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Difference between revisions of "STEM"
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| − | + | {| align="right" | |
| + | | __TOC__ | ||
| + | |} | ||
| + | == '''Ebola Community Efforts''' == | ||
| + | ==== [[Weekly Community Ebola Modeling Phone Call]] ==== | ||
| + | ==== [[Ebola Models]] ==== | ||
| + | ==== [https://wiki.eclipse.org/Ebola_How_To How to install the Ebola models]==== | ||
| + | ==== Literature [[Ebola References]]==== | ||
| + | ==== Data [[Ebola Reference Data]]==== | ||
| + | ==== Please sign up for the [https://dev.eclipse.org/mailman/listinfo/stem-ebola stem-ebola mailing list]==== | ||
| − | + | 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''' == |
| − | * | + | <!--outer table-->{| style="width:98% ; border="0" ; cellpadding="0" |
| − | #[http://www.youtube.com/watch?v=LfiibQX4IFE In English] | + | <!--outer table-->|- |
| − | #[http://www.youtube.com/watch?v=AFYXvazKkms In Hebrew] | + | <!--outer table-->| |
| − | #[http://www.youtube.com/watch?v=NM5X8-MaiKo In Japanese] | + | {| style="width: 100%; height: 100%; background: #f1f5fc" ; border="0" ; cellpadding="5" |
| − | #[http://www.youtube.com/watch?v=3S5DbjCHsx4 In Spanish] | + | |- style="background: #cceeff" |
| + | ! | ||
| + | === 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> | ||
| + | #[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=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] | |
| − | *[http://www.eclipse.org/stem/talksOnline.php Scientific Talks Online] | + | *[[STEM FAQ|STEM FAQ]] |
| − | *[ | + | *[[Publications and Presentations on STEM]] |
| − | *[[ | + | *[[Citing STEM]] |
| − | *[[ | + | *[[Join the STEM Community|How to Join the STEM Community]] |
| − | *[[STEM | + | *[[The STEM Development Team]] |
| − | *[[Join the STEM Community]] | + | *[[Join the STEM Community|Weekly phone call]] |
| + | |||
| + | ==== Getting Started ==== | ||
| − | |||
| − | |||
| − | |||
*[[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)]] |
| − | *[[ | + | *[[Importing and Exporting Projects]] |
| − | *[[ | + | *[[Analysis|Some Built in Tools for Analysis]] |
| − | *[[STEM | + | *[[Context-Sensitive Help]] |
| + | *[[STEM Model Creator|Using the '''''New!!''''' STEM Model Creator tool]] (''beta'') | ||
| − | |||
| − | + | |} | |
| − | + | <!--inner table start-->| | |
| − | + | {| style="width: 100%; height: 100%; background: #f1f5fc" ; border="0" ; cellpadding="5" | |
| − | + | |-style="background: #cceeff" | |
| − | + | ! | |
| − | + | ||
=== Tutorials === | === Tutorials === | ||
| + | |- | ||
| + | | | ||
| + | *'''[[Creating a STEM Scenario]]''' '''step by step''' | ||
| + | *'''[[How_scenarios_are_structured| 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)'']]''' | ||
| + | *'''[[STEM Import Discrete Transportation Events|Import Discrete Transportation Events]]''' | ||
| + | *'''[[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]] | + | #[[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]] | |
| − | + | #[[Visualizing STEM Simulations with Google Earth]] | |
| − | *[[ | + | |
| − | + | *'''''(new)'' Automated Model Creation''' | |
| − | + | #[[STEM Model Creator]] for users (''beta'') | |
| + | |||
| + | |} | ||
| + | <!--outer table-->|- style="width:45%" | ||
| + | <!--outer table-->| | ||
| + | {| style="width: 100%; background: #f1f5fc" ; border="0" ; cellpadding="5" | ||
| + | |-style="background: #cceeff" | ||
| + | ! | ||
=== Advanced Guides === | === Advanced Guides === | ||
| + | |- | ||
| + | | | ||
| + | ====Developers==== | ||
| + | *[[Welcome STEM Developers]] | ||
| + | *[[STEM Eclipse Setup|Setting up a STEM Development Environment]] | ||
| + | *[[STEM Design Document]] | ||
| + | *[[STEM National Language Support | National Language Support]] | ||
| + | *[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]] | ||
*[[Running STEM from the Development Environment]] | *[[Running STEM from the Development Environment]] | ||
| − | + | *[[Creating a Customized Color Provider|Customizing Colors]] | |
| − | *[[Creating a | + | *[[STEM Performance Tips |General tips when writing performance critical code]] |
| − | *[[ | + | |
| − | + | ||
| − | + | ||
| − | + | ||
| − | + | ||
| − | == [[ | + | ====Working with Graphs==== |
| − | + | #[[Composing a Graph]] | |
| + | #[[Creating a new Graph|Creating a Custom Graph]] (''new'') ''seasonal migration'' | ||
| + | #[[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==== |
| + | #[[STEM Model Creator|Using the '''''New!!''''' STEM Model Creator tool]] (''beta'') | ||
| + | #[[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]] | ||
| − | + | ==== STEM Solvers ==== | |
| − | + | *Available [[STEM_Solvers|Solvers]] | |
| − | + | **STEM Native Solvers | |
| − | + | **Apache Common Math Solvers | |
| + | **Stochastic Solver | ||
| + | === 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]] | ||
| + | #[[STEM_Population_Models#Multipopulation_Models|Demographic Models (and Aging)]] | ||
| + | *[[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]] | ||
| + | *[[Air Travel Model|Air Travel Model]] | ||
| − | + | |} | |
| + | {| style="width: 100%; height: 100%; background: #f1f5fc" ; border="0" ; cellpadding="5" | ||
| + | |-style="background: #cceeff" | ||
| + | ! | ||
| − | == | + | === Release Planning === |
| − | + | |- | |
| + | | | ||
| + | ''Please also see our [http://www.eclipse.org/stem website]'' and [[Whats New in STEM|What's New in STEM]] | ||
| − | == | + | ====Next Release To Come January 30, 2015==== |
| − | + | ====V2.0.2 Now Available==== | |
| − | + | * Bug Fixes | |
| − | + | * Updated Dengue Model and Scenario | |
| + | * New Campylobacter Scenario | ||
| − | * | + | ====V2.0.1 Included==== |
| − | * | + | * Bug Fixes |
| − | * | + | * Updated Code Generator |
| − | + | * New Campylobacter Model and Documentation | |
| − | + | * New Dengue Model and Scenario | |
| − | + | ||
| − | + | ||
| − | * New | + | |
| − | + | ||
| + | ====V2.0.0 Included==== | ||
| + | * 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 | ||
| + | ====...Future Features==== | ||
| + | * 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. | |
| − | + | |} | |
| − | + | ||
| − | + | ||
| − | + | ||
| − | + | ||
| − | + | <!--outer table-->|} | |
| − | + | ||
| + | ==[[Disclaimer]]== | ||
| − | + | <br> | |
| − | + | ||
| − | + | [[Category:Eclipse Technology Project]] | |
| + | |||
| + | Click on the header for this section to view the Disclaimer. | ||
Revision as of 11:26, 29 January 2015
Ebola Community Efforts
Weekly Community Ebola Modeling Phone Call
Ebola Models
How to install the Ebola models
Literature Ebola References
Data Ebola Reference Data
Please sign up for the stem-ebola mailing list
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
|
| ||||
|
Disclaimer
Click on the header for this section to view the Disclaimer.