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The _caIntegrator 1.3 User's Guide_ is the companion documentation to the caIntegrator software application. The user's guide includes information and instructions for using caIntegrator.

This chapter includes the following topics.

 
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h2. Organization of this Guide
The _caIntegrator 1.3 User's Guide_] contains the following chapters and appendices:

* *Using the caIntegrator User's Guide*--This chapter introduces you to the _caIntegrator 1.3 User's Guide_ and suggests ways you can maximize its use.

* *[1 - Getting Started with caIntegrator]*--This chapter provides details about launching caIntegrator, navigating the interface, accessing online help and performing basic tasks.

* *[2 - Creating a New Study]*--This chapter describes the processes for creating and managing clinical and genomic studies and adding imaging data to studies in caIntegrator.

* *[4 - Searching a caIntegrator Study]*--This chapter describes the procedures for searching studies within caIntegrator using the search and browse tools.

* *[5 - Viewing Query Results]*--This chapter describes search results that caIntegrator returns from study queries.

* *[6 - Analyzing Studies]*--This chapter describes how to use caIntegrator tools to analyze data in clinical or genomic studies that have been deployed in caIntegrator.

* *[7 - Administering User Accounts]*--This chapter describes the processes for creating and managing user accounts in caIntegrator.

* *[A - Data Import Configurations]*--This appendix describes how MAGE-TAB documents are parsed, validated and imported into caIntegrator. It also provides examples of the types of MAGE-TAB documents that are compatible with caIntegrator.

h2.

 User's Guide Text Conventions

The following table illustrates how text conventions are represented in this guide. The various typefaces differentiate between regular text and menu commands, keyboard keys, toolbar buttons, dialog box options and text that you type.

||*Convention*||*Description*||*Example*||
|*Bold & Capitalized Command*|Indicates a Menu command|*Admin > Refresh*|
|{{Monospace type}}|Used for file names, directory names, commands, code snippets, file listings, and anything that would appear in a Java program, such as methods, variables, and classes.|{{URL_definition}}|
|*Icon*|A toolbar button that you click|Click the *Refresh* button  (!refresh icon.png|height=25,width=25,alt="refresh icon"!) to update the screen.|
|*Boldface type*|Options that you select in dialog boxes or drop-down menus. Buttons or icons that you click.|In the Open dialog box, select the file and click the *Open* button.|
|_Italics_|Used to reference other documents, sections, figures, and tables.|_caArray 2.4 Technical Guide_|
|{{*Italic boldface monospace type*}}|Text that you type|In the New Subset text box, enter {{*Proprietary Proteins*}}|
|*Note:* |Highlights a concept of particular interest|*Note:* This concept is used throughout the installation manual.|
|*Warning!*|Highlights information of which you should be particularly aware.|*Warning!* Deleting an object will permanently delete it from the database.|
|\{ \}|Curly brackets are used for replaceable items.|Replace \{root directory\} with its proper value, such as {{c:\cabio}}||

h2. Credits and Resources
{include:caIntegrator Credits}
 
h2. Getting Support
* [Application Support Email|mailto:ncicb@pop.nci.nih.gov]
* Telephone: 301-451-4384
* Toll free: 888-478-4423

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