Skip to main content

Notice: this Wiki will be going read only early in 2024 and edits will no longer be possible. Please see: https://gitlab.eclipse.org/eclipsefdn/helpdesk/-/wikis/Wiki-shutdown-plan for the plan.

Jump to: navigation, search

Difference between revisions of "STEM"

(V2.0.0 is now Available)
(121 intermediate revisions by 5 users not shown)
Line 7: Line 7:
 
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.  
 
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''' ==
  
 
<!--outer table-->{| style="width:98% ; border="0" ; cellpadding="0"  
 
<!--outer table-->{| style="width:98% ; border="0" ; cellpadding="0"  
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)]]
 +
*[[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'')
  
<br/>
 
<br/>
 
  
 
|}
 
|}
<!--outer table start-->|
+
<!--inner table start-->|
 
{| 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 54: Line 57:
 
|-
 
|-
 
|  
 
|  
*'''[[Creating a STEM Scenario]]'''
+
*'''[[Creating a STEM Scenario]]''' '''step by step'''
*'''[[How_scenarios_are_structured|How Scenarios are Structured]]'''
+
*'''[[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_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]]'''
 
*'''[[Triggering interventions|Triggering Interventions]]'''
 
*'''[[Triggering interventions|Triggering Interventions]]'''
 
#[[Triggering interventions#Social Distancing Example|Social Distancing Example]]
 
#[[Triggering interventions#Social Distancing Example|Social Distancing Example]]
Line 76: Line 82:
 
#[[STEM Loggers|Simulation Data Logging]]
 
#[[STEM Loggers|Simulation Data Logging]]
  
*'''[[Importing and Exporting Projects]]'''
+
*'''''(new)'' Automated Model Creation'''
*'''[[Analysis|Some Built in Tools for Analysis]]'''
+
#[[STEM Model Creator]] for users (''beta'')
*'''[[Context-Sensitive Help]]'''
+
  
 
|}
 
|}
 
<!--outer table-->|- style="width:45%"
 
<!--outer table-->|- style="width:45%"
 
<!--outer table-->|
 
<!--outer table-->|
{| style="width: 100%; height: 100%; background: #f1f5fc" ; border="0" ; cellpadding="5"  
+
{| style="width: 100%; background: #f1f5fc" ; border="0" ; cellpadding="5"  
 
|-style="background: #cceeff"
 
|-style="background: #cceeff"
 
!
 
!
Line 104: Line 109:
 
====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]]
 
#[[Importing an Esri Shapefile|Importing a Graph from an Esri Shapefile]]
 
#[[Importing an Esri Shapefile|Importing a Graph from an Esri Shapefile]]
  
====Modeling new Diseases====
+
====Modeling New Diseases====
#[[Creating a new Disease Model Plug-in|Creating a New Disease Model Plug-in Using EMF]]  
+
#[[STEM Model Creator|Using the '''''New!!''''' STEM Model Creator tool]] (''beta'')
#[[Creating a new disease label|Creating a New Disease Label]]
+
#[[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]]
  
==== Epidemiological Modeling ====
+
==== STEM Solvers ====
 
+
*Available [[STEM_Solvers|Solvers]]
*[[Introduction to Compartment Models|Compartment Models]]  
+
**'''''New!!''''' [[STEM_Solvers#Stochastic_Solver|Stochastic Solver]]
*[[Available Models|Disease and Population Models]]
+
|}
 +
<!--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]]
 
*[[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 130: Line 155:
 
|-
 
|-
 
|  
 
|  
''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/>
+
  
====V1.3.1====
+
====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
  
Plan Features: (''Tentative Date 4/15/2012'')
+
==== V2.0.1 ====
* Bug Fixes to 1.3.0
+
 
* STEM EMF update to version 2.7.2
+
Planned for 12/11
* Generalized model replay mechanism
+
Features
* Modifiable Modifiers (batch mode)
+
* Bug Fixes
* Shape File Importer: Improvements to GUI
+
* Population Transformer: food mediated disease
+
* Graph Editor: improved features
+
* New Population re-scaler
+
* New Polio model
+
  
 
====...future====
 
====...future====
 
* Running Distributed STEM
 
* Running Distributed STEM
* parameter sensitivity analysis
 
* mcmc optimizer
 
* Simple creation of new Disease and Population models
 
* Pajek-file Importer:
 
** Enable import of discrete transportation events
 
** Enable integration between user graphs and existing STEM graphs &nbsp;&nbsp;
 
* Scenario ''"compile"'' proof of concept
 
* Ability to Delete Items inside a Graph from Designer Perspective
 
* Tools for generating new disease plugins
 
* Drag (and copy) built-in scenarios to scenario folders inside STEM
 
* Create new mixing edges.
 
 
<br>
 
  
 +
====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-->|}
  
Line 171: Line 195:
  
 
[[Category:Eclipse Technology Project]]
 
[[Category:Eclipse Technology Project]]
 +
 +
Click on the header for this section to view the Disclaimer.

Revision as of 13:39, 14 November 2013

STEM TOP BAR.gif

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 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

V2.0.1

Planned for 12/11 Features

  • Bug Fixes

...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.

Back to the top