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Difference between revisions of "STEM"

(Future STEM Releases (Planned))
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[[Image:STEM TOP BAR.gif|800px]]
 
[[Image:STEM TOP BAR.gif|800px]]
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{| align="right"
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  | __TOC__
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  |}
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== '''Ebola Community Efforts''' ==
 +
==== [[Weekly Community Ebola Modeling Phone Call]] ====
 +
==== [[Ebola Models]] ====
 +
==== [https://wiki.eclipse.org/Ebola_How_To How to install the Ebola models]====
 +
==== Literature [[Ebola References]]====
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==== 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]====
  
 
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.  
 
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 Documentation''' ==
  
== STEM Documentation ==
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<!--outer table-->{| style="width:98% ; border="0" ; cellpadding="0"
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<!--outer table-->|-
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<!--outer table-->|
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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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=== Introductory Resources  ===
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|-
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|
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*[http://www.eclipse.org/stem/ The STEM Website]
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*[[About STEM]]
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*[[Whats New in STEM|What's New in STEM]]
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*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''
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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)]
  
=== Introductory Resources ===
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*[http://www.eclipse.org/stem/talksOnline.php Scientific Talks Online] &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
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*[[STEM FAQ|STEM FAQ]]
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*[[Publications and Presentations on STEM]]
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*[[Join the STEM Community|How to Join the STEM Community]]
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*[[The STEM Development Team]]
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*[[Join the STEM Community|Weekly phone call]]
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==== Getting Started ====
  
*Full length STEM Tutorials on YouTube<sup>TM</sup>
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*[[STEM Installation Guide|Installing the STEM Application]]
#[http://www.youtube.com/watch?v=LfiibQX4IFE In English]
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*[[STEM Overview of the STEM UI|Overview of the STEM UI and menu items ''(new)'']]
#[http://www.youtube.com/watch?v=AFYXvazKkms In Hebrew]
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*[[STEM Addons|Installing Additional Features]]
#[http://www.youtube.com/watch?v=NM5X8-MaiKo In Japanese]
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*[[Sample Projects available for Download|Sample Projects (Downloadable Scenarios)]]
#[http://www.youtube.com/watch?v=3S5DbjCHsx4 In Spanish]
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*[[Importing and Exporting Projects]]
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*[[Analysis|Some Built in Tools for Analysis]]
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*[[Context-Sensitive Help]]
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*[[STEM Model Creator|Using the '''''New!!''''' STEM Model Creator tool]] (''beta'')
  
*[http://www.youtube.com/watch?v=OoiFLemepw4 5 min Video (English)]
 
*[http://www.eclipse.org/stem/talksOnline.php Scientific Talks Online]
 
*[http://www.eclipse.org/stem/ STEM Website]
 
*[[About STEM]]
 
*[[Whats New in STEM]]
 
*[[STEM FAQ|STEM FAQ]]
 
*[[Publications and Presentations on STEM]]
 
*[[Join the STEM Community]]
 
  
=== Getting Started ===
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|}
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<!--inner table start-->|
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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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=== Tutorials ===
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|-
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|
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*'''[[Creating a STEM Scenario]]''' '''step by step'''
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*'''[[How_scenarios_are_structured| Scenario Structure: Tutorial with Templates]]'''
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#[[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_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]]'''
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#[[Triggering interventions#Social Distancing Example|Social Distancing Example]]
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#[[Triggering interventions#Vaccination Example|Vaccination Example]]
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#[[Triggering interventions#Evacuation Example|Evacuation Example]]
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#[[Triggering interventions#Air Transportation Example|Air Transportation Example]]
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*'''Using Population Models'''
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# [[Initializing a Population]]
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#[[Using Structured Populations in STEM|Using Structured Populations in STEM]]
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#[[Using Aging Populations in STEM|Using Aging Populations in STEM]]
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*'''Running Simulations'''
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#[[STEM_Map_View|The STEM Map View]]
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#[[Batch Mode (Running Experiments)|Running Experiments in Batch Mode]]
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#[[Running an Automated Experiment]]
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#[[STEM Headless|Running STEM Headless]]
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#[[Importing Data from Files]]
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#[[STEM Loggers|Simulation Data Logging]]
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#[[Visualizing STEM Simulations with Google Earth]]
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*'''''(new)'' Automated Model Creation'''
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#[[STEM Model Creator]] for users (''beta'')
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 +
|}
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<!--outer table-->|- style="width:45%"
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<!--outer table-->|
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{| style="width: 100%; background: #f1f5fc" ; border="0" ; cellpadding="5"
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|-style="background: #cceeff"
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!
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=== Advanced Guides ===
 +
|-
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|
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====Developers====
 
*[[Welcome STEM Developers]]
 
*[[Welcome STEM Developers]]
*[[STEM Installation Guide|Installing the STEM Application]]
 
*[[STEM Addons|Installing Additional Features]]
 
 
*[[STEM Eclipse Setup|Setting up a STEM Development Environment]]
 
*[[STEM Eclipse Setup|Setting up a STEM Development Environment]]
 
*[[STEM Design Document]]
 
*[[STEM Design Document]]
*[[Sample Projects available for Download|Sample Projects Available for Download]]
 
 
*[[STEM National Language Support | National Language Support]]
 
*[[STEM National Language Support | National Language Support]]
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*[http://www.eclipse.org/projects/project.php?id=technology.stem Project Stats]
  
=== Available Models ===
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*[[Building the STEM RCP Application|Building the STEM RCP Application]]
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*[[Running STEM from the Development Environment]]
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*[[Creating a Customized Color Provider|Customizing Colors]]
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*[[STEM Performance Tips |General tips when writing performance critical code]]
  
*[[Introduction to Compartment Models|Compartment Models]]  
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====Working with Graphs====
*[[Available Models|Disease and Population Models]]
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#[[Composing a Graph]]
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#[[Creating a new Graph|Creating a Custom Graph]] (''new'') ''seasonal migration''
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#[[Visualizing and Editing Graphs]] ''with the STEM Graph Editor  ''&nbsp;&nbsp;
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#[[Importing a Pajek Graph|Importing a Graph from a Pajek File]]
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#[[Importing an Esri Shapefile|Importing a Graph from an Esri Shapefile]]
 +
 
 +
====Modeling New Diseases====
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#[[STEM Model Creator|Using the '''''New!!''''' STEM Model Creator tool]] (''beta'')
 +
#[[STEM Model Generator]] tool (for Developers)
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#*[[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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#[[Creating a new disease label|Manual Disease Label creation]]
 +
 
 +
==== STEM Solvers ====
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*Available [[STEM_Solvers|Solvers]]
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**STEM Native Solvers
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**Apache Common Math Solvers
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**Stochastic Solver
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 +
=== Epidemiological Modeling ===
 +
|-
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|
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*[[Sample Projects available for Download|Sample Projects (Downloadable Scenarios)]]
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*[[Introduction to Compartment Models|Intro to Compartment Models]]  
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*[[STEM Disease Models|Disease Models (basic to advanced)]]
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*[[STEM Population Models|Population Models]]
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#[[STEM_Population_Models#Standard_Population_Model|Standard Populations]]
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#[[STEM_Population_Models#Advanced_Models|Insect Vectors]]
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#[[STEM_Population_Models#Seasonal_Migratory_Population_Model|Migratory Birds]]
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#[[STEM_Population_Models#Multipopulation_Models|Demographic Models (and Aging)]]
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*[[STEM Food and Food Borne Disease|Food Borne Disease Models]]
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#[[Sample_Projects_available_for_Download#1._Beef_Production|Beef Production Example]]
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#[[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]]
 
*[[Disclaimer]]
 
  
=== Tutorials ===
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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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!
  
*[[Importing and Exporting Projects]]
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=== Release Planning ===
*[[Creating a STEM Scenario]]
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|-
*[[How scenarios are structured]]
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|  
*[[Initializing a Population]]
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''Please also see our [http://www.eclipse.org/stem website]'' and [[Whats New in STEM|What's New in STEM]]  
*[[Initializing Disease Compartments]]
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*[[STEM Loggers|Simulation Data Logging]]
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*[[Using Structured Populations in STEM|Using Structured Populations in STEM]]
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*[[Using Aging Populations in STEM|Using Aging Populations in STEM]]
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*[[Batch Mode (Running Experiments)|Running Experiments in Batch Mode]]
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*[[Running an Automated Experiment]]
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*[[STEM Headless|Running STEM Headless]]
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*[[Triggering interventions|Triggering Interventions]]
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*[[STEM_Map_View|The STEM Map View]]
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*[[Importing Data from Files]]
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*[[Analysis|Analysis: Four Tools]]
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*[[Context-Sensitive Help]]
+
  
=== Advanced Guides ===
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====Next Release To Come October 22, 2014====
  
*[[Building the STEM RCP Application|Building the STEM RCP Application]]
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====V2.0.2 Now Available====
*[[Running STEM from the Development Environment]]
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* Bug Fixes
*[[Composing a Graph]]
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* Updated Dengue Model and Scenario
*[[Creating a new Graph|Creating a Custom Graph]]
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* New Campylobacter Scenario
*[[Visualizing and Editing Graphs]] with the STEM Graph Editor
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*[[Importing a Pajek Graph|Importing a Graph from a Pajek File]]
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*[[Creating a new Disease Model Plug-in|Creating a New Disease Model Plug-in Using EMF]]
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*[[Creating a new disease label|Creating a New Disease Label]]
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*[[Creating a Customized Color Provider]]
+
  
== [[Join the STEM Community]] ==
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====V2.0.1 Included====
Click on [[Join the STEM Community]] to learn more about the STEM Community.
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* Bug Fixes
 +
* Updated Code Generator
 +
* New Campylobacter Model and Documentation
 +
* New Dengue Model and Scenario
  
[[Category:Eclipse Technology Project]]
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====V2.0.0 Included====
 +
* Bug Fixes
 +
* Performance Improvements
 +
* New Stochastic Model Solver
 +
* Draggable Solver Objects 
 +
* Visual Editor (Integrated UI for creating new models of disease including domain specific language for epi modeling)
 +
* New Measles Model
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* Directionally Biased Mixing Model
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* New Model Generator (Makes it easy for domain experts to create new STEM Models--no programming required!!)
 +
* New Apache Library
  
== Future STEM Releases (Planned)  ==
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====...Future Features====
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* Running Distributed STEM
  
'''V1.3.0'''
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====Release Engineering====
Planned Date 1/29/2012
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STEM releases are created by the team of STEM committers and uploaded to Eclipse on a regular basis.
Planned and Tentative Features:
+
  
Bug Fixes from 1.2.2
+
Documentation for the process may be found on the [[STEM Releng]] page.
* Ten years of Earth Science Data (2000-2010) available as STEM '''Features'''
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|}
* Malaria Disease Model (''Anopheles'' calibrated)
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* Dengue Fever Disease Model (''Aedes'' not yet calibrated)
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* New Differential Equation solver(s) from commons.math library
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* Additional NLS + User ability to switch languages
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* Logger Framework with new loggers
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* New feature: “Population Transformer” - enabling transformation of population members to allow modeling of e.g. food mediated disease transmission
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* Improvements to the graphical editor
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'''V1.3.1'''
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<!--outer table-->|}
Tentative Date 3/15/2012
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Tentative Features:
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* Bug Fixes to 1.3.0
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* auto-documenting run parameters
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* parameter sensitivity analysis
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* mcmc optimizer
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* Scenario ''"compile"'' proof of concept
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* STEM EMF update to version 2.7.2
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* Possible new feature to hide complexity of creating new plugins (for Disease and Population models).
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* Shape File Importer: Improvements to GUI
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* Population Transformer: “realistic” sample model on food mediated disease transmission
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* Pajek-file Importer: enable import of discrete transportation events. enable the import of edges into existing STEM graphs
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* Graph Editor: improved zooming;  deleting nodes and edges, improved GUI for new population generation
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* STEM -integration inside KNIME: creating a Node within the KNIME, Node-repository that allows STEM headless execution
+
  
'''...future'''
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==[[Disclaimer]]==
* Running Distributed STEM
+
  
 +
<br>
  
{| align="right"
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[[Category:Eclipse Technology Project]]
  | __TOC__
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  |}
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Click on the header for this section to view the Disclaimer.

Revision as of 19:53, 9 October 2014

STEM TOP BAR.gif

Ebola Community Efforts

Weekly 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

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 Documentation

Introductory Resources

  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)

Getting Started


Tutorials

  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

Developers

Working with Graphs

  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

Modeling New Diseases

  1. Using the New!! STEM Model Creator tool (beta)
  2. STEM Model Generator tool (for Developers)
  3. Manual Model Plug-in generation
  4. Manual Disease Label creation

STEM Solvers

  • Available Solvers
    • STEM Native Solvers
    • Apache Common Math Solvers
    • Stochastic Solver

Epidemiological Modeling

  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

Release Planning

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

Next Release To Come October 22, 2014

V2.0.2 Now Available

  • Bug Fixes
  • Updated Dengue Model and Scenario
  • New Campylobacter Scenario

V2.0.1 Included

  • Bug Fixes
  • Updated Code Generator
  • New Campylobacter Model and Documentation
  • New Dengue Model and Scenario

V2.0.0 Included

  • Bug Fixes
  • Performance Improvements
  • New Stochastic Model Solver
  • Draggable Solver Objects
  • Visual Editor (Integrated UI for creating new models of disease including domain specific language for epi modeling)
  • New Measles Model
  • Directionally Biased Mixing Model
  • New Model Generator (Makes it easy for domain experts to create new STEM Models--no programming required!!)
  • New Apache Library

...Future Features

  • Running Distributed STEM

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.

Disclaimer


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

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