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(STEM Documentation)
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[[Image:STEM TOP BAR.gif|800px]]
 
[[Image:STEM TOP BAR.gif|800px]]
  
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.
+
{| align="right"
 +
  | __TOC__
 +
  |}
  
 +
== '''STEM Community Phone Call''' ==
  
== Introductory Resources ==
+
The STEM community runs a [[Join the STEM Community|monthly phone call]] anyone is free to join. The agenda is posted on stem-dev.org every month early in the week of the call for you to view.  
*[http://www.eclipse.org/stem/ The STEM Website]
+
The special series of [[Community Ebola Modeling Phone Call]]s held during the epidemic was merged back with our regular [[Join the STEM Community|monthly phone call]].
*[[About STEM]]
+
You can still see all the Ebola content [[Join the STEM Community#Ebola Community Efforts|here]]
*[[What's New in STEM]]
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*STEM Tutorials on YouTube<sup>TM</sup>
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#Full length video [http://www.youtube.com/watch?v=LfiibQX4IFE In English]
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#Full length video [http://www.youtube.com/watch?v=AFYXvazKkms In Hebrew]
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#Full length video [http://www.youtube.com/watch?v=NM5X8-MaiKo In Japanese]
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#Full length video [http://www.youtube.com/watch?v=3S5DbjCHsx4 In Spanish]
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#[http://www.youtube.com/watch?v=OoiFLemepw4 5 min Video (English)]
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*[http://www.eclipse.org/stem/talksOnline.php Scientific Talks Online]
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*[[STEM FAQ|STEM FAQ]]
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*[[Publications and Presentations on STEM]]
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*[[Join the STEM Community|How to Join the STEM Community]]
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*[[The STEM Development Team]]
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*[[Join the STEM Community|Weekly phone call]]
+
  
== STEM Documentation ==
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== '''STEM Documentation''' ==
  
=== Getting Started ===
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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.
 
+
*[[STEM Installation Guide|Installing the STEM Application]]
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*[[STEM Addons|Installing Additional Features]]
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*[[Sample Projects available for Download|Sample Projects (Downloadable Scenarios)]]
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*[[Welcome STEM Developers|Information for STEM Software Developers]]
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*[[STEM Eclipse Setup|Setting up a STEM Development Environment]]
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*[[STEM Design Document]]
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*[[STEM National Language Support | National Language Support]]
+
  
 +
{| style="width: 90%" border="1" cellpadding="5" cellspacing="0" align="center"
 +
|+ 
 +
|-
 +
! style="width: 45%; background: #cceeff;" |
 +
=== Introductory Resources  ===
 +
! colspan="2" style="width: 45%; background: #cceeff;" |
 
=== Tutorials ===
 
=== Tutorials ===
 +
|-
 +
|
 +
<!-- upper left (INTRODUCTORY RESOURCES GO HERE) -->
 +
*[[Installation Guide]]
 +
*[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)]
 +
#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]]
  
*[[Creating a STEM Scenario]]  
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*[http://www.eclipse.org/stem/talksOnline.php Scientific Talks Online] &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
*[[How_scenarios_are_structured|How Scenarios are Structured]]
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*[[STEM FAQ|STEM FAQ]]
*[[Initializing Disease Compartments|Initializing Diseases ''(Infectors, Inoculators, and Initializers)'']]
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*[[Publications and Presentations on STEM]]
*[[Triggering interventions|Triggering Interventions]]  
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*[[Citing STEM]]
 +
*[[Join the STEM Community|How to Join the STEM Community]]
 +
*[[The STEM Development Team]]
 +
*[[Join the STEM Community|Weekly phone call]]
 +
|
 +
<!-- upper right (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'''
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*'''Using Population Models'''
 
# [[Initializing a Population]]  
 
# [[Initializing a Population]]  
 
#[[Using Structured Populations in STEM|Using Structured Populations in STEM]]  
 
#[[Using Structured Populations in STEM|Using Structured Populations in STEM]]  
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#[[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]]
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#[[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]]
  
*[[Importing and Exporting Projects]]
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*'''''(new)'' Automated Model Creation'''
*[[Analysis|Some Built in Tools for Analysis]]
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#[[STEM Model Creator]] for users (''beta'')
*[[Context-Sensitive Help]]
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|-
 
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! style="background: #cceeff;" |
=== Advanced Guides ===
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=== '''Advanced Guides''' ===
 +
! colspan="2" style="background: #cceeff;" |
  
 +
=== Epidemiological Modeling ===
 +
|-
 +
|
 +
<!-- middle left (ADVANCED GUIDES GOES HERE) -->
 +
*[[Welcome STEM Developers]]
 +
*[[STEM Eclipse Setup|Setting up a STEM Development Environment]]
 +
*[[STEM Design Document]] ''(updated 4/29/2016)''
 +
*[[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]]
 +
*[[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]]
 
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*[[STEM Performance Tips |General tips when writing performance critical code]]
*'''Working with Graphs'''
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*Working with Graphs
 
#[[Composing a Graph]]
 
#[[Composing a Graph]]
#[[Creating a new Graph|Creating a Custom Graph]]
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#[[Creating a new Graph|Creating a Custom Graph]] (''new'') ''seasonal migration''
#[[Visualizing and Editing Graphs]] with the STEM Graph Editor
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#[[Visualizing and Editing Graphs]] ''with the STEM Graph Editor ''&nbsp;&nbsp;
 
#[[Importing a Pajek Graph|Importing a Graph from a Pajek File]]
 
#[[Importing a Pajek Graph|Importing a Graph from a Pajek File]]
 
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#[[Importing an Esri Shapefile|Importing a Graph from an Esri Shapefile]]
*'''Modeling new Diseases'''
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*[[STEM_Solvers|Available STEM Solvers]]
#[[Creating a New Disease Model Plug-in|Creating a New Disease Model Plug-in Using EMF]]  
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**STEM Native Solvers
#[[Creating a New Disease Label|Creating a New Disease Label]]
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**Apache Common Math Solvers
 
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**Stochastic Solver
=== Epidemiological Modeling ===
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|
 
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<!-- middle right (EPIDEMIOLOGICAL MODELING GOES HERE)-->
*[[Introduction to Compartment Models|Compartment Models]]  
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*[[Sample Projects available for Download|Sample Projects (Downloadable Scenarios)]]
*[[Available Models|Disease and Population Models]]
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* ''(new!!)'' [[Epidemiological Parameters]]
 +
*[[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]]
 
*[[Transportation Models|Transportation Models]]
 
*[[Air Travel Model|Air Travel Model]]
 
*[[Air Travel Model|Air Travel Model]]
*[[STEM_Solvers|Solvers]]
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*'''Modeling New Diseases'''
 +
#[[STEM Model Creator|Using the '''''New!!''''' STEM Model Creator tool]] (''beta'')
 +
#[[STEM Model Generator]] tool (for Developers)
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#[[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]]
  
<br/>
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|-
 +
! style="background: #ffdead;" |
 +
=== Release Planning ===
 +
! colspan="2" style="background: #ffdead;" |
 +
=== Disclaimer ===
 +
|-
 +
|
 +
<!-- 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]]
 +
* V3.0.0 Milestone 1 is now Available
 +
* Based on and compatible with Eclipse 4.5.1 (Mars)
 +
* STEM V3.0.0M1 supports (J2SE) 8.0 JVM. ''In fact - it's required''
  
== [[Disclaimer]] ==
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* V2.0.3 Now Available (Feb. 2015)
 +
** Bug Fixes
 +
** Updated Admin 0 borders added
 +
** New models
 +
** Updated Google Earth(tm) Interface
  
<br/><br/>
+
* 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) -->
  
== Release Planning ==
+
 
 +
<br>
 +
Click on the header for this section to view the [[Disclaimer]].
 +
|-
 +
| colspan="3" align="center" |
 +
|}
  
 
[[Category:Eclipse Technology Project]]
 
[[Category:Eclipse Technology Project]]
 
''please also see our [http://www.eclipse.org/stem website]''
 
 
'''V1.3.0'''
 
Revised Date 2/7/2012
 
Planned 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
 
 
'''V1.3.1'''
 
Tentative Date 4/15/2012
 
Tentative Features:
 
* Bug Fixes to 1.3.0
 
* Scenario ''"compile"'' proof of concept
 
* STEM EMF update to version 2.7.2
 
* Shape File Importer: Improvements to GUI
 
* Population Transformer: “realistic” sample model on food mediated disease transmission
 
* Pajek-file Importer: Enable integration between user graphs and existing STEM graphs
 
* Graph Editor: improved zooming, deleting nodes and edges, improved GUI for new population generation
 
* Ability to Delete Items inside a Graph from Designer Perspective
 
* STEM -integration inside KNIME: creating a Node within the KNIME, Node-repository that allows STEM headless execution
 
 
'''...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.
 
 
 
{| align="left"
 
  | __TOC__
 
  |}
 

Revision as of 15:05, 20 July 2017

STEM TOP BAR.gif

STEM Community Phone Call

The STEM community runs a monthly phone call anyone is free to join. The agenda is posted on stem-dev.org every month early in the week of the call for you to view. 
The special series of Community Ebola Modeling Phone Calls held during the epidemic was merged back with our regular monthly phone call.
You can still see all the Ebola content here

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 (new!!) requires STEM V2.0 milestone
  2. Full length video In English
  3. Full length video In Hebrew
  4. Full length video In Japanese
  5. Full length video In Spanish
  6. 5 min Video (English)
  7. 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 Map View
  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 (beta)

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 (beta)
  2. STEM Model Generator tool (for Developers)
  3. Model Generator Installation
  4. Manual Model Plug-in generation
  5. Manual Disease Label creation

Release Planning

Disclaimer

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

  • V3.0.0 Milestone 1 is now Available
  • Based on and compatible with Eclipse 4.5.1 (Mars)
  • STEM V3.0.0M1 supports (J2SE) 8.0 JVM. In fact - it's required
  • V2.0.3 Now Available (Feb. 2015)
    • Bug Fixes
    • Updated Admin 0 borders added
    • New models
    • Updated Google Earth(tm) Interface
  • 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.



Click on the header for this section to view the Disclaimer.

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