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STEM Community Phone Call

The STEM community runs a monthly phone call anyone is free to join. 
If you wish to join, please subscribe to the mailing list
where you can see the announcements and agenda for scheduled calls.

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


  1. STEM Model Generator
    narration by Sarah Kaufman
  2. A Presentation on STEM
    1. In English
  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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