Jump to: navigation, search

Difference between revisions of "STEM"

(Epidemiological Modeling)
(Ebola Community Efforts)
 
(78 intermediate revisions by 2 users not shown)
Line 5: Line 5:
 
   |}
 
   |}
  
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.  
+
== '''Ebola Community Efforts''' ==
 +
==== [[Weekly Community Ebola Modeling Phone Call]] ====
 +
==== [[Ebola Models]] ====
 +
==== [https://wiki.eclipse.org/Ebola_How_To How to install the Ebola models]====
 +
==== Literature [[Ebola References]]====
 +
==== Data [[Ebola Reference Data]]====
 +
==== Please sign up for the [https://dev.eclipse.org/mailman/listinfo/stem-ebola stem-ebola mailing list]====
 +
 
 +
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''' ==
 
== '''STEM Documentation''' ==
Line 22: Line 30:
 
*[[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 47:
  
 
*[[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'')
  
  
Line 53: Line 66:
 
|  
 
|  
 
*'''[[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| 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 76: Line 89:
 
#[[Importing Data from Files]]  
 
#[[Importing Data from Files]]  
 
#[[STEM Loggers|Simulation Data Logging]]
 
#[[STEM Loggers|Simulation Data Logging]]
 +
#[[Visualizing STEM Simulations with Google Earth]]
  
 
*'''''(new)'' Automated 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 Creator|Using the '''''New!!''''' STEM Model Creator tool]] (''beta'')
 
 
|}
 
|}
 
<!--outer table-->|- style="width:45%"
 
<!--outer table-->|- style="width:45%"
Line 93: Line 102:
  
 
=== Advanced Guides ===
 
=== Advanced Guides ===
 
 
|-
 
|-
 
|  
 
|  
Line 110: Line 118:
 
====Working with Graphs====
 
====Working with Graphs====
 
#[[Composing a Graph]]
 
#[[Composing a Graph]]
#[[Creating a new Graph|Creating a Custom Graph]] (''new'' , seasonal migration)
+
#[[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]]
Line 122: Line 130:
 
#[[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]]
 +
**STEM Native Solvers
 +
**Apache Common Math Solvers
 +
**Stochastic Solver
 +
 
 +
=== 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]]  
Line 129: Line 145:
 
#[[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#Seasonal_Migratory_Population_Model|Migratory Birds]]
 
#[[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''']]
+
*[[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#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]]
 
#[[Sample_Projects_available_for_Download#2._A_scenario_for_modelling_the_transmission_of_Salmonella_to_pigs.2C_pork_and_humans|Salmonella in Pork Example]]
Line 137: Line 153:
 
*[[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"
Line 150: Line 163:
 
|  
 
|  
 
''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 ====
+
====Next Release To Come October 22, 2014====
Planning
+
  
 +
====V2.0.2 Now Available====
 
* Bug Fixes
 
* Bug Fixes
* New Stochastic model solver
+
* Updated Dengue Model and Scenario
* Visual Editor initial checkin
+
* New Campylobacter Scenario
* 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====
+
====V2.0.1 Included====
 +
* Bug Fixes
 +
* Updated Code Generator
 +
* New Campylobacter Model and Documentation
 +
* New Dengue Model and Scenario
 +
 
 +
====V2.0.0 Included====
 +
* 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
 +
 
 +
====...Future Features====
 
* Running Distributed STEM
 
* 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.
 
|}
 
|}
 +
 
<!--outer table-->|}
 
<!--outer table-->|}
  

Latest revision as of 12:12, 3 November 2014

STEM TOP BAR.gif

Ebola Community Efforts

Weekly Community Ebola Modeling Phone Call

Ebola Models

How to install the Ebola models

Literature Ebola References

Data Ebola Reference Data

Please sign up for the stem-ebola mailing list

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
  7. Visualizing STEM Simulations with Google Earth
  • (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

  • Available Solvers
    • STEM Native Solvers
    • Apache Common Math Solvers
    • Stochastic Solver

Epidemiological Modeling

  1. Standard Populations
  2. Insect Vectors
  3. Migratory Birds
  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

Next Release To Come October 22, 2014

V2.0.2 Now Available

  • Bug Fixes
  • Updated Dengue Model and Scenario
  • New Campylobacter Scenario

V2.0.1 Included

  • Bug Fixes
  • Updated Code Generator
  • New Campylobacter Model and Documentation
  • New Dengue Model and Scenario

V2.0.0 Included

  • 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

...Future Features

  • 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.