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This section includes the following topics.

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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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This chaptersection section 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

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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:

  • 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

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Registering as a New caIntegrator User*
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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:

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# Go to the CBIIT caIntegrator login page   or use the URL provided by your System Administrator for the caIntegrator instance at your institution.

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# Click the hypertext link, under the caIntegrator login section in the upper left of the page. This opens the account registration form ()

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* _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 \[NCICB or your institution\]{*}?*

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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{*}

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#ff0000}*

LDAP Password*
–Requested ">*</span> –{*}LDAP Password{*}<span style="color: #ff0000">*</span> *–Requested role(s){*}<span style="color: #ff0000">{<strong>}</strong>{*}</span>– 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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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. 

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  • 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. 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.
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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 ().

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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:

  1. On the login page, enter your and .
  2. 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.
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caIntegrator Functions

caIntegrator(). Once a study is created, its caIntegratorsidebar caIntegrator sidebar on the left side of the page. The following table describes each caIntegrator option in the workspace ().

caIntegrator tabs 

Sidebar Option

Function

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[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.

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Home

Click this to return to the home page for the selected study.

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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 .

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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 on page 62.
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 on page 69.
Click Saved Copy Number Analysis to open an Edit GISTIC Analysis page. You can review genes retrived from the analysis or, with appropriate permissions, you can edit the metadata for the analysis. See on page 74.

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 on page 82.
  • Generate a Gene Expression Plots. See on page 88.
  • Launch GenePattern Analysis. on page 101.

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 on page 45.
  • Click Create a New Study. See on page 16.

Application Management

Click Manage Platforms to identify, add or remove platforms that caIntegrator supports. For more information, see on page 47.

caIntegrator Menu

  • Click Support to view contact information for Application Support.
  • Click Tutorials to view a tutorial to help you get started using caIntegrator.
  • Click User Guide to open the caIntegrator v.1.3 User's Guide in PDF format.
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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

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Viewing Existing Studies

caIntegrator:viewing existing studies;study:viewing an existingIf 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, 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. 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 in the following screen shot.
  • From 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

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A link on a study home page, as shown in the following screen shot, opens a data dictionary summary. Image Added

data dictionaryThe 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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For more information about study details, see on page 17.
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Study Log

The study log which you can open by clicking the Study Log > View link on the study summary page lists step the steps used to create a study. For more information, see on page 18.
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Using the User's Guide/Online Help

caIntegrator:online help;online help, usingThe The user's guide/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.

Icon or Button

Description

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Locates and highlights your current topic in the table of contents.

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Select a topic from the complete online help table of contents.

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Select a topic from the online help index.

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Perform word searches of Help by entering query text in the search text box.

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Create a list of your frequently-accessed topics.

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Opens other closely related topics.

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Prints the current topic.

Topic Name > Topic Name

The breadcrumb trail shows the relative location of the current help topic relative to neighboring topics. Click a breadcrumb link to display that help topic.

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Navigates through previously viewed topics.

  • Online help tips

 

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Logging Out

To caIntegrator:logging outlog out of caIntegrator, click the link in the upper right-hand corner of the page. AnchorRTF34373932333a204865616469RTF34373932333a204865616469

Application Support

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

Email:

When submitting support requests via email, please include:

  • Your contact information, including your telephone number.
  • The name of the application/tool you are using
  • The URL if it is a Web-based application
  • A description of the problem and steps to recreate it.
  • The text of any error messages you have received

Application Support URL

 

Telephone: 301-451-4384Toll free: 888-478-4423

Telephone support is available:
Monday to Friday, 8 am – 8 pm Eastern Time,
excluding government holidays.

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