1 - 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 Register Now hypertext link, under the caIntegrator login section in the lower center of the page. This opens the account registration form.
3. 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. Note: 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: Role Description Permissible Actions Study Manager Creates, owns and manages studies Configures and deploys studies Updates studies Adds or removes study data Performs analyses on study data Knows which data should be included in a study Knows which users should be given access to the data within a study Study Investigator Investigates and queries study data Queries study data Saves queries Analyzes using K-M Plot Analyzes using Gene Expression Plots Analyzes using GenePattern Cannot update a study Can see only data authorized by study manager UPT Admin Has administrative privileges in UPT Creates or deletes user groups .

4. Enter your account details. Field names followed by asterisks are required.
5. 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.

1. The caIntegrator system administrator receives an email containing all of the information you specified in the new user request form.
2. An account request confirmation email is also sent to you, the prospective user, at your specified email address.
3. The system administrator creates your user account and sends you an email verification.
4. You can log in to caIntegrator.

   Note

   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 Administering User Accounts Using UPT.

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.

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, identified in the accompanying figure.

To log into caIntegrator, 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 These options are described in #caIntegrator Functions.

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.
  

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. 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 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.

For more information about study details, see Creating/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/Editing a Log.

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.