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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''' ==
 +
 
 +
The STEM community runs a [[Join the STEM Community|monthly phone call]] anyone is free to join. The agenda 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 held during the epidemic was 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]]
  
 
== '''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 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.
<!--outer table-->|-
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<!--outer table-->|
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{| style="width: 90%" border="1" cellpadding="5" cellspacing="0" align="center"
{| 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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! style="width: 45%; background: #cceeff;" |  
 
=== Introductory Resources  ===
 
=== Introductory Resources  ===
 +
! colspan="2" style="width: 45%; background: #cceeff;" |
 +
=== Tutorials ===
 
|-
 
|-
 
|  
 
|  
 +
<!-- upper left (INTRODUCTORY RESOURCES GO HERE) -->
 +
*[[Installation Guide]]
 +
*[[STEM_Add-ons|STEM Denominator Data]]
 
*[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] <br /> ''narration by'' [https://www.sarahkaufmannyc.com ''Sarah Kaufman'']
#Full length video [http://www.youtube.com/watch?v=LfiibQX4IFE In English]  
+
#A Presentation on STEM
#Full length video [http://www.youtube.com/watch?v=AFYXvazKkms In Hebrew]  
+
## [http://www.youtube.com/watch?v=LfiibQX4IFE In English]  
#Full length video [http://www.youtube.com/watch?v=NM5X8-MaiKo In Japanese]  
+
## [http://www.youtube.com/watch?v=AFYXvazKkms In Hebrew]  
#Full length video [http://www.youtube.com/watch?v=3S5DbjCHsx4 In Spanish]  
+
## [http://www.youtube.com/watch?v=NM5X8-MaiKo In Japanese]  
 +
## [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]
 +
*Download a step by step guide: [[Media:STEM_HowToGuide.pdf|Ebola Example]]
  
 
*[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;
 
*[[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/>
 
 
 
|}
 
<!--inner table start-->|
 
{| 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|How Scenarios are Structured]]'''
+
*'''[[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]]
 +
#[[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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*'''Running Simulations'''
 
*'''Running Simulations'''
#[[STEM_Map_View|The STEM Map View]]  
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# [[STEM_Map_View|The STEM UI and Map View]] ''(updated)''
 
#[[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]]'''
+
*'''''(new)'' Automated Model Creation'''
*'''[[Analysis|Some Built in Tools for Analysis]]'''
+
#[[STEM Model Creator]] for users
*'''[[Context-Sensitive Help]]'''
+
|-
|}
+
! style="background: #cceeff;" |
<!--outer table-->|- style="width:45%"
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=== '''Advanced Guides''' ===
<!--outer table-->|
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! colspan="2" style="background: #cceeff;" |
{| 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 ===
+
  
 +
=== 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]]
*[[STEM Design Document]]
+
*[[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]
 
*[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]]
 +
*[[Configuring the STEM Build on Eclipse CI|STEM CI Build]] ''(Eclipse committers only)''
 +
*[[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]]
 
*[[STEM Performance Tips |General tips when writing performance critical code]]
 
*[[STEM Performance Tips |General tips when writing performance critical code]]
 
+
*Working with Graphs
====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]]
 
+
*[[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]]  
+
**Apache Common Math Solvers
#[[Creating a new disease label|Creating a New Disease Label]]
+
**Stochastic Solver
 
+
|
==== Epidemiological Modeling ====
+
<!-- middle right (EPIDEMIOLOGICAL MODELING GOES HERE)-->
 
*[[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]]
+
*[[STEM Disease Models|Disease Models (basic to advanced)]]
 
*[[STEM Population Models|Population Models]]
 
*[[STEM Population Models|Population Models]]
 +
#[[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]]
 
*[[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]]
+
*'''Modeling New Diseases'''
 
+
#[[STEM Model Creator|Using the '''''New!!''''' STEM Model Creator tool]]  
 
+
#[[STEM Model Generator]] tool (for Developers)
|}
+
#[[STEM_Model_Generator/Install|Model Generator Installation]]
<!--outer table-->|
+
#[[Creating a new Disease Model Plug-in|Manual Model Plug-in generation]]
{| style="width: 100%; height: 100%; background: #f1f5fc" ; border="0" ; cellpadding="5"
+
#[[Creating a new disease label|Manual Disease Label creation]]
|-style="background: #cceeff"
+
!
+
  
 +
|-
 +
! style="background: #ffdead;" |
 
=== Release Planning ===
 
=== Release Planning ===
 +
! colspan="2" style="background: #ffdead;" |
 +
=== Important Links ===
 
|-
 
|-
 
|  
 
|  
''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]]  
<br/>
+
* V4.0.0 Release is now Available
 +
* Based on and compatible with Eclipse e4
 +
* STEM V4.0.0M1 supports (J2SE) 8.0 JVM. ''In fact - it's required''
  
====V1.4.0 ====
 
'''Plan Features: (''Tentative Date 9/15/2012'')'''
 
*Performance improvements
 
*Simplified creation of new Disease and Population models (Tools for generating new disease plugins)
 
*Pajek-file Importer:
 
**Enable import of discrete transportation events
 
**Enable integration between user graphs and existing STEM graphs
 
*New improved MapView
 
**Enable visualization of discrete transportation events
 
**Enable multiple views of the same simulation 
 
*Polio Example
 
*Stochastic Modeling Framework
 
*Ability to delete items inside a graph from Designer Perspective
 
*Deep copy drag and drop for models
 
*Refactor
 
*Create new mixing edges (chris to put edges back, jk to do generator)
 
*Improved UI for decorators view
 
  
====V1.3.1====
+
* Release Engineering
 
+
** STEM releases are created by the team of STEM committers and uploaded to Eclipse on a regular basis.
'''Current Release'''
+
** Documentation for the process may be found on the [[STEM Releng]] page.
* Bug Fixes to 1.3.0
+
|
* STEM EMF update to version 2.7.2
+
<!-- bottom right (DISCLAIMER GOES HERE) -->
* Generalized model replay mechanism
+
* Modifiable Modifiers (batch mode)
+
* Shape File Importer: Improvements to GUI
+
* Population Transformer: food mediated disease
+
* Graph Editor: improved features
+
* New Population re-scaler
+
* New Polio model
+
 
+
====...future====
+
* Running Distributed STEM
+
* parameter sensitivity analysis
+
* mcmc optimizer
+
* Scenario ''"compile"'' proof of concept
+
  
  
 +
<br>
 +
* Our [[Disclaimer]].
 +
* [http://www.eclipse.org Main Eclipse Foundation website]
 +
* [http://www.eclipse.org/legal/privacy.php Privacy policy]
 +
* [http://www.eclipse.org/legal/termsofuse.php Website terms of use]
 +
* [http://www.eclipse.org/legal/copyright.php Copyright agent]
 +
* [http://www.eclipse.org/legal Legal]
 +
|-
 +
| colspan="3" align="center" |
 
|}
 
|}
<!--outer table-->|}
 
 
==[[Disclaimer]]==
 
 
<br>
 
  
 
[[Category:Eclipse Technology Project]]
 
[[Category:Eclipse Technology Project]]

Latest revision as of 16:14, 3 September 2019

STEM TOP BAR.gif

STEM Community Phone Call

The STEM community runs a monthly phone call anyone is free to join. The agenda 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 held during the epidemic was 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
    narration by Sarah Kaufman
  2. A Presentation on STEM
    1. In English
    2. In Hebrew
    3. In Japanese
    4. In Spanish
  3. 5 min Video (English)
  4. 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 UI and Map View (updated)
  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

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
  2. STEM Model Generator tool (for Developers)
  3. Model Generator Installation
  4. Manual Model Plug-in generation
  5. Manual Disease Label creation

Release Planning

Important Links

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

  • V4.0.0 Release is now Available
  • Based on and compatible with Eclipse e4
  • STEM V4.0.0M1 supports (J2SE) 8.0 JVM. In fact - it's required


  • 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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