Difference between revisions of "STEM"

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(V2.0.0 is now Available)
 
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*[[Whats New in STEM|What's New in STEM]]  
 
*[[Whats New in STEM|What's New in STEM]]  
 
*STEM Tutorials on YouTube<sup>TM</sup>
 
*STEM Tutorials on YouTube<sup>TM</sup>
 
+
#[http://www.youtube.com/watch?v=MtQlS7g7Qnw STEM Model Generator (new!!)] ''requires STEM V2.0 milestone''
 
#Full length video [http://www.youtube.com/watch?v=LfiibQX4IFE In English]  
 
#Full length video [http://www.youtube.com/watch?v=LfiibQX4IFE In English]  
 
#Full length video [http://www.youtube.com/watch?v=AFYXvazKkms In Hebrew]  
 
#Full length video [http://www.youtube.com/watch?v=AFYXvazKkms In Hebrew]  
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*[[STEM Installation Guide|Installing the STEM Application]]
 
*[[STEM Installation Guide|Installing the STEM Application]]
 +
*[[STEM Overview of the STEM UI|Overview of the STEM UI and menu items ''(new)'']]
 
*[[STEM Addons|Installing Additional Features]]
 
*[[STEM Addons|Installing Additional Features]]
 
*[[Sample Projects available for Download|Sample Projects (Downloadable Scenarios)]]
 
*[[Sample Projects available for Download|Sample Projects (Downloadable Scenarios)]]
 +
*[[Importing and Exporting Projects]]
 +
*[[Analysis|Some Built in Tools for Analysis]]
 +
*[[Context-Sensitive Help]]
 +
*[[STEM Model Creator|Using the '''''New!!''''' STEM Model Creator tool]] (''beta'')
  
  
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|  
 
|  
 
*'''[[Creating a STEM Scenario]]''' '''step by step'''
 
*'''[[Creating a STEM Scenario]]''' '''step by step'''
*'''[[How_scenarios_are_structured|(New!) Scenario Structure: tutorial with templates]]'''
+
*'''[[How_scenarios_are_structured|(New!) Scenario Structure: Tutorial with Templates]]'''
#[[How_scenarios_are_structured#Template_for_a_Basic_Scenario_with_a_Human_Disease|Model with human-human transmission]]
+
#[[How_scenarios_are_structured#Template_for_a_Basic_Scenario_with_a_Human_Disease|Model with Human-Human Transmission]]
#[[How_scenarios_are_structured#Template_for_a_Food_Borne_Disease_Scenario|Model of food borne disease]]
+
#[[How_scenarios_are_structured#Template_for_a_Food_Borne_Disease_Scenario|Model of Food Borne disease]]
 
*'''[[Initializing Disease Compartments|Initializing Diseases ''(Infectors, Inoculators, and Initializers)'']]'''
 
*'''[[Initializing Disease Compartments|Initializing Diseases ''(Infectors, Inoculators, and Initializers)'']]'''
 
*'''[[STEM Import Discrete Transportation Events|Import Discrete Transportation Events]]'''
 
*'''[[STEM Import Discrete Transportation Events|Import Discrete Transportation Events]]'''
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#[[STEM Loggers|Simulation Data Logging]]
 
#[[STEM Loggers|Simulation Data Logging]]
  
*'''''(new)'' Automatic Model Creation'''
+
*'''''(new)'' Automated Model Creation'''
*[[STEM Model Creator]] for users (-''beta'')
+
#[[STEM Model Creator]] for users (''beta'')
  
*'''[[Importing and Exporting Projects]]''' 
 
*'''[[Analysis|Some Built in Tools for Analysis]]'''
 
*'''[[Context-Sensitive Help]]'''
 
 
*[[STEM Model Generator|Using the '''''New!!''''' STEM Model Generation tool]]
 
 
|}
 
|}
 
<!--outer table-->|- style="width:45%"
 
<!--outer table-->|- style="width:45%"
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=== Advanced Guides ===
 
=== Advanced Guides ===
 
 
|-
 
|-
 
|  
 
|  
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====Working with Graphs====
 
====Working with Graphs====
 
#[[Composing a Graph]]
 
#[[Composing a Graph]]
#[[Creating a new Graph|Creating a Custom Graph]]
+
#[[Creating a new Graph|Creating a Custom Graph]] (''new'') ''seasonal migration''
 
#[[Visualizing and Editing Graphs]] ''with the STEM Graph Editor  ''&nbsp;&nbsp;
 
#[[Visualizing and Editing Graphs]] ''with the STEM Graph Editor  ''&nbsp;&nbsp;
 
#[[Importing a Pajek Graph|Importing a Graph from a Pajek File]]
 
#[[Importing a Pajek Graph|Importing a Graph from a Pajek File]]
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====Modeling New Diseases====
 
====Modeling New Diseases====
#'''''New!!''''' [[STEM Model Generator]] tool
+
#[[STEM Model Creator|Using the '''''New!!''''' STEM Model Creator tool]] (''beta'')
 +
#[[STEM Model Generator]] tool (for Developers)
 
#*[[STEM_Model_Generator/Install|Model Generator Installation]]
 
#*[[STEM_Model_Generator/Install|Model Generator Installation]]
 
#[[Creating a new Disease Model Plug-in|Manual Model Plug-in generation]]  
 
#[[Creating a new Disease Model Plug-in|Manual Model Plug-in generation]]  
 
#[[Creating a new disease label|Manual Disease Label creation]]
 
#[[Creating a new disease label|Manual Disease Label creation]]
  
==== Epidemiological Modeling ====
+
==== STEM Solvers ====
 +
*Available [[STEM_Solvers|Solvers]]
 +
**'''''New!!''''' [[STEM_Solvers#Stochastic_Solver|Stochastic Solver]]
 +
|}
 +
<!--outer table-->|
 +
{| style="width: 100%; height: 100%; background: #f1f5fc" ; border="0" ; cellpadding="5"
 +
|-style="background: #cceeff"
 +
!
 +
=== Epidemiological Modeling ===
 +
|-
 +
|
 
*[[Sample Projects available for Download|Sample Projects (Downloadable Scenarios)]]
 
*[[Sample Projects available for Download|Sample Projects (Downloadable Scenarios)]]
 
*[[Introduction to Compartment Models|Intro to Compartment Models]]  
 
*[[Introduction to Compartment Models|Intro to Compartment Models]]  
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#[[STEM_Population_Models#Standard_Population_Model|Standard Populations]]
 
#[[STEM_Population_Models#Standard_Population_Model|Standard Populations]]
 
#[[STEM_Population_Models#Advanced_Models|Insect Vectors]]
 
#[[STEM_Population_Models#Advanced_Models|Insect Vectors]]
 +
#[[STEM_Population_Models#Seasonal_Migratory_Population_Model|Migratory Birds ''(new)'']]
 
#[[STEM_Population_Models#Multipopulation_Models|Demographic Models (and Aging)]]
 
#[[STEM_Population_Models#Multipopulation_Models|Demographic Models (and Aging)]]
 
*'''''New!!''''' [[STEM Food and Food Borne Disease|Food Borne Disease Models''']]
 
*'''''New!!''''' [[STEM Food and Food Borne Disease|Food Borne Disease Models''']]
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*[[Transportation Models|Transportation Models]]
 
*[[Transportation Models|Transportation Models]]
 
*[[Air Travel Model|Air Travel Model]]
 
*[[Air Travel Model|Air Travel Model]]
*[[STEM_Solvers|Solvers]]
 
 
  
 
|}
 
|}
<!--outer table-->|
 
 
{| style="width: 100%; height: 100%; background: #f1f5fc" ; border="0" ; cellpadding="5"  
 
{| style="width: 100%; height: 100%; background: #f1f5fc" ; border="0" ; cellpadding="5"  
 
|-style="background: #cceeff"
 
|-style="background: #cceeff"
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|  
 
|  
 
''Please also see our [http://www.eclipse.org/stem website]'' and [[Whats New in STEM|What's New in STEM]]  
 
''Please also see our [http://www.eclipse.org/stem website]'' and [[Whats New in STEM|What's New in STEM]]  
<br/>
 
<br/>
 
  
====V2.0.0 M1 ====
+
====V2.0.0 is now Available ====
Planning
+
Features
* Integrated UI for creating new models of disease including domain specific language for epi modeling
+
Features
* Parameter sensitivity analysis
+
* Bug Fixes
* mcmc optimizer
+
* Performance improvements
* Advanced Dengue Example
+
* New Stochastic model solver
* New Food Distribution Analysis view (incubation)  
+
* Draggable solver objects 
 +
* Visual Editor (Integrated UI for creating new models of disease including domain specific language for epi modeling)
 +
* New Measles model
 +
* Directionally biased mixing model
 +
* New Model Generator makes it easy for domain experts to create new STEM Models (no programming required) !!
 
* New Apache library
 
* New Apache library
 +
 +
==== V2.0.1 ====
 +
 +
Planned for 12/11
 +
Features
 +
* Bug Fixes
  
 
====...future====
 
====...future====
 
* Running Distributed STEM
 
* Running Distributed STEM
  
 +
====Release Engineering====
 +
STEM releases are created by the team of STEM committers and uploaded
 +
<br/>
 +
to Eclipse on a regular basis.
 +
Documentation for the process may be found
 +
<br/>
 +
on the [[STEM Releng]] page.
 
|}
 
|}
 +
 
<!--outer table-->|}
 
<!--outer table-->|}
  

Latest revision as of 13:39, 14 November 2013

STEM TOP BAR.gif

Contents

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.

[edit] STEM Documentation

[edit] Introductory Resources

  1. STEM Model Generator (new!!) requires STEM V2.0 milestone
  2. Full length video In English
  3. Full length video In Hebrew
  4. Full length video In Japanese
  5. Full length video In Spanish
  6. 5 min Video (English)

[edit] Getting Started


[edit] Tutorials

  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
  • (new) Automated Model Creation
  1. STEM Model Creator for users (beta)

[edit] Advanced Guides

[edit] Developers

[edit] Working with Graphs

  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

[edit] Modeling New Diseases

  1. Using the New!! STEM Model Creator tool (beta)
  2. STEM Model Generator tool (for Developers)
  3. Manual Model Plug-in generation
  4. Manual Disease Label creation

[edit] STEM Solvers

[edit] Epidemiological Modeling

  1. Standard Populations
  2. Insect Vectors
  3. Migratory Birds (new)
  4. Demographic Models (and Aging)
  1. Beef Production Example
  2. Salmonella in Pork Example
  3. How to Structure a Food Borne Disease Scenario

[edit] Release Planning

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

[edit] V2.0.0 is now Available

Features Features

  • Bug Fixes
  • Performance improvements
  • New Stochastic model solver
  • Draggable solver objects
  • Visual Editor (Integrated UI for creating new models of disease including domain specific language for epi modeling)
  • New Measles model
  • Directionally biased mixing model
  • New Model Generator makes it easy for domain experts to create new STEM Models (no programming required) !!
  • New Apache library

[edit] V2.0.1

Planned for 12/11 Features

  • Bug Fixes

[edit] ...future

  • Running Distributed STEM

[edit] 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.

[edit] Disclaimer


Click on the header for this section to view the Disclaimer.