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Difference between revisions of "STEM"

(V1.4.0)
(Modeling New Diseases)
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*[[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)]]
 
 
<br/>
 
<br/>
 
  
  
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|-style="background: #cceeff"
 
|-style="background: #cceeff"
 
!
 
!
 +
 
=== Tutorials ===
 
=== 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|(New!) 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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#[[Importing Data from Files]]  
 
#[[Importing Data from Files]]  
 
#[[STEM Loggers|Simulation Data Logging]]
 
#[[STEM Loggers|Simulation Data Logging]]
 +
 +
*'''''(new)'' Automated Model Creation'''
 +
#[[STEM Model Creator]] for users (''beta'')
  
 
*'''[[Importing and Exporting Projects]]'''   
 
*'''[[Importing and Exporting Projects]]'''   
 
*'''[[Analysis|Some Built in Tools for Analysis]]'''
 
*'''[[Analysis|Some Built in Tools for Analysis]]'''
 
*'''[[Context-Sensitive Help]]'''
 
*'''[[Context-Sensitive Help]]'''
 +
 +
*[[STEM Model Creator|Using the '''''New!!''''' STEM Model Creator tool]] (''beta'')
 
|}
 
|}
 
<!--outer table-->|- style="width:45%"
 
<!--outer table-->|- style="width:45%"
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====Modeling New Diseases====
 
====Modeling New Diseases====
#[[Creating a new Disease Model Plug-in|Creating a New Disease Model Plug-in Using EMF]]  
+
#[[STEM Model Creator|Using the '''''New!!''''' STEM Model Creator tool]] (''beta'')
#[[Creating a new disease label|Creating a New Disease Label]]
+
#[[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]]
  
 
==== Epidemiological Modeling ====
 
==== Epidemiological Modeling ====
 
*[[Sample Projects available for Download|Sample Projects (Downloadable Scenarios)]]
 
*[[Sample Projects available for Download|Sample Projects (Downloadable Scenarios)]]
 
*[[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 Food and Food Borne Disease|Food Borne Disease Models]]
+
#[[STEM_Population_Models#Standard_Population_Model|Standard Populations]]
 +
#[[STEM_Population_Models#Advanced_Models|Insect Vectors]]
 +
#[[STEM_Population_Models#Multipopulation_Models|Demographic Models (and Aging)]]
 +
*'''''New!!''''' [[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]]
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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]]  
 
<br/>
 
<br/>
 
<br/>
 
<br/>
  
====V1.4.0 ====
+
====V2.0.0 M1 ====
'''Plan Features: (''Tentative Date 9/25/2012'')'''
+
Planning
*Performance improvements
+
* Integrated UI for creating new models of disease including domain specific language for epi modeling
*Simplified creation of new Disease and Population models (Tools for generating new disease plugins)
+
* Parameter sensitivity analysis
*Pajek-file Importer:
+
* mcmc optimizer
**Enable import of discrete transportation events
+
* Advanced Dengue Example
**Enable integration between user graphs and existing STEM graphs
+
* New Food Distribution Analysis view (incubation)  
*New improved MapView
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* New Apache library
**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
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*Refactor
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*Create new mixing edges (edges back in, generator created)
+
*Improved UI for decorators view
+
*Time adaptive external data source models
+
 
+
====V1.3.1====
+
 
+
'''Current Release'''
+
* Bug Fixes to 1.3.0
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* STEM EMF update to version 2.7.2
+
* 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====
 
====...future====
 
* Running Distributed STEM
 
* Running Distributed STEM
* parameter sensitivity analysis
 
* mcmc optimizer
 
* Scenario ''"compile"'' proof of concept
 
 
  
 
|}
 
|}
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[[Category:Eclipse Technology Project]]
 
[[Category:Eclipse Technology Project]]
 +
 +
Click on the header for this section to view the Disclaimer.

Revision as of 10:50, 4 April 2013

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. Full length video In English
  2. Full length video In Hebrew
  3. Full length video In Japanese
  4. Full length video In Spanish
  5. 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
  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

Epidemiological Modeling

  1. Standard Populations
  2. Insect Vectors
  3. 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

V2.0.0 M1

Planning

  • Integrated UI for creating new models of disease including domain specific language for epi modeling
  • Parameter sensitivity analysis
  • mcmc optimizer
  •  Advanced Dengue Example
  • New Food Distribution Analysis view (incubation)
  • New Apache library

...future

  • Running Distributed STEM

Disclaimer


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