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(Introductory Resources)
(STEM Solvers)
 
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*[[STEM Installation Guide|Installing the STEM Application]]
 
*[[STEM Installation Guide|Installing the STEM Application]]
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*[[STEM Overview of the STEM UI|Overview of the STEM UI and menu items ''(new)'']]
 
*[[STEM Addons|Installing Additional Features]]
 
*[[STEM Addons|Installing Additional Features]]
 
*[[Sample Projects available for Download|Sample Projects (Downloadable Scenarios)]]
 
*[[Sample Projects available for Download|Sample Projects (Downloadable Scenarios)]]
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|  
 
|  
 
*'''[[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]]
 
#[[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]]
 
#[[How_scenarios_are_structured#Template_for_a_Food_Borne_Disease_Scenario|Model of Food Borne disease]]
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==== STEM Solvers ====
 
==== STEM Solvers ====
 
*Available [[STEM_Solvers|Solvers]]
 
*Available [[STEM_Solvers|Solvers]]
**'''''New!!''''' [[STEM_Solvers#Stochastic_Solver|Stochastic Solver]]
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**STEM Native Solvers
|}
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**Apache Common Math Solvers
<!--outer table-->|
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**Stochastic Solver
{| 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 ===
 
=== Epidemiological Modeling ===
 
|-
 
|-
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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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''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]]  
  
====V2.0.0 Milestone 3 ====
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====Next Release To Come October 22, 2014====
Planning
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 +
====V2.0.2 Now Available====
 
* Bug Fixes
 
* Bug Fixes
* New Stochastic model solver
+
* Updated Dengue Model and Scenario
* Visual Editor initial checkin
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* New Campylobacter Scenario
* 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
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====...future====
+
====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
 
* Running Distributed STEM
  
 
====Release Engineering====
 
====Release Engineering====
STEM releases are created by the team of STEM committers and uploaded  
+
STEM releases are created by the team of STEM committers and uploaded to Eclipse on a regular basis.
<br/>
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to Eclipse on a regular basis.
+
Documentation for the process may be found on the [[STEM Releng]] page.
Documentation for the process may be found  
+
<br/>
+
on the [[STEM Releng]] page.
+
 
|}
 
|}
  

Latest revision as of 16:47, 19 June 2014

STEM TOP BAR.gif

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
  • (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.