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Revision as of 20:47, 12 November 2012 by (Talk | contribs) (Release Planning)


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

Advanced Guides


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. New!! STEM Model Generator tool
  2. Manual Model Plug-in generation
  3. 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



  • Bug Fixes from 1.4.0
  • Performance improvements
  • Polio Vaccination Example
  • New STEM Update mechanism ***
  • More solvers from Apache Library


  • Running Distributed STEM
  • Integrated UI for creating new models of disease including domain specific language for epi modeling
  • parameter sensitivity analysis
  • mcmc optimizer
  • Polio
  •  Graphical Model Design (GUI for code generation)
  •  Advanced Dengue Example
  • New Food Distribution Analysis view (incubation)
  • New Apache library


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