Getting Started with caIntegrator

This section includes the following topics.

Welcome to the caIntegrator. This document is designed to provide contextual definitions and examples that will help explain key terms and concepts used with .

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Getting Started with caIntegrator
This chaptersection introduces general caIntegrator procedures and how to obtain help to use caIntegrator.
Topics in this chaptersection include:

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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 usercaIntegrator:requesting user account; account, requesting new user;registering new user 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 hypertext link, under the caIntegrator login section in the upper left of the page. This opens the account registration form ().
• New user account registration form
• In the Register form, enter the appropriate informationItems 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]?

• [jpm] study manager configures and deploys the study, adds or removes study data. Study Investigator - queries the study after the study manager deploys it.

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• Click Submit Registration Request to execute the 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 and 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). When your account is created, the system administrator sends you an email to alert you, after which you can login to caIntegrator.
When your account is registered, the user ID and password you are assigned determine your access rights for the software.
Welcome to the caIntegrator Workspace
The caIntegrator:workspacecaIntegrator:using workspacecaIntegrator Welcome workspace enables quick access to all caIntegrator functions and information before you login. The Welcome page also displays after you log in, 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 ().
To log into caIntegrator:logging incaIntegrator, follow these steps:

• On the login page, enter your and .
• Click the button. 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.
See also:

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caIntegrator Functions
caIntegrator(). Once a study is created, its caIntegratorsidebar on the left side of the page.The following table describes each caIntegrator 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
caIntegrator:viewing existing studies;study:viewing an existingIf 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, select the study you want to review or work in ().

• Drop-down list for selecting existing studies

The study you select opens in the browser. You can review the study data for which you have been granted permission.
After selecting the study name, in the My Studies drop-down list, a study summary should appear, including a status field. 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 the 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 ().
• study:log view;log view of studyFrom 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 opens a data dictionary summary

data dictionaryThe Data Dictionary consists of a table that 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 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 step used to create a study. For more information, see on page 18.
Using Online Help
caIntegrator:online help;online help, usingThe online help explains how to use all of the features.
To access online help, click the help icon at the top of each page to open a context-sensitive topic. Context-sensitive help displays information that corresponds to the page from which help was opened.
When you open online help, the table of contents displays in the left panel.
Once you are in online help, several buttons and/or options help you locate topics of interest.

Logging Out
To caIntegrator:logging outlog out of caIntegrator, click the 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; Application SupportNCICB Application Support.