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This chapter introduces general caIntegrator procedures and how to obtain help to use caIntegrator.

Topics in this chapter include:

About caIntegrator

NCI Center for Biomedical Informatics and Information Technology (CBIIT) is developing a novel translational informatics platform called caIntegrator that allows researchers and bioinformaticians to access and analyze subject annotation and experimental data across multiple subject annotation trials and studies. The caIntegrator framework provides a mechanism for integrating and aggregating biomedical research data and provides access to a variety of data types (for example, immunohistochemistry (IHC), microarray-based gene expression, SNPs, subject annotation trials data, imaging data, etc.) in a cohesive fashion.

caIntegrator is a web based or locally installed portal that allows researchers and study managers to access the biomedical informatics infrastructure and data analysis tools established by caIntegrator from one common software platform. As a caIntegrator user, you can perform the following tasks:

Integrate subject annotation data with genomic and/or imaging data
Import data of various types in a predefined flat format, and create new studies with multiple study data
Update an existing study to add new attributes or to add/modify data
Perform analyses on study data

Registering as a New caIntegrator User

To request a caIntegrator account, you must register as a new user, completing the following steps:

Go to the CBIIT caIntegrator login page or use the URL provided by your System Administrator for the caIntegrator instance at your institution.
Click the Register Now hypertext link, under the caIntegrator login section in the lower center of the page. This opens the account registration form.

Enter the appropriate information. Fields with an asterisk are required.

Security Information

Entry

Do you have an LDAP account?

An LDAP account is a user profile you may have with your institution or CBIIT. If you answer Yes, enter your username and password. This allows caIntegrator to verify that your credentials are correct.

If caIntegrator does not validate your LDAP profile, you are asked to reenter your credentials. You can choose to answer No. In this case, the System Administrator will manually ensure that you do not get a duplicate LDAP account during provisioning. You can then cancel the action or talk with your System Administrator about the problem.

If you select No (you do not have an LDAP account), the text boxes for entering the LDAP account information disappear. You must indicate the role you would like to be assigned in caIntegrator, and continue entering the appropriate information in the Account Details section.

After you submit your registration request, you can continue to use caIntegrator without an account to browse and search available data while your account is verified and activated.

Username

Enter your LDAP user name.

LDAP Password

Enter your password. Your password is case-sensitive.

Requested role(s)

Select one or more of the roles, described in this table:.

Enter your account details. Field names followed by asterisks are required.
Click Submit Registration Request. Click Cancel to terminate the registration. A Registration Request confirmation page appears if you submit the request.

The registration workflow continues as follows.

The caIntegrator system administrator receives an email containing all of the information you specified in the new user request form.
An account request confirmation email is also sent to you, the prospective user, at your specified email address.
The system administrator creates your user account and sends you an email verification.
You can log in to caIntegrator.
Once you register, you can continue to use caIntegrator without an account to browse and search publicly available data and download data while your account is being activated.

When your account is registered, the UserID and password you are assigned determines your access rights for the data in the system. Access rights include roles for the application as well as instance level security; they are provisioned to your account by the system administrator.

For information about administering user accounts, see 7 - Administering User Accounts.

Welcome to the caIntegrator Workspace

The caIntegrator Welcome workspace enables quick access to all caIntegrator functions and information before and after you login, before you open any studies.

Logging In

Without logging in, you can browse any public studies. To do so, select from the drop-down list of Public Studies in the upper center of your browser.

Use the customary steps to log into caIntegrator. If your login is successful, the Welcome to Browse/Study page appears.

If your local installation of caIntegrator is configured with single sign-on, when you click the login button, you are redirected to the single sign-on login page hosted by a separate SSO server. Once you enter your credentials there, you are logged into both caIntegrator and caArray. You can navigate between the two applications without being challenged to provide login credentials again.

If SSO is not enabled, continue working in caIntegrator after you log-in as you always have done.
If SSO is enabled, you might want to check for data updates in caArray upon user login. This is applicable only to studies that you have access to.

caIntegrator Functions

To access caIntegrator functions, use the options listed on the left sidebar of the workspace and described in the following table.

*Sidebar Option*	*Function*
[Study Name]	When you log in, one study displays in the left sidebar by default. Any study that you select in the My Studies drop-down list in the upper right of the page replaces this default selection.
Home	Click this to return to the home page for the selected study.
Search [Study Name]	Click this option to open the Search [Study Name] page from which you can launch queries into your selected study. For more information, see 4 - Searching a caIntegrator Study.
Study Data	Click Saved Queries > My Queries to open the list of previous queries you saved. Click any item in the list to open the saved query, which displays on the Criteria, Columns and Sorting tabs. From those tabs, you can modify criteria and/or launch the query again. For more information, see Saving a Query. Click Saved Lists > Global Lists or > My Lists to open gene lists that have been saved for a study. From any page in caIntegrator that shows such a group, you can save a such a list of genes to be used for searches or analyses. See Creating a Gene or Subject List. Click Saved Copy Number Analysis to open an Edit GISTIC Analysis page. You can review genes retrieved from the analysis or, with appropriate permissions, you can edit the metadata for the analysis. See Editing a GISTICAnalysis.
Analysis Tools	Click any of the listed options to open a page where you can launch an analysis of the data in the selected study. Generate a K-M Plot. See Creating Kaplan-Meier Plots. Generate a Gene Expression Plot. See Creating Gene Expression Plots. Launch GenePattern Analysis. See Analyzing Data with GenePattern
Study Management	Click either of the listed options to manage the selected study through editing or deleting it or by creating a new study. Click Manage Studies. See Managing a Study. Click Create a New Study. See Creating or Editing a Study.
Application Management	Click Manage Platforms to identify, add or remove platforms that caIntegrator supports. For more information, see Managing Platforms.
caIntegrator Menu	Click Support to view contact information for Application Support. Click User Guide to open the caIntegrator User's Guide.
Help	Click the Help icon at the top of each page to open a context-sensitive topic. The help page displays information (from this user's guide) that corresponds to the page from which help was opened.

In the My Studies drop-down list in the upper right of the page, select the study you want to use for your current session. (The list includes all studies to which you are subscribed as well as public studies.) As you do so, the following left sidebar contents change to reflect options relevant to your study selection:

the logo for the selected study (if it exists)
the name for the selected study
the list of saved queries and/or saved lists for that study

Viewing Existing Studies

If you have not logged into caIntegrator, you can view any public studies in your browser.
After logging in, you can view existing studies for which you have been granted permission as well as public studies. In the upper right corner of the page, in the My Studies drop down list, shown in the following figure, select the study you want to review or work in.

A study summary including a status field should appear for the study you selected. If the status is not deployed, or if the study summary does not appear, then the study is not deployed and available for analysis.

When annotations are uploaded during the creation of the study, each field is defined by the study manager.

Because in looking at the study, you may not know the meaning of all the annotations, you can open a reference page with a summary of the annotations. Click the Data Dictionary: View link on the study home page, as described in the following section.
From the study summary page, you can also open a log for the study. Click the Study Log: View link on the page to see all log entries with descriptions. See Study Log for more information.

Data Dictionary

A link on a study home page, as shown by the arrow in the following screen shot, opens a data dictionary summary.
The link to open the Data Dictionary is identified by an arrow

The Data Dictionary table, shown in the following figure, clarifies all annotations used in the study. It displays their field descriptors, descriptions, caDSR identifiers (if used), caDSR IDs and definitions, data type, and permissible settings. The Restrictions column indicates whether or not masks have been applied to numeric data in the study. For more information, see Assigning an Identifier or Annotation.
The table for viewing details in the data dictionary

For more information about study details, see Creating or Editing a Study.

Study Log

The study log which you can open by clicking the Study Log > View link on the study summary page lists the steps used to create a study. For more information, see Viewing or Editing a Log.

Logging Out

To log out of caIntegrator, click the logout link in the upper right-hand corner of the page.

Using caIntegrator Online Help

The caIntegrator online help is in user's guide format. It explains how to use all of the features of the caIntegrator portal.

You can open the user's guide without being logged into caIntegrator.

To access the user's guide in caIntegrator, click the Help icon/menu options available in the upper right corner of the user interface ( help button ) and on the left sidebar under the caIntegrator Menu section. When you click the help icon, context sensitive topics relevant to the page open for your assistance.

Help and additional resource links remain fixed through all the user interface pages.