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STEM
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
- Full length STEM Tutorials on YouTubeTM
- 5 min Video (English)
- Scientific Talks Online
- STEM Website
- About STEM
- Whats New in STEM
- STEM FAQ
- Publications and Presentations on STEM
- Join the STEM Community
Getting Started
- Welcome STEM Developers
- Installing the STEM Application
- Installing Additional Features
- Setting up a STEM Development Environment
- STEM Design Document
- Sample Projects Available for Download
- National Language Support
Available Models
- Compartment Models
- Disease and Population Models
- Transportation Models
- Air Travel Model
- Solvers
- Disclaimer
Tutorials
- Importing and Exporting Projects
- Creating a STEM Scenario
- How scenarios are structured
- Initializing a Population
- Initializing Disease Compartments
- Simulation Data Logging
- Using Structured Populations in STEM
- Using Aging Populations in STEM
- Running Experiments in Batch Mode
- Running an Automated Experiment
- Running STEM Headless
- Triggering Interventions
- The STEM Map View
- Importing Data from Files
- Analysis: Four Tools
- Context-Sensitive Help
Advanced Guides
- Building the STEM RCP Application
- Running STEM from the Development Environment
- Composing a Graph
- Creating a Custom Graph
- Visualizing and Editing Graphs with the STEM Graph Editor
- Importing a Graph from a Pajek File
- Creating a New Disease Model Plug-in Using EMF
- Creating a New Disease Label
- Creating a Customized Color Provider
Join the STEM Community
Click on Join the STEM Community to learn more about the STEM Community.
Eclipse Project Mentors
Our Eclipse Project Mentors are: Ed Merks mailto:ed.merks@gmail.com and Chris Aniszczyk mailto:zx@eclipsesource.com
Future STEM Releases (Planned)
V1.3.0 Planned Date 1/29/2012 Planned and Tentative Features:
- Ten years of Earth Science Data (2000-2010) available as STEM Features
- Malaria Disease Model (Anopheles calibrated)
- Dengue Fever Disease Model (Aedes not yet calibrated)
- Additional NLS + User ability to switch languages
- Logger Framework with new loggers
- Shape File Import Utility (Dependency on Open Map CQ)
- Integrating external models for study of food based transmission
- New Differential Equation solver(s) from commons.math library
- Bug Fixes from 1.2.2
V1.3.1
Tentative Date 1/15/2012
Tentative Features:
- Bug Fixes to 1.3.0
- auto-documenting run parameters
- parameter sensitivity analysis
...future
- Running Distributed STEM