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Difference between revisions of "STEM"

(Tutorials)
(Next Release To Come October 22, 2014)
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[[Image:STEM TOP BAR.gif|800px]]
 
[[Image:STEM TOP BAR.gif|800px]]
  
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.
+
{| align="right"
 +
  | __TOC__
 +
  |}
  
 +
== '''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]====
  
== Introductory Resources ==
+
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.
*[http://www.eclipse.org/stem/ The STEM Website]
+
 
*[[About STEM]]
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== '''STEM Documentation''' ==
*[[Whats New in STEM]]
+
 
 +
<!--outer table-->{| style="width:98% ; border="0" ; cellpadding="0"
 +
<!--outer table-->|-
 +
<!--outer table-->|
 +
{| style="width: 100%; height: 100%; background: #f1f5fc" ; border="0" ; cellpadding="5"
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|- style="background: #cceeff"
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!
 +
=== Introductory Resources ===
 +
|-
 +
|
 +
*[http://www.eclipse.org/stem/ The STEM Website]  
 +
*[[About STEM]]  
 +
*[[Whats New in STEM|What's New in STEM]]  
 
*STEM Tutorials on YouTube<sup>TM</sup>
 
*STEM Tutorials on YouTube<sup>TM</sup>
#Full length video [http://www.youtube.com/watch?v=LfiibQX4IFE In English]
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#[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=AFYXvazKkms In Hebrew]
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#Full length video [http://www.youtube.com/watch?v=LfiibQX4IFE In English]  
#Full length video [http://www.youtube.com/watch?v=NM5X8-MaiKo In Japanese]
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#Full length video [http://www.youtube.com/watch?v=AFYXvazKkms In Hebrew]  
#Full length video [http://www.youtube.com/watch?v=3S5DbjCHsx4 In Spanish]
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#Full length video [http://www.youtube.com/watch?v=NM5X8-MaiKo In Japanese]  
 +
#Full length video [http://www.youtube.com/watch?v=3S5DbjCHsx4 In Spanish]  
 
#[http://www.youtube.com/watch?v=OoiFLemepw4 5 min Video (English)]
 
#[http://www.youtube.com/watch?v=OoiFLemepw4 5 min Video (English)]
*[http://www.eclipse.org/stem/talksOnline.php Scientific Talks Online]
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*[[STEM FAQ|STEM FAQ]]
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*[http://www.eclipse.org/stem/talksOnline.php Scientific Talks Online] &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
*[[Publications and Presentations on STEM]]
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*[[STEM FAQ|STEM FAQ]]  
*[[Join the STEM Community|How to Join the STEM Community]]
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*[[Publications and Presentations on STEM]]
*[[The STEM Development Team]]
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*[[Citing STEM]]  
 +
*[[Join the STEM Community|How to Join the STEM Community]]  
 +
*[[The STEM Development Team]]  
 
*[[Join the STEM Community|Weekly phone call]]
 
*[[Join the STEM Community|Weekly phone call]]
 
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== STEM Documentation ==
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==== Getting Started ====
 
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=== Getting Started ===
+
  
 
*[[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 Available for Download]]
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*[[Sample Projects available for Download|Sample Projects (Downloadable Scenarios)]]
*[[Welcome STEM Developers|Information for STEM Software Developers]]
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*[[Importing and Exporting Projects]]
*[[STEM Eclipse Setup|Setting up a STEM Development Environment]]
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*[[Analysis|Some Built in Tools for Analysis]]
*[[STEM Design Document]]
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*[[Context-Sensitive Help]]
*[[STEM National Language Support | National Language Support]]
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*[[STEM Model Creator|Using the '''''New!!''''' STEM Model Creator tool]] (''beta'')
 +
 
 +
 
 +
|}
 +
<!--inner table start-->|
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{| style="width: 100%; height: 100%; background: #f1f5fc" ; border="0" ; cellpadding="5"
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|-style="background: #cceeff"
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!
  
 
=== Tutorials ===
 
=== Tutorials ===
 +
|-
 +
|
 +
*'''[[Creating a STEM Scenario]]''' '''step by step'''
 +
*'''[[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_Food_Borne_Disease_Scenario|Model of Food Borne disease]]
 +
*'''[[Initializing Disease Compartments|Initializing Diseases ''(Infectors, Inoculators, and Initializers)'']]'''
 +
*'''[[STEM Import Discrete Transportation Events|Import Discrete Transportation Events]]'''
 +
*'''[[Triggering interventions|Triggering Interventions]]'''
 +
#[[Triggering interventions#Social Distancing Example|Social Distancing Example]]
 +
#[[Triggering interventions#Vaccination Example|Vaccination Example]]
 +
#[[Triggering interventions#Evacuation Example|Evacuation Example]]
 +
#[[Triggering interventions#Air Transportation Example|Air Transportation Example]]
  
*[[Importing and Exporting Projects]]
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*'''Using Population Models'''
*[[Creating a STEM Scenario]]
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# [[Initializing a Population]]  
*[[How scenarios are structured]]
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#[[Using Structured Populations in STEM|Using Structured Populations in STEM]]  
*[[Initializing Disease Compartments]]
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#[[Using Aging Populations in STEM|Using Aging Populations in STEM]]  
*[[Triggering interventions|Triggering Interventions]]
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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'''
 
*'''Running Simulations'''
**[[STEM_Map_View|The STEM Map View]]  
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#[[STEM_Map_View|The STEM Map View]]  
**[[Batch Mode (Running Experiments)|Running Experiments in Batch Mode]]  
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#[[Batch Mode (Running Experiments)|Running Experiments in Batch Mode]]  
**[[Running an Automated Experiment]]  
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#[[Running an Automated Experiment]]  
**[[STEM Headless|Running STEM Headless]]
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#[[STEM Headless|Running STEM Headless]]
**[[Importing Data from Files]]  
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#[[Importing Data from Files]]  
**[[STEM Loggers|Simulation Data Logging]]
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#[[STEM Loggers|Simulation Data Logging]]
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#[[Visualizing STEM Simulations with Google Earth]]
*[[Analysis|Analysis: Four Tools]]  
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*[[Context-Sensitive Help]]
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*'''''(new)'' Automated Model Creation'''
 +
#[[STEM Model Creator]] for users (''beta'')
 +
 
 +
|}
 +
<!--outer table-->|- style="width:45%"
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<!--outer table-->|
 +
{| style="width: 100%; background: #f1f5fc" ; border="0" ; cellpadding="5"
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|-style="background: #cceeff"
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!
  
 
=== Advanced Guides ===
 
=== Advanced Guides ===
 +
|-
 +
|
 +
====Developers====
 +
*[[Welcome STEM Developers]]
 +
*[[STEM Eclipse Setup|Setting up a STEM Development Environment]]
 +
*[[STEM Design Document]]
 +
*[[STEM National Language Support | National Language Support]]
 +
*[http://www.eclipse.org/projects/project.php?id=technology.stem Project Stats]
  
 
*[[Building the STEM RCP Application|Building the STEM RCP Application]]
 
*[[Building the STEM RCP Application|Building the STEM RCP Application]]
 
*[[Running STEM from the Development Environment]]
 
*[[Running STEM from the Development Environment]]
*[[Composing a Graph]]
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*[[Creating a Customized Color Provider|Customizing Colors]]
*[[Creating a new Graph|Creating a Custom Graph]]
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*[[STEM Performance Tips |General tips when writing performance critical code]]
*[[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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*[[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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*[[Creating a Customized Color Provider]]
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=== Epidemiological Modeling ===
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====Working with Graphs====
 +
#[[Composing a Graph]]
 +
#[[Creating a new Graph|Creating a Custom Graph]] (''new'') ''seasonal migration''
 +
#[[Visualizing and Editing Graphs]] ''with the STEM Graph Editor  ''&nbsp;&nbsp;
 +
#[[Importing a Pajek Graph|Importing a Graph from a Pajek File]]
 +
#[[Importing an Esri Shapefile|Importing a Graph from an Esri Shapefile]]
  
*[[Introduction to Compartment Models|Compartment Models]]  
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====Modeling New Diseases====
*[[Available Models|Disease and Population Models]]
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#[[STEM Model Creator|Using the '''''New!!''''' STEM Model Creator tool]] (''beta'')
 +
#[[STEM Model Generator]] tool (for Developers)
 +
#*[[STEM_Model_Generator/Install|Model Generator Installation]]
 +
#[[Creating a new Disease Model Plug-in|Manual Model Plug-in generation]]
 +
#[[Creating a new disease label|Manual Disease Label creation]]
 +
 
 +
==== 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)]]
 +
*[[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]]
 +
#[[STEM_Population_Models#Multipopulation_Models|Demographic Models (and Aging)]]
 +
*[[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]]
 
*[[Transportation Models|Transportation Models]]
 
*[[Air Travel Model|Air Travel Model]]
 
*[[Air Travel Model|Air Travel Model]]
*[[STEM_Solvers|Solvers]]
 
*[[Disclaimer]]
 
  
== Release Planning ==
+
|}
 +
{| style="width: 100%; height: 100%; background: #f1f5fc" ; border="0" ; cellpadding="5"
 +
|-style="background: #cceeff"
 +
!
  
[[Category:Eclipse Technology Project]]
+
=== Release Planning ===
 +
|-
 +
|
 +
''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]''
+
====Next Release To Come January 30, 2015====
  
'''V1.3.0'''
+
====V2.0.2 Now Available====
Revised Date 2/7/2012
+
* Bug Fixes
Planned and Tentative Features:
+
* Updated Dengue Model and Scenario
 +
* New Campylobacter Scenario
  
* Bug Fixes from 1.2.2
+
====V2.0.1 Included====
* Ten years of Earth Science Data (2000-2010) available as STEM '''Features'''
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* Bug Fixes
* Malaria Disease Model (''Anopheles'' calibrated)
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* Updated Code Generator
* Dengue Fever Disease Model (''Aedes'' not yet calibrated)
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* New Campylobacter Model and Documentation
* New Differential Equation solver(s) from commons.math library
+
* New Dengue Model and Scenario
* Additional NLS + User ability to switch languages
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* Logger Framework with new loggers
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* New feature: “Population Transformer” - enabling transformation of population members to allow modeling of e.g. food mediated disease transmission
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* Improvements to the graphical editor
+
  
'''V1.3.1'''
+
====V2.0.0 Included====
Tentative Date 4/15/2012
+
* Bug Fixes
Tentative Features:
+
* Performance Improvements
* Bug Fixes to 1.3.0
+
* New Stochastic Model Solver
* Scenario ''"compile"'' proof of concept
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* Draggable Solver Objects 
* STEM EMF update to version 2.7.2
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* Visual Editor (Integrated UI for creating new models of disease including domain specific language for epi modeling)
* Shape File Importer: Improvements to GUI
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* New Measles Model
* Population Transformer: “realistic” sample model on food mediated disease transmission
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* Directionally Biased Mixing Model
* Pajek-file Importer: Enable integration between user graphs and existing STEM graphs
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* New Model Generator (Makes it easy for domain experts to create new STEM Models--no programming required!!)
* Graph Editor: improved zooming, deleting nodes and edges, improved GUI for new population generation
+
* New Apache Library
* Ability to Delete Items inside a Graph from Designer Perspective
+
* STEM -integration inside KNIME: creating a Node within the KNIME, Node-repository that allows STEM headless execution
+
  
'''...future'''
+
====...Future Features====
 
* Running Distributed STEM
 
* Running Distributed STEM
* parameter sensitivity analysis
 
* mcmc optimizer
 
* New feature to hide complexity of creating new plugins (for Disease and Population models).
 
* Pajek-file Importer: enable import of discrete transportation events.
 
  
 +
====Release Engineering====
 +
STEM releases are created by the team of STEM committers and uploaded to Eclipse on a regular basis.
  
{| align="left"
+
Documentation for the process may be found on the [[STEM Releng]] page.
  | __TOC__
+
|}
  |}
+
 
 +
<!--outer table-->|}
 +
 
 +
==[[Disclaimer]]==
 +
 
 +
<br>
 +
 
 +
[[Category:Eclipse Technology Project]]
 +
 
 +
Click on the header for this section to view the Disclaimer.

Revision as of 11:26, 29 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 January 30, 2015

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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