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(Tutorials)
(Epidemiological Modeling)
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====Working with Graphs====
 
====Working with Graphs====
 
#[[Composing a Graph]]
 
#[[Composing a Graph]]
#[[Creating a new Graph|Creating a Custom Graph]]
+
#[[Creating a new Graph|Creating a Custom Graph]] (''new'') ''seasonal migration''
 
#[[Visualizing and Editing Graphs]] ''with the STEM Graph Editor  ''  
 
#[[Visualizing and Editing Graphs]] ''with the STEM Graph Editor  ''  
 
#[[Importing a Pajek Graph|Importing a Graph from a Pajek File]]
 
#[[Importing a Pajek Graph|Importing a Graph from a Pajek File]]
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====Modeling New Diseases====
 
====Modeling New Diseases====
#'''''New!!''''' [[STEM Model Generator]] tool
+
#[[STEM Model Creator|Using the '''''New!!''''' STEM Model Creator tool]] (''beta'')
 +
#[[STEM Model Generator]] tool (for Developers)
 
#*[[STEM_Model_Generator/Install|Model Generator Installation]]
 
#*[[STEM_Model_Generator/Install|Model Generator Installation]]
 
#[[Creating a new Disease Model Plug-in|Manual Model Plug-in generation]]  
 
#[[Creating a new Disease Model Plug-in|Manual Model Plug-in generation]]  
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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)'']]
 
#[[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''']]
 
*'''''New!!''''' [[STEM Food and Food Borne Disease|Food Borne Disease Models''']]
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*[[Air Travel Model|Air Travel Model]]
 
*[[Air Travel Model|Air Travel Model]]
 
*[[STEM_Solvers|Solvers]]
 
*[[STEM_Solvers|Solvers]]
 +
**'''''New!!''''' [[STEM_Solvers#Stochastic_Solver|Stochastic Solver]]
  
  
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<br/>
 
<br/>
  
====V2.0.0 M1 ====
+
====V2.0.0 M3 ====
 
Planning
 
Planning
* Integrated UI for creating new models of disease including domain specific language for epi modeling
+
 
* Parameter sensitivity analysis
+
* Bug Fixes
* mcmc optimizer
+
* New Stochastic model solver
* Advanced Dengue Example
+
* Visual Editor initial checkin
* New Food Distribution Analysis view (incubation)  
+
* New Measles model
* New Apache library
+
* On Track: UI, model development workflow, builder tools, xtext, all in STEM
 +
* Add model generator Feature to STEM-core (with required plugins)  
 +
* Customize Project Explorer (show/hide generated Java code)                           
 +
* Hot injection of generated plugins
  
 
====...future====
 
====...future====

Revision as of 07:29, 17 June 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 (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

Epidemiological Modeling

  1. Standard Populations
  2. Insect Vectors
  3. Migratory Birds (new)
  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

V2.0.0 M3

Planning

  • Bug Fixes
  • New Stochastic model solver
  • Visual Editor initial checkin
  • New Measles model
  • On Track: UI, model development workflow, builder tools, xtext, all in STEM
  • Add model generator Feature to STEM-core (with required plugins)
  • Customize Project Explorer (show/hide generated Java code)
  • Hot injection of generated plugins

...future

  • Running Distributed STEM

Disclaimer


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