Difference between revisions of "STEM"

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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]]'''
*'''[[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_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]]
*'''[[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]]'''

Revision as of 10:17, 25 July 2013



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


  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


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

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 Milestone 3


  • 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


  • 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.


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