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Difference between revisions of "STEM"

(Modeling New Diseases)
(V2.0.0)
(14 intermediate revisions by 3 users not shown)
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*'''[[Analysis|Some Built in Tools for Analysis]]'''
 
*'''[[Analysis|Some Built in Tools for Analysis]]'''
 
*'''[[Context-Sensitive Help]]'''
 
*'''[[Context-Sensitive Help]]'''
 +
 +
*[[STEM Model Generator|Using the '''''New!!''''' STEM Model Generation tool]]
 
|}
 
|}
 
<!--outer table-->|- style="width:45%"
 
<!--outer table-->|- style="width:45%"
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====Modeling New Diseases====
 
====Modeling New Diseases====
#New!! [[STEM Model Generator]] tool
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#'''''New!!''''' [[STEM Model Generator]] tool
 
#*[[STEM_Model_Generator/Install|Model Generator Installation]]
 
#*[[STEM_Model_Generator/Install|Model Generator Installation]]
#[[Creating a new Disease Model Plug-in|manual Model Plug-in generation]]  
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#[[Creating a new Disease Model Plug-in|Manual Model Plug-in generation]]  
#[[Creating a new disease label|manual Disease Label creation]]
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#[[Creating a new disease label|Manual Disease Label creation]]
  
 
==== Epidemiological Modeling ====
 
==== Epidemiological Modeling ====
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*[[STEM Disease Models|Disease Models (basic to advanced)]]
 
*[[STEM Disease Models|Disease Models (basic to advanced)]]
 
*[[STEM Population Models|Population Models]]
 
*[[STEM Population Models|Population Models]]
#[[STEM_Population_Models#Standard_Population_Model|standard populations]]
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#[[STEM_Population_Models#Standard_Population_Model|Standard Populations]]
#[[STEM_Population_Models#Advanced_Models|insect vectors]]
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#[[STEM_Population_Models#Advanced_Models|Insect Vectors]]
#[[STEM_Population_Models#Multipopulation_Models|demographic models (and aging)]]
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#[[STEM_Population_Models#Multipopulation_Models|Demographic Models (and Aging)]]
*[[STEM Food and Food Borne Disease|'''(new!) Food Borne Disease Models''']]
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*'''''New!!''''' [[STEM Food and Food Borne Disease|Food Borne Disease Models''']]
#[[Sample_Projects_available_for_Download#1._Beef_Production|Beef production example]]
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#[[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]]
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#[[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]]
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#[[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]]
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|-
 
|-
 
|  
 
|  
''please also see our [http://www.eclipse.org/stem website]'' and [[Whats New in STEM|What's New in STEM]]  
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''Please also see our [http://www.eclipse.org/stem website]'' and [[Whats New in STEM|What's New in STEM]]  
 
<br/>
 
<br/>
 
<br/>
 
<br/>
  
====V1.4.0 ====
+
====V2.0.0 M1 ====
"Current Release"
+
Planning
*Performance improvements
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*Simplified creation of new Disease and Population models (Tools for generating new disease plugins)
+
*Pajek-file Importer:
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**Enable import of discrete transportation events
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**Enable integration between user graphs and existing STEM graphs
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*New improved MapView
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**Enable visualization of discrete transportation events
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**Enable multiple views of the same simulation 
+
*Stochastic Modeling Framework
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*Deep copy drag and drop for models
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*Refactor
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*Create new mixing edges (edges back in, generator created)
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*Improved UI for decorators view
+
*Time adaptive external data source models
+
*New preferences
+
 
+
====...future====
+
* Running Distributed STEM
+
 
* Integrated UI for creating new models of disease including domain specific language for epi modeling
 
* Integrated UI for creating new models of disease including domain specific language for epi modeling
* parameter sensitivity analysis
+
* Parameter sensitivity analysis
 
* mcmc optimizer
 
* mcmc optimizer
* Polio
 
* Graphical Model Design (GUI for code generation)
 
 
* Advanced Dengue Example  
 
* Advanced Dengue Example  
 +
* New Food Distribution Analysis view (incubation)
 +
* New Apache library
 +
 +
====...future====
 +
* Running Distributed STEM
  
 
|}
 
|}
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[[Category:Eclipse Technology Project]]
 
[[Category:Eclipse Technology Project]]
 +
 +
Click on the header for this section to view the Disclaimer.

Revision as of 13:07, 31 January 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. Full length video In English
  2. Full length video In Hebrew
  3. Full length video In Japanese
  4. Full length video In Spanish
  5. 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

Advanced Guides

Developers

Working with Graphs

  1. Composing a Graph
  2. Creating a Custom Graph
  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. New!! STEM Model Generator tool
  2. Manual Model Plug-in generation
  3. Manual Disease Label creation

Epidemiological Modeling

  1. Standard Populations
  2. Insect Vectors
  3. 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 M1

Planning

  • Integrated UI for creating new models of disease including domain specific language for epi modeling
  • Parameter sensitivity analysis
  • mcmc optimizer
  •  Advanced Dengue Example
  • New Food Distribution Analysis view (incubation)
  • New Apache library

...future

  • Running Distributed STEM

Disclaimer


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