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"

(STEM Community Phone Call)
m
(41 intermediate revisions by 2 users not shown)
Line 7: Line 7:
 
== '''STEM Community Phone Call''' ==
 
== '''STEM Community Phone Call''' ==
  
  The STEM community runs a [[Join the STEM Community|monthly phone call]] anyone is free to join.
+
  The STEM community runs a [[Join the STEM Community|monthly phone call]] anyone is free to join.  
  The special series of [[Community Ebola Modeling Phone Call]]s has been merged back with our regular [[Join the STEM Community|monthly phone call]].
+
  If you wish to join, please subscribe to the [http://dev.eclipse.org/mailman/listinfo/stem-dev mailing list]
  You can still see all the Ebola content [[Join the STEM Community#Ebola Community Efforts|here]]
+
  where you can see the announcements and agenda for scheduled calls.
  
 
== '''STEM Documentation''' ==
 
== '''STEM Documentation''' ==
  
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 who 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.
  
 
{| style="width: 90%" border="1" cellpadding="5" cellspacing="0" align="center"
 
{| style="width: 90%" border="1" cellpadding="5" cellspacing="0" align="center"
Line 26: Line 26:
 
<!-- upper left (INTRODUCTORY RESOURCES GO HERE) -->
 
<!-- upper left (INTRODUCTORY RESOURCES GO HERE) -->
 
*[[Installation Guide]]
 
*[[Installation Guide]]
 +
*[[STEM_Add-ons|STEM Denominator Data]]
 
*[http://www.eclipse.org/stem/ The STEM Website]  
 
*[http://www.eclipse.org/stem/ The STEM Website]  
 
*[[About STEM]]  
 
*[[About STEM]]  
 
*[[Whats New in STEM|What's New in STEM]]  
 
*[[Whats New in STEM|What's New in STEM]]  
 +
*[[Importing and Exporting Projects|Importing and Exporting Projects]]
 
*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''
+
#[http://www.youtube.com/watch?v=MtQlS7g7Qnw STEM Model Generator] <br /> ''narration by'' [https://www.sarahkaufmannyc.com ''Sarah Kaufman'']
#Full length video [http://www.youtube.com/watch?v=LfiibQX4IFE In English]  
+
#A Presentation on STEM
#Full length video [http://www.youtube.com/watch?v=AFYXvazKkms In Hebrew]  
+
## [http://www.youtube.com/watch?v=LfiibQX4IFE In English]  
#Full length video [http://www.youtube.com/watch?v=NM5X8-MaiKo In Japanese]  
+
## [http://www.youtube.com/watch?v=AFYXvazKkms In Hebrew]  
#Full length video [http://www.youtube.com/watch?v=3S5DbjCHsx4 In Spanish]  
+
## [http://www.youtube.com/watch?v=NM5X8-MaiKo In Japanese]  
 +
## [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)]
 
#Avian Influenza
 
#Avian Influenza
 
##Only [https://youtu.be/tI0Ogy-8O10 Poultry-Human Transmission]  
 
##Only [https://youtu.be/tI0Ogy-8O10 Poultry-Human Transmission]  
 
##Including  [https://youtu.be/0YJ6FxdhFm8 Human-Human Transmission]  
 
##Including  [https://youtu.be/0YJ6FxdhFm8 Human-Human Transmission]  
 +
*Download a step by step guide: [[Media:STEM_HowToGuide.pdf|Ebola Example]]
  
 
*[http://www.eclipse.org/stem/talksOnline.php Scientific Talks Online] &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 
*[http://www.eclipse.org/stem/talksOnline.php Scientific Talks Online] &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
Line 46: Line 50:
 
*[[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]]  
*[[Join the STEM Community|Weekly phone call]]
+
*[[Join the STEM Community|Monthly phone call]]
 
|  
 
|  
 
<!-- upper right (TUTORIALS) -->
 
<!-- upper right (TUTORIALS) -->
Line 67: Line 71:
  
 
*'''Running Simulations'''
 
*'''Running Simulations'''
#[[STEM_Map_View|The STEM Map View]]  
+
# [[STEM_Map_View|The STEM UI and Map View]] ''(updated)''
 
#[[Batch Mode (Running Experiments)|Running Experiments in Batch Mode]]  
 
#[[Batch Mode (Running Experiments)|Running Experiments in Batch Mode]]  
 
#[[Running an Automated Experiment]]  
 
#[[Running an Automated Experiment]]  
#[[STEM Headless|Running STEM Headless]]
+
#[[STEM Headless|Running STEM Headless]] ''(STEM on Server)''
 
#[[Importing Data from Files]]  
 
#[[Importing Data from Files]]  
 
#[[STEM Loggers|Simulation Data Logging]]
 
#[[STEM Loggers|Simulation Data Logging]]
Line 76: Line 80:
  
 
*'''''(new)'' Automated Model Creation'''
 
*'''''(new)'' Automated Model Creation'''
#[[STEM Model Creator]] for users (''beta'')
+
#[[STEM Model Creator]] for users  
 
|-
 
|-
 
! style="background: #cceeff;" |  
 
! style="background: #cceeff;" |  
=== Advanced Guides ===
+
=== '''Advanced Guides''' ===
! colspan="2" style="background: #cceeff;" |  
+
! colspan="2" style="background: #cceeff;" |
 +
 
 
=== Epidemiological Modeling ===
 
=== Epidemiological Modeling ===
 
|-
 
|-
Line 87: Line 92:
 
*[[Welcome STEM Developers]]
 
*[[Welcome STEM Developers]]
 
*[[STEM Eclipse Setup|Setting up a STEM Development Environment]]
 
*[[STEM Eclipse Setup|Setting up a STEM Development Environment]]
*[[STEM Design Document]]
+
*[[STEM Design Document]] ''(updated 4/29/2016)''
 
*[[STEM National Language Support | National Language Support]]
 
*[[STEM National Language Support | National Language Support]]
 
*[http://www.eclipse.org/projects/project.php?id=technology.stem Project Stats]
 
*[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]]
 +
*[[Configuring the STEM Build on Eclipse CI|STEM CI Build]] ''(Eclipse committers only)''
 +
*[[STEM Create EMF Project|Example: Create a STEM JSON Logger (a new EMF Project)]]
 
*[[Running STEM from the Development Environment]]
 
*[[Running STEM from the Development Environment]]
 +
*[[STEM Headless|Running STEM Headless]] ''(STEM on Server)''
 
*[[Creating a Customized Color Provider|Customizing Colors]]
 
*[[Creating a Customized Color Provider|Customizing Colors]]
 
*[[STEM Performance Tips |General tips when writing performance critical code]]
 
*[[STEM Performance Tips |General tips when writing performance critical code]]
Line 111: Line 118:
 
*[[Introduction to Compartment Models|Intro to Compartment Models]]  
 
*[[Introduction to Compartment Models|Intro to Compartment Models]]  
 
*[[STEM Disease Models|Disease Models (basic to advanced)]]
 
*[[STEM Disease Models|Disease Models (basic to advanced)]]
 +
** ''(new)'' [[2019 novel Corona Virus Model|''three'' Sars-CoV-2 models]]
 
*[[STEM Population Models|Population Models]]
 
*[[STEM Population Models|Population Models]]
 
#[[STEM_Population_Models#Standard_Population_Model|Standard Populations]]
 
#[[STEM_Population_Models#Standard_Population_Model|Standard Populations]]
Line 123: Line 131:
 
*[[Air Travel Model|Air Travel Model]]
 
*[[Air Travel Model|Air Travel Model]]
 
*'''Modeling New Diseases'''  
 
*'''Modeling New Diseases'''  
#[[STEM Model Creator|Using the '''''New!!''''' STEM Model Creator tool]] (''beta'')
+
#[[STEM Model Creator|Using the '''''New!!''''' STEM Model Creator tool]]  
 
#[[STEM Model Generator]] tool (for Developers)
 
#[[STEM Model Generator]] tool (for Developers)
 
#[[STEM_Model_Generator/Install|Model Generator Installation]]
 
#[[STEM_Model_Generator/Install|Model Generator Installation]]
Line 133: Line 141:
 
=== Release Planning ===
 
=== Release Planning ===
 
! colspan="2" style="background: #ffdead;" |  
 
! colspan="2" style="background: #ffdead;" |  
=== Disclaimer ===
+
=== Important Links ===
 
|-
 
|-
 
|  
 
|  
 
<!-- bottom left (RELEASE PLANNING GOES HERE) -->
 
<!-- bottom left (RELEASE PLANNING GOES HERE) -->
 
''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]]  
* Next Release To Come September 2015
+
* V4.0.0 Release is now Available
* V2.0.3 Now Available (Feb. 2015)
+
* Based on and compatible with Eclipse e4
** Bug Fixes
+
* STEM V4.0.0M1 supports (J2SE) 8.0 JVM. ''In fact - it's required''
** Updated Admin 0 borders added
+
 
** New models
+
** Updated Google Earth(tm) Interface
+
  
 
* Release Engineering
 
* Release Engineering
Line 153: Line 159:
  
 
<br>
 
<br>
Click on the header for this section to view the [[Disclaimer]].
+
* Our [[Disclaimer]].
 +
* [http://www.eclipse.org Main Eclipse Foundation website]
 +
* [http://www.eclipse.org/legal/privacy.php Privacy policy]
 +
* [http://www.eclipse.org/legal/termsofuse.php Website terms of use]
 +
* [http://www.eclipse.org/legal/copyright.php Copyright agent]
 +
* [http://www.eclipse.org/legal Legal]
 
|-
 
|-
 
| colspan="3" align="center" |
 
| colspan="3" align="center" |

Revision as of 15:34, 15 May 2020

STEM TOP BAR.gif

STEM Community Phone Call

The STEM community runs a monthly phone call anyone is free to join. 
If you wish to join, please subscribe to the mailing list
where you can see the announcements and agenda for scheduled calls.

STEM Documentation

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 who 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.

Introductory Resources

Tutorials

  1. STEM Model Generator
    narration by Sarah Kaufman
  2. A Presentation on STEM
    1. In English
    2. In Hebrew
    3. In Japanese
    4. In Spanish
  3. 5 min Video (English)
  4. Avian Influenza
    1. Only Poultry-Human Transmission
    2. Including Human-Human Transmission
  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 UI and Map View (updated)
  2. Running Experiments in Batch Mode
  3. Running an Automated Experiment
  4. Running STEM Headless (STEM on Server)
  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

Advanced Guides

Epidemiological Modeling

  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
  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
  1. Using the New!! STEM Model Creator tool
  2. STEM Model Generator tool (for Developers)
  3. Model Generator Installation
  4. Manual Model Plug-in generation
  5. Manual Disease Label creation

Release Planning

Important Links

Please also see our website and What's New in STEM

  • V4.0.0 Release is now Available
  • Based on and compatible with Eclipse e4
  • STEM V4.0.0M1 supports (J2SE) 8.0 JVM. In fact - it's required


  • 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.



Back to the top