Difference between revisions of "STEM"

From Eclipsepedia

Jump to: navigation, search
(Tutorials)
(Getting Started)
(18 intermediate revisions by 2 users not shown)
Line 22: Line 22:
 
*[[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]  
Line 39: Line 39:
  
 
*[[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)]]
Line 46: Line 47:
 
*[[STEM Model Creator|Using the '''''New!!''''' STEM Model Creator tool]] (''beta'')
 
*[[STEM Model Creator|Using the '''''New!!''''' STEM Model Creator tool]] (''beta'')
  
==== Running Simulations ====
 
*[[STEM_Map_View|The STEM Map View]]
 
*[[Batch Mode (Running Experiments)|Running Experiments in Batch Mode]]
 
*[[Running an Automated Experiment]]
 
*[[STEM Headless|Running STEM Headless]]
 
*[[Importing Data from Files]]
 
*[[STEM Loggers|Simulation Data Logging]]
 
  
 
|}
 
|}
Line 64: Line 58:
 
|  
 
|  
 
*'''[[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]]'''
Line 79: Line 73:
 
#[[Using Structured Populations in STEM|Using Structured Populations in STEM]]  
 
#[[Using Structured Populations in STEM|Using Structured Populations in STEM]]  
 
#[[Using Aging Populations in STEM|Using Aging Populations in STEM]]  
 
#[[Using Aging Populations in STEM|Using Aging Populations in STEM]]  
 +
 +
*'''Running Simulations'''
 +
#[[STEM_Map_View|The STEM Map View]]
 +
#[[Batch Mode (Running Experiments)|Running Experiments in Batch Mode]]
 +
#[[Running an Automated Experiment]]
 +
#[[STEM Headless|Running STEM Headless]]
 +
#[[Importing Data from Files]]
 +
#[[STEM Loggers|Simulation Data Logging]]
  
 
*'''''(new)'' Automated Model Creation'''
 
*'''''(new)'' Automated Model Creation'''
Line 91: Line 93:
  
 
=== Advanced Guides ===
 
=== Advanced Guides ===
 
 
|-
 
|-
 
|  
 
|  
Line 121: Line 122:
  
 
==== STEM Solvers ====
 
==== STEM Solvers ====
 
 
*Available [[STEM_Solvers|Solvers]]
 
*Available [[STEM_Solvers|Solvers]]
 
**'''''New!!''''' [[STEM_Solvers#Stochastic_Solver|Stochastic Solver]]
 
**'''''New!!''''' [[STEM_Solvers#Stochastic_Solver|Stochastic Solver]]
 
 
 
|}
 
|}
 
<!--outer table-->|
 
<!--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)]]
 +
*[[Introduction to Compartment Models|Intro to Compartment Models]]
 +
*[[STEM Disease Models|Disease Models (basic to advanced)]]
 +
*[[STEM Population Models|Population Models]]
 +
#[[STEM_Population_Models#Standard_Population_Model|Standard Populations]]
 +
#[[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)]]
 +
*'''''New!!''''' [[STEM Food and Food Borne Disease|Food Borne Disease Models''']]
 +
#[[Sample_Projects_available_for_Download#1._Beef_Production|Beef Production Example]]
 +
#[[Sample_Projects_available_for_Download#2._A_scenario_for_modelling_the_transmission_of_Salmonella_to_pigs.2C_pork_and_humans|Salmonella in Pork Example]]
 +
#[[How_scenarios_are_structured#Template_for_a_Food_Borne_Disease_Scenario|How to Structure a Food Borne Disease Scenario]]
 +
*[[Transportation Models|Transportation Models]]
 +
*[[Air Travel Model|Air Travel Model]]
 +
 +
|}
 
{| 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"
Line 136: Line 156:
 
|  
 
|  
 
''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 M3 ====
+
====V2.0.0 Milestone 3 ====
 
Planning
 
Planning
 
 
* Bug Fixes
 
* Bug Fixes
 
* New Stochastic model solver
 
* New Stochastic model solver
Line 149: Line 166:
 
* Add model generator Feature to STEM-core (with required plugins)  
 
* Add model generator Feature to STEM-core (with required plugins)  
 
* Customize Project Explorer (show/hide generated Java code)                             
 
* Customize Project Explorer (show/hide generated Java code)                             
* Hot injection of generated plugins  
+
* Hot injection of generated plugins
  
 
====...future====
 
====...future====
Line 161: Line 178:
 
<br/>
 
<br/>
 
on the [[STEM Releng]] page.
 
on the [[STEM Releng]] page.
 
 
|}
 
 
 
{| 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)]]
 
*[[Introduction to Compartment Models|Intro to Compartment Models]]
 
*[[STEM Disease Models|Disease Models (basic to advanced)]]
 
*[[STEM Population Models|Population Models]]
 
#[[STEM_Population_Models#Standard_Population_Model|Standard Populations]]
 
#[[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)]]
 
*'''''New!!''''' [[STEM Food and Food Borne Disease|Food Borne Disease Models''']]
 
#[[Sample_Projects_available_for_Download#1._Beef_Production|Beef Production Example]]
 
#[[Sample_Projects_available_for_Download#2._A_scenario_for_modelling_the_transmission_of_Salmonella_to_pigs.2C_pork_and_humans|Salmonella in Pork Example]]
 
#[[How_scenarios_are_structured#Template_for_a_Food_Borne_Disease_Scenario|How to Structure a Food Borne Disease Scenario]]
 
*[[Transportation Models|Transportation Models]]
 
*[[Air Travel Model|Air Travel Model]]
 
 
 
 
|}
 
|}
  

Revision as of 18:04, 26 September 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.

STEM Documentation

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)

Getting Started


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)

Advanced Guides

Developers

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

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

STEM Solvers

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

Release Planning

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

V2.0.0 Milestone 3

Planning

  • Bug Fixes
  • New Stochastic model solver
  • Visual Editor initial checkin
  • New Measles model
  • On Track: UI, model development workflow, builder tools, xtext, all in STEM
  • Add model generator Feature to STEM-core (with required plugins)
  • Customize Project Explorer (show/hide generated Java code)
  • Hot injection of generated plugins

...future

  • Running Distributed STEM

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.

Disclaimer


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