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Difference between revisions of "STEM"
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| − | |+ | + | |+ == STEM Documentation == |
| | | | ||
| − | + | == 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> | ||
| + | |||
| + | #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=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.eclipse.org/stem/talksOnline.php Scientific Talks Online] | ||
| + | *[[STEM FAQ|STEM FAQ]] | ||
| + | *[[Publications and Presentations on STEM]] | ||
| + | *[[Join the STEM Community|How to Join the STEM Community]] | ||
| + | *[[The STEM Development Team]] | ||
| + | *[[Join the STEM Community|Weekly phone call]] | ||
| + | |||
| + | === Getting Started === | ||
| + | |||
| + | *[[STEM Installation Guide|Installing the STEM Application]] | ||
| + | *[[STEM Addons|Installing Additional Features]] | ||
| + | *[[Sample Projects available for Download|Sample Projects (Downloadable Scenarios)]] | ||
| + | *[[Welcome STEM Developers|Information for STEM Software Developers]] | ||
| + | *[[STEM Eclipse Setup|Setting up a STEM Development Environment]] | ||
| + | *[[STEM Design Document]] | ||
| + | *[[STEM National Language Support | National Language Support]] | ||
| + | |||
|| | || | ||
| − | + | === Tutorials === | |
| + | |||
| + | *[[Creating a STEM Scenario]] | ||
| + | *[[How_scenarios_are_structured|How Scenarios are Structured]] | ||
| + | *[[Initializing Disease Compartments|Initializing Diseases ''(Infectors, Inoculators, and Initializers)'']] | ||
| + | *[[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]] | ||
| + | |||
| + | * '''Using Population Models''' | ||
| + | # [[Initializing a Population]] | ||
| + | #[[Using Structured Populations in STEM|Using Structured Populations in STEM]] | ||
| + | #[[Using Aging Populations in STEM|Using Aging Populations in STEM]] | ||
| + | |||
| + | *'''Running Simulations''' | ||
| + | #[[STEM_Map_View|The STEM Map View]] | ||
| + | #[[Batch Mode (Running Experiments)|Running Experiments in Batch Mode]] | ||
| + | #[[Running an Automated Experiment]] | ||
| + | #[[STEM Headless|Running STEM Headless]] | ||
| + | #[[Importing Data from Files]] | ||
| + | #[[STEM Loggers|Simulation Data Logging]] | ||
| + | |||
| + | *[[Importing and Exporting Projects]] | ||
| + | *[[Analysis|Some Built in Tools for Analysis]] | ||
| + | *[[Context-Sensitive Help]] | ||
| + | |||
| + | === Advanced Guides === | ||
| + | |||
| + | *[[Building the STEM RCP Application|Building the STEM RCP Application]] | ||
| + | *[[Running STEM from the Development Environment]] | ||
| + | *[[Creating a Customized Color Provider|Customizing Colors]] | ||
| + | |||
| + | *'''Working with Graphs''' | ||
| + | #[[Composing a Graph]] | ||
| + | #[[Creating a new Graph|Creating a Custom Graph]] | ||
| + | #[[Visualizing and Editing Graphs]] with the STEM Graph Editor | ||
| + | #[[Importing a Pajek Graph|Importing a Graph from a Pajek File]] | ||
| + | #[[Importing an Esri Shapefile|Importing a Graph from an Esri Shapefile]] | ||
| + | |||
| + | *'''Modeling new Diseases''' | ||
| + | #[[Creating a new Disease Model Plug-in|Creating a New Disease Model Plug-in Using EMF]] | ||
| + | #[[Creating a new disease label|Creating a New Disease Label]] | ||
| + | |||
| + | === Epidemiological Modeling === | ||
| + | |||
| + | *[[Introduction to Compartment Models|Compartment Models]] | ||
| + | *[[Available Models|Disease and Population Models]] | ||
| + | *[[Transportation Models|Transportation Models]] | ||
| + | *[[Air Travel Model|Air Travel Model]] | ||
| + | *[[STEM_Solvers|Solvers]] | ||
| + | |||
|- | |- | ||
Revision as of 14:16, 19 March 2012
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.
Introductory Resources
- The STEM Website
- About STEM
- What's New in STEM
- STEM Tutorials on YouTubeTM
- Full length video In English
- Full length video In Hebrew
- Full length video In Japanese
- Full length video In Spanish
- 5 min Video (English)
- Scientific Talks Online
- STEM FAQ
- Publications and Presentations on STEM
- How to Join the STEM Community
- The STEM Development Team
- Weekly phone call
STEM Documentation
Getting Started
- Installing the STEM Application
- Installing Additional Features
- Sample Projects (Downloadable Scenarios)
- Information for STEM Software Developers
- Setting up a STEM Development Environment
- STEM Design Document
- National Language Support
Tutorials
- Creating a STEM Scenario
- How Scenarios are Structured
- Initializing Diseases (Infectors, Inoculators, and Initializers)
- Triggering Interventions
- Using Population Models
- Running Simulations
- The STEM Map View
- Running Experiments in Batch Mode
- Running an Automated Experiment
- Running STEM Headless
- Importing Data from Files
- Simulation Data Logging
Advanced Guides
- Working with Graphs
- Composing a Graph
- Creating a Custom Graph
- Visualizing and Editing Graphs with the STEM Graph Editor
- Importing a Graph from a Pajek File
- Importing a Graph from an Esri Shapefile
- Modeling new Diseases
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