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Difference between revisions of "STEM"

(→‎STEM Documentation)
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== STEM Documentation ==
 
== STEM Documentation ==
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=== Getting Started ===
 
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*[[STEM Installation Guide|Installing the STEM Application]]
 
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*[[STEM Addons|Installing Additional Features]]
 
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*[[Sample Projects available for Download|Sample Projects (Downloadable Scenarios)]]
 
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*[[Welcome STEM Developers|Information for STEM Software Developers]]
 
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*[[STEM Eclipse Setup|Setting up a STEM Development Environment]]
 
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*[[STEM Design Document]]
 
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*[[STEM National Language Support | National Language Support]]
 
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=== Tutorials ===
 
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*[[Creating a STEM Scenario]]
 
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*[[How_scenarios_are_structured|How Scenarios are Structured]]
 
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*[[Initializing Disease Compartments|Initializing Diseases ''(Infectors, Inoculators, and Initializers)'']]
 
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*[[Triggering interventions|'''Triggering Interventions''']]
 
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#[[Triggering interventions#Social Distancing Example|Social Distancing Example]]
 
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#[[Triggering interventions#Vaccination Example|Vaccination Example]]
 
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#[[Triggering interventions#Evacuation Example|Evacuation Example]]
 
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#[[Triggering interventions#Air Transportation Example|Air Transportation Example]]
 
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* '''Using Population Models'''
 
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# [[Initializing a Population]]
 
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#[[Using Structured Populations in STEM|Using Structured Populations in STEM]]
 
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#[[Using Aging Populations in STEM|Using Aging Populations in STEM]]
 
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*'''Running Simulations'''
 
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#[[STEM_Map_View|The STEM Map View]]
 
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#[[Batch Mode (Running Experiments)|Running Experiments in Batch Mode]]
 
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#[[Running an Automated Experiment]]
 
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#[[STEM Headless|Running STEM Headless]]
 
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#[[Importing Data from Files]]
 
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#[[STEM Loggers|Simulation Data Logging]]
 
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*[[Importing and Exporting Projects]] 
 
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*[[Analysis|Some Built in Tools for Analysis]]
 
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*[[Context-Sensitive Help]]
 
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=== Advanced Guides ===
 
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*[[Building the STEM RCP Application|Building the STEM RCP Application]]
 
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*[[Running STEM from the Development Environment]]
 
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*[[Creating a Customized Color Provider|Customizing Colors]]
 
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*'''Working with Graphs'''
 
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#[[Composing a Graph]]
 
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#[[Creating a new Graph|Creating a Custom Graph]]
 
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#[[Visualizing and Editing Graphs]] with the STEM Graph Editor
 
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#[[Importing a Pajek Graph|Importing a Graph from a Pajek File]]
 
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#[[Importing an Esri Shapefile|Importing a Graph from an Esri Shapefile]]
 
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*'''Modeling new Diseases'''
 
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#[[Creating a new Disease Model Plug-in|Creating a New Disease Model Plug-in Using EMF]]
 
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#[[Creating a new disease label|Creating a New Disease Label]]
 
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=== Epidemiological Modeling ===
 
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*[[Introduction to Compartment Models|Compartment Models]]
 
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*[[Available Models|Disease and Population Models]]
 
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*[[Transportation Models|Transportation Models]]
 
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*[[Air Travel Model|Air Travel Model]]
 
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*[[STEM_Solvers|Solvers]]
 
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<br/>
 
  
 
== [[Disclaimer]] ==
 
== [[Disclaimer]] ==

Revision as of 14:41, 19 March 2012

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


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

Epidemiological Modeling

Release Planning

please also see our website

V1.3.1 Tentative Date 4/15/2012

Plan Features:

  • Bug Fixes to 1.3.0
  • STEM EMF update to version 2.7.2
  • Generalized model replay mechanism
  • Shape File Importer: Improvements to GUI
  • Population Transformer: food mediated disease
  • Graph Editor: improved features
  • New Population re-scaler

...future

  • Running Distributed STEM
  • parameter sensitivity analysis
  • mcmc optimizer
  • Simple creation of new Disease and Population models
  • Pajek-file Importer:
    • Enable import of discrete transportation events
    • Enable integration between user graphs and existing STEM graphs
  • Scenario "compile" proof of concept
  • Ability to Delete Items inside a Graph from Designer Perspective
  • Tools for generating new disease plugins

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)

STEM Documentation

Disclaimer





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