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

Topics in this chaptersection chapter include:

Table of Contents
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About caIntegrator

NCI , Center for Biomedical informatics Informatics and Information Technology (CBIIT) is developing a novel translational informatics platform called

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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.

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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:

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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:

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 (). Image Removed

• New user account registration form

2. Enter the appropriate information. Items In the Register form, enter the appropriate informationItems with an asterisk or highlight are required..

• Security Information

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    *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 **-–Username
**-–*LDAP Password*
–Requested
**--Requested role(s){}{*}– :Select one or more of the roles. Roles are described in 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.

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

• Account Details
• First Name{}*
• Last Name{}*

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  *Email \[address\]{*}<span style="color: #ff0000">{<strong>}</strong>*</span>

• Organization{}*

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  *Address \[Lines 1{*}<span style="color: #ff0000">{<strong>}</strong>*</span> *and 2\}*

• City{}*
• State{}*
• Country{}*

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  *Postal \[or Zip\] Code{*}<span style="color: #ff0000">{<strong>}</strong>*</span>

• Phone{}*
• Fax

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

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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 . 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 You will recieve an email when your account is created, the system administrator sends you an email to alert you, after which you can login log in to caIntegrator.
When your account is registered, the 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 and after you login. The Welcome page also displays after you log in, before you open any studies ().

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  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 the button 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.

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

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• 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.
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  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 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 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, as shown described in the following screen shotsection.
• 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.

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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 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, 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..

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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

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Context Sensitive Online Help

To access online help, click the help icon at the top of each page to open a . The topic that opens is context-sensitive topic. Context-sensitive help displays information , 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 caIntegrator:logging outlog log out of caIntegrator, click the logout link in the upper right-hand corner of the page.

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