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

Topics in this chapter include:
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h2. 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 (for example, immunohistochemistry (IHC), microarray-based gene expression, SNPs, subject annotation trials data, imaging 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 

h2. Registering as a New caIntegrator User 
To request a caIntegrator account, you must register as a new user, completing the following steps:
# Go to the [CBIIT caIntegrator login page|http://caIntegrator.nci.nih.gov] or use the URL provided by your System Administrator for the caIntegrator instance at your institution.
# Click the *Register Now* hypertext link, under the caIntegrator login section in the lower center of the page. This opens the account registration form. 
# 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. \\ \\
{info:title=Not logged in?}  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.{info} |
|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:{include:caIntegrator roles}. \\ \\
|
# Enter your account details. Field names followed by asterisks are required.
# 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.
# The caIntegrator system administrator receives an email containing all of the information you specified in the new user request form. 
# An account request confirmation email is also sent to you, the prospective user, at your specified email address. 
# The system administrator creates your user account and sends you an email verification.
# You can log in to caIntegrator.
{info:title=While your account is activated} 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.{info}

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 [caIntegrator:7 - Administering User Accounts].
 
h2. 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.

h3. {anchor:login}Logging In  

* 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.

* Use the customary steps to log into caIntegrator. If your login is successful, the Welcome to Browse/Study page appears.

{info:title=Single Sign-on (SSO).} If your local installation of caIntegrator is configured with single sign-on, when you click the login button, you are redirected to the single sign-on login page hosted by a separate SSO server. Once you enter your credentials there, you are logged into both caIntegrator and caArray. You can navigate between the two applications without being challenged to provide login credentials again.
* If SSO is not enabled, continue working in caIntegrator after you log-in as you always have done.
* If SSO is enabled, you might want to check for data updates in caArray upon user login. This is applicable only to studies that you have access to.{info}

h3. caIntegrator Functions
To access caIntegrator functions, use the options listed on the left sidebar of the workspace and described in the following table.
||*_Sidebar Option_*||*_Function_*||
|*\[Study Name\]*|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.|
|*Home*|Click this to return to the home page for the selected study.|
|*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 [4 - Searching a caIntegrator Study].|
|*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 [Saving a Query|caIntegrator:4 - Searching a caIntegrator Study#SavingaQuery]. \\
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 [Creating a Gene or Subject List|caIntegrator:5 - Viewing Query Results#CreatingaGeneorSubjectList]. \\
Click *Saved Copy Number Analysis* to open an Edit GISTIC Analysis page. You can review genes retrieved from the analysis or, with appropriate permissions, you can edit the metadata for the analysis. See [Editing a GISTICAnalysis|caIntegrator:6 - Analyzing Studies#EditingaGISTICAnalysis]. |
|*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 [Creating Kaplan-Meier Plots|caIntegrator:6 - Analyzing Studies#CreatingKaplanMeierPlots].   \\
* Generate a Gene Expression Plot. See [Creating Gene Expression Plots|caIntegrator:6 - Analyzing Studies#CreatingGeneExpressionPlots]. \\
* Launch GenePattern Analysis. See [Analyzing Data with GenePattern|caIntegrator:6 - Analyzing Studies#AnalyzingDatawithGenePattern]|
|*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 [Managing a Study|caIntegrator:3 - Managing a Study or Platform#ManagingaStudy]. \\
* Click *Create a New Study.* See [Creating or Editing a Study|caIntegrator:2 - Creating a New Study#CreatingorEditingaStudy].|
|*Application Management*|Click *Manage Platforms* to identify, add or remove platforms that caIntegrator supports. For more information, see [Managing Platforms|caIntegrator:3 - Managing a Study or Platform#ManagingPlatforms].|
|*caIntegrator Menu*|* Click *Support* to view contact information for Application Support. \\
* Click *User Guide* to open the caIntegrator User's Guide.|
|*Help*|Click the *Help* icon at the top of each page to open a context-sensitive topic. The help page displays information (from this user's guide) that corresponds to the page from which help was opened.| 

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

h2. 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 as well as public studies. 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. 
!home page80.png|vspace=4, alt="Drop-down list for selecting existing studies"!

A study summary including a status field should appear for the study you selected.  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.

h3. Data Dictionary
A link on a study home page, as shown by the arrow in the following screen shot, opens a data dictionary summary. 
!home page3 arrow80.png|vspace=4, alt="The link to open the Data Dictionary is identified by an arrow"! 

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|caIntegrator:2 - Creating a New Study#AssigningAnIdentifierorAnnotation]. 
!view data dictionary80.png|vspace=4, alt="The table for viewing details in the data dictionary"!

For more information about study details, see [Creating or Editing a Study|caIntegrator:2 - Creating a New Study#CreatingorEditingaStudy].

h3. 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 or Editing a Log|caIntegrator:2 - Creating a New Study#ViewingorEditingaLog].

h2. Logging Out
To log out of caIntegrator, click the *logout* link in the upper right-hand corner of the page.

h2. Using caIntegrator Online Help
The caIntegrator online help is in user's guide format. It explains how to use all of the features of the caIntegrator portal.
{info:title=Not logged in?} You can open the user's guide without being logged into caIntegrator.{info}

To access the user's guide in caIntegrator, click the *Help* icon/menu options available in the upper right corner of the user interface (!help icon.png|alt="help button"!) and on the left sidebar under the *caIntegrator Menu* section. When you click the help icon, context sensitive topics relevant to the page open for your assistance. 

Help and additional resource links remain fixed through all the user interface pages.

h2. Application Support
For any general information about the application, application support or to report a bug, contact NCICB 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|[http://ncicb.nci.nih.gov/NCICB/support

] |
|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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