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Difference between revisions of "STEM"

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== [[Disclaimer]] ==
 
 
<br/><br/>
 
 
== Release Planning ==
 
 
[[Category:Eclipse Technology Project]]
 
 
''please also see our [http://www.eclipse.org/stem website]''
 
  
 
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*[[Air Travel Model|Air Travel Model]]
 
*[[Air Travel Model|Air Travel Model]]
 
*[[STEM_Solvers|Solvers]]
 
*[[STEM_Solvers|Solvers]]
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|
 +
 +
== Release Planning ==
 +
 +
[[Category:Eclipse Technology Project]]
 +
 +
''please also see our [http://www.eclipse.org/stem website]''
 +
 +
 +
 +
==='''V1.3.1'''===
 +
Tentative Date 4/15/2012
 +
 +
Plan Features:
 +
* Bug Fixes to 1.3.0
 +
* STEM EMF update to version 2.7.2
 +
* Generalized model replay mechanism
 +
* Shape File Importer: Improvements to GUI
 +
* Population Transformer: “realistic” sample model on food mediated disease transmission
 +
* Graph Editor: improved zooming, deleting nodes and edges, improved GUI for new population generation
 +
* Replace population rewinding with an explicit population re-scaler
 +
 +
'''...future'''
 +
* 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
 +
** Enable integration between user graphs and existing STEM graphs
 +
* Scenario ''"compile"'' proof of concept
 +
* STEM -integration inside KNIME: creating a Node within the KNIME, Node-repository that allows STEM headless execution
 +
* Ability to Delete Items inside a Graph from Designer Perspective
 +
* Tools for generating new disease plugins
 +
 +
 +
 +
'''Current Release'''
 +
 +
==='''V1.3.0'''===
 +
''Completed'' Date 2/7/2012
 +
Features
 +
 +
* Bug Fixes from 1.2.2
 +
* Ten years of Earth Science Data (2000-2010) available as STEM '''Features'''
 +
* Malaria Disease Model (''Anopheles'' calibrated)
 +
* Dengue Fever Disease Model (''Aedes'' not yet calibrated)
 +
* New Differential Equation solver(s) from commons.math library
 +
* Additional NLS + User ability to switch languages
 +
* Logger Framework with new loggers
 +
* New feature: “Population Transformer” - enabling transformation of population members to allow modeling of e.g. food mediated disease transmission
 +
* Improvements to the graphical editor
 +
 +
== [[Disclaimer]] ==
 +
 +
<br/><br/>
 +
 +
== Release Planning ==
 +
 +
[[Category:Eclipse Technology Project]]
 +
 +
''please also see our [http://www.eclipse.org/stem website]''
  
 
|}
 
|}

Revision as of 14:22, 19 March 2012

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. 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

  • 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. Creating a New Disease Model Plug-in Using EMF
  2. Creating a New Disease Label

Epidemiological Modeling

Release Planning

please also see our website


V1.3.1

Tentative Date 4/15/2012

Plan Features:

  • Bug Fixes to 1.3.0
  • STEM EMF update to version 2.7.2
  • Generalized model replay mechanism
  • Shape File Importer: Improvements to GUI
  • Population Transformer: “realistic” sample model on food mediated disease transmission
  • Graph Editor: improved zooming, deleting nodes and edges, improved GUI for new population generation
  • Replace population rewinding with an explicit population re-scaler

...future

  • 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
    • Enable integration between user graphs and existing STEM graphs
  • Scenario "compile" proof of concept
  • STEM -integration inside KNIME: creating a Node within the KNIME, Node-repository that allows STEM headless execution
  • Ability to Delete Items inside a Graph from Designer Perspective
  • Tools for generating new disease plugins


Current Release

V1.3.0

Completed Date 2/7/2012 Features

  • Bug Fixes from 1.2.2
  • Ten years of Earth Science Data (2000-2010) available as STEM Features
  • Malaria Disease Model (Anopheles calibrated)
  • Dengue Fever Disease Model (Aedes not yet calibrated)
  • New Differential Equation solver(s) from commons.math library
  • Additional NLS + User ability to switch languages
  • Logger Framework with new loggers
  • New feature: “Population Transformer” - enabling transformation of population members to allow modeling of e.g. food mediated disease transmission
  • Improvements to the graphical editor

Disclaimer



Release Planning

please also see our website

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)

STEM Documentation

Getting Started

Tutorials

  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

  • 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. Creating a New Disease Model Plug-in Using EMF
  2. Creating a New Disease Label

Epidemiological Modeling


Disclaimer



Release Planning

please also see our website


V1.3.1

Tentative Date 4/15/2012

Plan Features:

  • Bug Fixes to 1.3.0
  • STEM EMF update to version 2.7.2
  • Generalized model replay mechanism
  • Shape File Importer: Improvements to GUI
  • Population Transformer: “realistic” sample model on food mediated disease transmission
  • Graph Editor: improved zooming, deleting nodes and edges, improved GUI for new population generation
  • Replace population rewinding with an explicit population re-scaler

...future

  • 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
    • Enable integration between user graphs and existing STEM graphs
  • Scenario "compile" proof of concept
  • STEM -integration inside KNIME: creating a Node within the KNIME, Node-repository that allows STEM headless execution
  • Ability to Delete Items inside a Graph from Designer Perspective
  • Tools for generating new disease plugins


Current Release

V1.3.0

Completed Date 2/7/2012 Features

  • Bug Fixes from 1.2.2
  • Ten years of Earth Science Data (2000-2010) available as STEM Features
  • Malaria Disease Model (Anopheles calibrated)
  • Dengue Fever Disease Model (Aedes not yet calibrated)
  • New Differential Equation solver(s) from commons.math library
  • Additional NLS + User ability to switch languages
  • Logger Framework with new loggers
  • New feature: “Population Transformer” - enabling transformation of population members to allow modeling of e.g. food mediated disease transmission
  • Improvements to the graphical editor


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