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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.

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.

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 () 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`

Organization of this Guide

User's Guide Text Conventions

Credits and Resources

Application Support