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Difference between revisions of "STEM"

(V2.0.0 is now Available)
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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.  
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== '''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''' ==
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*[[STEM FAQ|STEM FAQ]]  
 
*[[STEM FAQ|STEM FAQ]]  
 
*[[Publications and Presentations on STEM]]  
 
*[[Publications and Presentations on STEM]]  
 +
*[[Citing STEM]]
 
*[[Join the STEM Community|How to Join the STEM Community]]  
 
*[[Join the STEM Community|How to Join the STEM Community]]  
 
*[[The STEM Development Team]]  
 
*[[The STEM Development Team]]  
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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]]'''
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*'''[[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]]
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#[[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'''
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==== STEM Solvers ====
 
==== STEM Solvers ====
 
*Available [[STEM_Solvers|Solvers]]
 
*Available [[STEM_Solvers|Solvers]]
**'''''New!!''''' [[STEM_Solvers#Stochastic_Solver|Stochastic Solver]]
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**STEM Native Solvers
|}
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**Apache Common Math Solvers
<!--outer table-->|
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**Stochastic Solver
{| style="width: 100%; height: 100%; background: #f1f5fc" ; border="0" ; cellpadding="5"
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|-style="background: #cceeff"
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!
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=== Epidemiological Modeling ===
 
=== Epidemiological Modeling ===
 
|-
 
|-
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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)'']]
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#[[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''']]
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*[[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]]
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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]]  
  
====V2.0.2 will be Available Friday, June 13====
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====Next Release To Come October 22, 2014====
Features
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* Bug fixes
+
* Updated Dengue Model and Scenario
+
  
====V2.0.1 NOW Available====
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====V2.0.2 Now Available====
* Bug fixes
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* Bug Fixes
 +
* Updated Dengue Model and Scenario
 +
* New Campylobacter Scenario
 +
 
 +
====V2.0.1 Included====
 +
* Bug Fixes
 
* Updated Code Generator
 
* Updated Code Generator
 
* New Campylobacter Model and Documentation
 
* New Campylobacter Model and Documentation
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====V2.0.0 Included====
 
====V2.0.0 Included====
Features
 
Features
 
 
* Bug Fixes
 
* Bug Fixes
* Performance improvements
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* Performance Improvements
* New Stochastic model solver
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* New Stochastic Model Solver
* Draggable solver objects    
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* Draggable Solver Objects    
 
* Visual Editor (Integrated UI for creating new models of disease including domain specific language for epi modeling)
 
* Visual Editor (Integrated UI for creating new models of disease including domain specific language for epi modeling)
 
* New Measles Model  
 
* New Measles Model  
* Directionally biased mixing model
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* Directionally Biased Mixing Model
* New Model Generator makes it easy for domain experts to create new STEM Models (no programming required) !!
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* New Model Generator (Makes it easy for domain experts to create new STEM Models--no programming required!!)
* New Apache library
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* New Apache Library
  
==== V2.0.1 ====
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====...Future Features====
 
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Planned for 12/11
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Features
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* Bug Fixes
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====...future====
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* Running Distributed STEM
 
* Running Distributed STEM
  
 
====Release Engineering====
 
====Release Engineering====
STEM releases are created by the team of STEM committers and uploaded  
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STEM releases are created by the team of STEM committers and uploaded to Eclipse on a regular basis.
<br/>
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to Eclipse on a regular basis.
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Documentation for the process may be found on the [[STEM Releng]] page.
Documentation for the process may be found  
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<br/>
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on the [[STEM Releng]] page.
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|}
 
|}
  

Revision as of 13:50, 8 January 2015

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.

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