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.
Difference between revisions of "STEM"
(→Tutorials) |
|||
| (145 intermediate revisions by 2 users not shown) | |||
| Line 5: | Line 5: | ||
|} | |} | ||
| − | + | == '''STEM Community Phone Call''' == | |
| + | |||
| + | The STEM community runs a [[Join the STEM Community|monthly phone call]] anyone is free to join. | ||
| + | If you wish to join, please subscribe to the [http://dev.eclipse.org/mailman/listinfo/stem-dev mailing list] | ||
| + | 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 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: 45%; background: #cceeff;" | | |
=== Introductory Resources === | === Introductory Resources === | ||
| + | ! colspan="2" style="width: 45%; background: #cceeff;" | | ||
| + | === Tutorials === | ||
|- | |- | ||
| | | | ||
| + | <!-- upper left (INTRODUCTORY RESOURCES GO HERE) --> | ||
| + | *[[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> | ||
| − | + | #[https://www.youtube.com/watch?v=iw-M0SkIK50 STEM Model Generator] <br /> ''narration by'' [https://www.sarahkaufmannyc.com ''Sarah Kaufman''] | |
| − | # | + | #A Presentation on STEM |
| − | # | + | ## [https://www.youtube.com/watch?v=2bm-1ktbsmU In English] |
| − | # | + | <!-- |
| − | # | + | ## [http://www.youtube.com/watch?v=AFYXvazKkms In Hebrew] |
| − | #[ | + | ## [http://www.youtube.com/watch?v=NM5X8-MaiKo In Japanese] |
| + | ## [http://www.youtube.com/watch?v=3S5DbjCHsx4 In Spanish] | ||
| + | --> | ||
| + | #[https://www.youtube.com/watch?v=2aMQyutaCaA 5 min Video (English)] | ||
| + | #Avian Influenza | ||
| + | ##Only [https://youtu.be/tI0Ogy-8O10 Poultry-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] | *[http://www.eclipse.org/stem/talksOnline.php Scientific Talks Online] | ||
*[[STEM FAQ|STEM FAQ]] | *[[STEM FAQ|STEM FAQ]] | ||
*[[Publications and Presentations on STEM]] | *[[Publications and Presentations on STEM]] | ||
| + | *[[Citing STEM]] | ||
*[[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| | + | *[[Join the STEM Community|Monthly phone call]] |
| − | + | ||
| − | + | ||
| − | + | ||
| − | + | ||
| − | + | ||
| − | + | ||
| − | + | ||
| − | + | ||
| − | + | ||
| − | + | ||
| − | + | ||
| − | + | ||
| − | + | ||
| − | + | ||
| − | + | ||
| − | + | ||
| − | + | ||
| − | + | ||
| − | + | ||
| − | + | ||
| | | | ||
| + | <!-- upper right (TUTORIALS) --> | ||
*'''[[Creating a STEM Scenario]]''' '''step by step''' | *'''[[Creating a STEM Scenario]]''' '''step by step''' | ||
| − | *'''[[How_scenarios_are_structured| | + | *'''[[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_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]] | #[[How_scenarios_are_structured#Template_for_a_Food_Borne_Disease_Scenario|Model of Food Borne disease]] | ||
| Line 74: | Line 73: | ||
*'''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]] | ||
| + | #[[Visualizing STEM Simulations with Google Earth]] | ||
*'''''(new)'' Automated Model Creation''' | *'''''(new)'' Automated Model Creation''' | ||
| − | #[[STEM Model Creator]] for users | + | #[[STEM Model Creator]] for users |
| + | |- | ||
| + | ! style="background: #cceeff;" | | ||
| + | === '''Advanced Guides''' === | ||
| + | ! colspan="2" style="background: #cceeff;" | | ||
| − | + | === Epidemiological Modeling === | |
| − | + | ||
| − | + | ||
| − | + | ||
| − | + | ||
| − | + | ||
| − | + | ||
| − | + | ||
|- | |- | ||
| − | | | + | | |
| − | + | <!-- middle left (ADVANCED GUIDES GOES HERE) --> | |
*[[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]] | ||
| − | + | *Working with Graphs | |
| − | + | ||
#[[Composing a Graph]] | #[[Composing a Graph]] | ||
#[[Creating a new Graph|Creating a Custom Graph]] (''new'') ''seasonal migration'' | #[[Creating a new Graph|Creating a Custom Graph]] (''new'') ''seasonal migration'' | ||
| Line 112: | Line 110: | ||
#[[Importing a Pajek Graph|Importing a Graph from a Pajek File]] | #[[Importing a Pajek Graph|Importing a Graph from a Pajek File]] | ||
#[[Importing an Esri Shapefile|Importing a Graph from an Esri Shapefile]] | #[[Importing an Esri Shapefile|Importing a Graph from an Esri Shapefile]] | ||
| − | + | *[[STEM_Solvers|Available STEM Solvers]] | |
| − | + | **STEM Native Solvers | |
| − | + | **Apache Common Math Solvers | |
| − | + | **Stochastic Solver | |
| − | + | | | |
| − | + | <!-- middle right (EPIDEMIOLOGICAL MODELING GOES HERE)--> | |
| − | + | ||
| − | + | ||
| − | + | ||
| − | * | + | |
| − | ** | + | |
| − | | | + | |
| − | <!-- | + | |
| − | + | ||
| − | + | ||
| − | + | ||
| − | + | ||
| − | + | ||
| − | + | ||
*[[Sample Projects available for Download|Sample Projects (Downloadable Scenarios)]] | *[[Sample Projects available for Download|Sample Projects (Downloadable Scenarios)]] | ||
| + | * ''(new!!)'' [[Epidemiological Parameters]] | ||
*[[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]] | ||
#[[STEM_Population_Models#Advanced_Models|Insect Vectors]] | #[[STEM_Population_Models#Advanced_Models|Insect Vectors]] | ||
| − | #[[STEM_Population_Models#Seasonal_Migratory_Population_Model|Migratory Birds | + | #[[STEM_Population_Models#Seasonal_Migratory_Population_Model|Migratory Birds]] |
#[[STEM_Population_Models#Multipopulation_Models|Demographic Models (and Aging)]] | #[[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#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]] | #[[Sample_Projects_available_for_Download#2._A_scenario_for_modelling_the_transmission_of_Salmonella_to_pigs.2C_pork_and_humans|Salmonella in Pork Example]] | ||
| Line 145: | Line 132: | ||
*[[Transportation Models|Transportation Models]] | *[[Transportation Models|Transportation Models]] | ||
*[[Air Travel Model|Air Travel Model]] | *[[Air Travel Model|Air Travel Model]] | ||
| + | *'''Modeling New Diseases''' | ||
| + | #[[STEM Model Creator|Using the '''''New!!''''' STEM Model Creator tool]] | ||
| + | #[[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]] | ||
| − | | | + | |- |
| − | + | ! style="background: #ffdead;" | | |
| − | | | + | |
| − | + | ||
| − | + | ||
=== Release Planning === | === Release Planning === | ||
| + | ! colspan="2" style="background: #ffdead;" | | ||
| + | === Important Links === | ||
|- | |- | ||
| | | | ||
| + | <!-- 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]] | ||
| + | * 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. | ||
| + | | | ||
| + | <!-- bottom right (DISCLAIMER GOES HERE) --> | ||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
<br> | <br> | ||
| + | * 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" | | ||
| + | |} | ||
[[Category:Eclipse Technology Project]] | [[Category:Eclipse Technology Project]] | ||
| − | |||
| − | |||
Latest revision as of 21:55, 18 November 2020
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.