding="5"
 
|-style="background: #cceeff"
 
!
 
 
=== Tutorials ===
 
|-
 
 
|  
 
|  
 +
<!-- upper right (TUTORIALS) -->
 
*'''[[Creating a STEM Scenario]]''' '''step by step'''
 
*'''[[Creating a STEM Scenario]]''' '''step by step'''
*'''[[How_scenarios_are_structured|(New!) Scenario Structure: tutorial with templates]]'''
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*'''[[How_scenarios_are_structured| Scenario Structure: Tutorial with Templates]]'''
#[[How_scenarios_are_structured#Template_for_a_Basic_Scenario_with_a_Human_Disease|Model with human-human transmission]]
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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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#[[How_scenarios_are_structured#Template_for_a_Food_Borne_Disease_Scenario|Model of Food Borne disease]]
 
*'''[[Initializing Disease Compartments|Initializing Diseases ''(Infectors, Inoculators, and Initializers)'']]'''
 
*'''[[Initializing Disease Compartments|Initializing Diseases ''(Infectors, Inoculators, and Initializers)'']]'''
 
*'''[[STEM Import Discrete Transportation Events|Import Discrete Transportation Events]]'''
 
*'''[[STEM Import Discrete Transportation Events|Import Discrete Transportation Events]]'''
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#[[Importing Data from Files]]  
 
#[[Importing Data from Files]]  
 
#[[STEM Loggers|Simulation Data Logging]]
 
#[[STEM Loggers|Simulation Data Logging]]
 +
#[[Visualizing STEM Simulations with Google Earth]]
  
 
*'''''(new)'' Automated Model Creation'''
 
*'''''(new)'' Automated Model Creation'''
 
#[[STEM Model Creator]] for users (''beta'')
 
#[[STEM Model Creator]] for users (''beta'')
 
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|-
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{| style="width: 100%; background: #f1f5fc" ; border="0" ; cellpadding="5"
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!
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=== Advanced Guides ===
 
=== Advanced Guides ===
 +
! colspan="2" style="background: #cceeff;" |
 +
=== Epidemiological Modeling ===
 
|-
 
|-
|  
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|
====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]]
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*[[Creating a Customized Color Provider|Customizing Colors]]
 
*[[Creating a Customized Color Provider|Customizing Colors]]
 
*[[STEM Performance Tips |General tips when writing performance critical code]]
 
*[[STEM Performance Tips |General tips when writing performance critical code]]
 
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*Working with Graphs
====Working with Graphs====
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#[[Composing a Graph]]
 
#[[Composing a Graph]]
 
#[[Creating a new Graph|Creating a Custom Graph]] (''new'') ''seasonal migration''
 
#[[Creating a new Graph|Creating a Custom Graph]] (''new'') ''seasonal migration''
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#[[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
#[[STEM Model Creator|Using the '''''New!!''''' STEM Model Creator tool]] (''beta'')
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**Apache Common Math Solvers
#[[STEM Model Generator]] tool (for Developers)
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**Stochastic Solver
#*[[STEM_Model_Generator/Install|Model Generator Installation]]
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|
#[[Creating a new Disease Model Plug-in|Manual Model Plug-in generation]]
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<!-- middle right (EPIDEMIOLOGICAL MODELING GOES HERE)-->
#[[Creating a new disease label|Manual Disease Label creation]]
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==== STEM Solvers ====
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*Available [[STEM_Solvers|Solvers]]
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**'''''New!!''''' [[STEM_Solvers#Stochastic_Solver|Stochastic Solver]]
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|}
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{| style="width: 100%; height: 100%; background: #f1f5fc" ; border="0" ; cellpadding="5"
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|-style="background: #cceeff"
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!
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=== Epidemiological Modeling ===
+
|-
+
|
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*[[Sample Projects available for Download|Sample Projects (Downloadable Scenarios)]]
 
*[[Sample Projects available for Download|Sample Projects (Downloadable Scenarios)]]
 +
* ''(new!!)'' [[Epidemiological Parameters]]
 
*[[Introduction to Compartment Models|Intro to Compartment Models]]  
 
*[[Introduction to Compartment Models|Intro to Compartment Models]]  
 
*[[STEM Disease Models|Disease Models (basic to advanced)]]
 
*[[STEM Disease Models|Disease Models (basic to advanced)]]
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#[[STEM_Population_Models#Standard_Population_Model|Standard Populations]]
 
#[[STEM_Population_Models#Standard_Population_Model|Standard Populations]]
 
#[[STEM_Population_Models#Advanced_Models|Insect Vectors]]
 
#[[STEM_Population_Models#Advanced_Models|Insect Vectors]]
#[[STEM_Population_Models#Seasonal_Migratory_Population_Model|Migratory Birds ''(new)'']]
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#[[STEM_Population_Models#Seasonal_Migratory_Population_Model|Migratory Birds]]
 
#[[STEM_Population_Models#Multipopulation_Models|Demographic Models (and Aging)]]
 
#[[STEM_Population_Models#Multipopulation_Models|Demographic Models (and Aging)]]
*'''''New!!''''' [[STEM Food and Food Borne Disease|Food Borne Disease Models''']]
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*[[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#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]]
 
#[[Sample_Projects_available_for_Download#2._A_scenario_for_modelling_the_transmission_of_Salmonella_to_pigs.2C_pork_and_humans|Salmonella in Pork Example]]
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*[[Transportation Models|Transportation Models]]
 
*[[Transportation Models|Transportation Models]]
 
*[[Air Travel Model|Air Travel Model]]
 
*[[Air Travel Model|Air Travel Model]]
 +
*'''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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|-
{| style="width: 100%; height: 100%; background: #f1f5fc" ; border="0" ; cellpadding="5"
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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 ===
 
|-
 
|-
 
|  
 
|  
 +
<!-- 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
 +
* V2.0.3 Now Available (Feb. 2015)
 +
** Bug Fixes
 +
** Updated Admin 0 borders added
 +
** New models
 +
** Updated Google Earth(tm) Interface
  
====V2.0.0 Milestone 3 ====
+
* Release Engineering
Planning
+
** STEM releases are created by the team of STEM committers and uploaded to Eclipse on a regular basis.
* Bug Fixes
+
** Documentation for the process may be found on the [[STEM Releng]] page.
* New Stochastic model solver
+
|
* Visual Editor initial checkin
+
<!-- bottom right (DISCLAIMER GOES HERE) -->
* New Measles model
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* On Track: UI, model development workflow, builder tools, xtext, all in STEM  
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* Add model generator Feature to STEM-core (with required plugins)  
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* Customize Project Explorer (show/hide generated Java code)                           
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* Hot injection of generated plugins
+
  
====...future====
 
* Running Distributed STEM
 
  
====Release Engineering====
+
<br>
STEM releases are created by the team of STEM committers and uploaded
+
Click on the header for this section to view the [[Disclaimer]].
<br/>
+
|-
to Eclipse on a regular basis.
+
| colspan="3" align="center" |
Documentation for the process may be found
+
<br/>
+
on the [[STEM Releng]] page.
+
 
|}
 
|}
 
<!--outer table-->|}
 
 
==[[Disclaimer]]==
 
 
<br>
 
  
 
[[Category:Eclipse Technology Project]]
 
[[Category:Eclipse Technology Project]]
 
Click on the header for this section to view the Disclaimer.
 

Latest revision as of 14:42, 29 April 2015

STEM TOP BAR.gif

Ebola Community Efforts

Community Ebola Modeling Phone Call 
Ebola Models
How to install the Ebola models 
Literature Ebola References
Data Ebola Reference Data
Please sign up for the stem-ebola mailing list

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.

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)
  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

  • Next Release To Come September 2015
  • 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.