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STEM

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. 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
  7. Visualizing Discrete Transportation Events

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. Creating a New Disease Model Plug-in Using EMF
  2. Creating a New Disease Label

Epidemiological Modeling


Release Planning

please also see our website and What's New in STEM

V1.4.0

Plan Features: (Tentative Date 9/15/2012)

  • Performance improvements
  • Simplified creation of new Disease and Population models (Tools for generating new disease plugins)
  • Pajek-file Importer:
    • Enable import of discrete transportation events
    • Enable integration between user graphs and existing STEM graphs
  • New improved MapView
    • 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
  • Refactor
  • Create new mixing edges (chris to put edges back, jk to do generator)
  • Improved UI for decorators view

V1.3.1

Current Release

  • Bug Fixes to 1.3.0
  • 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

  • Running Distributed STEM
  • parameter sensitivity analysis
  • mcmc optimizer
  • Scenario "compile" proof of concept


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