Getting Started with caIntegrator

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 (e.g. Immunohistochemistry (IHC), microarray-based gene expression, SNPs, subject annotation trials 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:

1. Go to the CBIIT caIntegrator login page or use the URL provided by your System Administrator for the caIntegrator instance at your institution.
2. Click the hypertext link, under the caIntegrator login section in the upper left of the page. This opens the account registration form.
3. Enter the appropriate information. Items with an asterisk or highlight are required..

• Security Information

  • Do you have an LDAP account [a user profile with your institution] at [NCICB or your institution]?

If Yes, enter your username and case-sensitive password for the purposes of verifying that it is correct. After you submit your request, you can continue to use caIntegrator without an account to browse and search available experiments and download data while your account is verified and activated.
**-–Username
**-–*LDAP Password
**--Requested role(s):Select one or more of the roles. Roles are described in the following table.

If your LDAP profile is not validated, caIntegrator indicates that the LDAP credentials do not check out. You are asked to reenter them, but you can choose to answer no, and the System Administrator will manually ensure you don't get a duplicate LDAP account during provisioning. You can Cancel 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.

1. Complete the Account Details requested on the form.
2. Click Submit Registration Request, or click Cancel to abort the registration.

After registration is sent, the screen displays a confirmation message.

At this point, an email containing all of the information you specified in the new user request form is sent to the caIntegrator system administrator. An account request confirmation email is also sent to you, the prospective user, at your specified email address. In response, the caIntegrator system administrator uses UPT to create your user account and assign the requested roles (in predefined groups like Study Investigator). You will recieve an email when your account is created, after which you can log in to caIntegrator.
The user ID and password you are assigned determine your access rights for the software.

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.

• Welcome page that displays before and after login

Without logging in, you can browse any public studies. To do so, select from the drop-down list of public studies in the upper right-hand corner of your browser, identified in the accompanying figure.

To log into caIntegrator:logging incaIntegrator, follow these steps:

1. On the login page, enter your username and password.
2. Click Login. If your login is successful, the Welcome to Browse/Study page appears.

To access caIntegrator functions, use the options listed on the left sidebar of the workspace.

caIntegrator Functions

Once a study is created, its name appears at the top of the left sidebar. The following table describes each caIntegrator sidebar option in the workspace.

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. 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.
  
• Drop-down list for selecting existing studies

After selecting the study name in the My Studies drop-down list, a study summary including a status field should appear. 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.

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 Data Dictionary table 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, shown in the following figure. The Restrictions column indicates whether or not masks have been applied to numeric data in the study. For more information, see on page 23..

• Page for viewing data dictionary details

For more information about study details, see on page 17.

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 on page 18.

Using Context Sensitive Online Help

To access online help, click the help icon at the top of each page. The topic that opens is context-sensitive topic, which means that the page displays information (from this user's guide) that corresponds to the page from which help was opened.

Logging Out

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

Application Support

For any general information about the application, application support or to report a bug, contact NCICB Application Support.