User Guide

User Interface

When first opened in your browser, GenePattern displays the home page. To return to this page at any time, click the GenePattern icon in the title bar or the Modules & Pipelines item in the navigation bar.

	The title bar includes: GenePattern icon: Click the icon to return to this page. My Settings: Click this link to modify your GenePattern account settings (see My Settings). Sign Out: Click this link to exit from GenePattern. Your username: The username of the person currently logged into GenePattern.
	The navigation bar provides access to other GenePattern pages (see Navigation Bar).
	Use the search box to quickly find a module or pipeline.
	The Modules & Pipelines pane lists the analysis modules and pipelines that you can run. Modules and pipelines not installed from the Broad repository are shown in red. Use the radio buttons to organize the modules and pipelines as you prefer: Category (default): Organizes analysis modules by functional category; pipelines are in the pipeline category. Each module is assigned to a category when it is created. To change the category, you must edit the module definition. Suite: Organizes modules and pipelines by suite. Suites are arbitrary collections of modules and pipelines. You can install suites from the Broad repository or create your own. All: Organizes modules and pipelines alphabetically by name.
	The center pane is the main display pane. GenePattern uses this pane to display information and to prompt you for input. Initially, the center pane contains a welcome page, which provides instructions for running common analysis protocols. To redisplay the welcome page, click the GenePattern icon in the title bar.
	The far right pane provides access to several tabs: The Recent Jobs tab lists the most recent analyses that you have run and the result files generated by those analyses, as well as any currently running analyses. Click the icon next to a job or file name to display a menu of commands for working with the job or file (see Job Menu and File Menu). Click My Settings to modify the History setting, which controls the number of analyses displayed in the Recent Jobs pane. The Uploads tab lists the files in your uploads directory on the GenePattern server. Click the icon next to a directory or file name to display a menu of commands for working with the uploaded files (see Upload Menu). A GenomeSpace-enabled GenePattern installation includes a GenomeSpace tab that can be used to help move data files from GenomeSpace and analysis results to GenomeSpace. For more information, see www.genomespace.org.

Navigation Bar

The navigation bar provides access to GenePattern pages and operations. When you log into a GenePattern server on which GenomeSpace is not enabled, you see the following navigation bar:

If you log into another GenePattern server, such as your own local GenePattern server or a GenomeSpace-enabled GenePattern server, you may see additional items in the navigation bar:

The following table describes all possible options in the navigation bar. Not all of these options are available on the GenePattern public server.

Modules & Pipelines	Display the GenePattern home page.
New Pipeline	Create a pipeline.
New Module¹	Create a module.
Install from repository¹	Install a module or pipeline from the Broad repository.
Install from ZIP	Install a module or pipeline from a ZIP file.
Manage	Display installed modules or pipelines; delete modules or pipelines.
Suites	Display the Manage Suites page.
New	Create a suite.
Install from repository¹	Install a suite from the Broad repository.
Install from ZIP	Install a suite from a ZIP file.
Manage	Display installed suites; delete suites.
Job Results	Display the Results Summary page.
Results Summary	Display jobs run on the server; delete jobs.
Resources	Display an overview of the resources.
Mailing List	Display the form you use to join a low-traffic GenePattern mailing list.
Report Bugs	Display the form you use to contact the GenePattern team to report bugs, provide feedback, or ask questions.
Contact Us	Display a form, which you can use to send questions and comments to the GenePattern team.
Downloads	Display an overview of the available downloads.
Programming Libraries	Download and install GenePattern libraries for use with Java, MATLAB, or R.
Public Datasets	Download sample datasets for use with GenePattern.
GParc¹	Display the GenePattern Archive web site, which is a repository and community where users can share and discuss their own GenePattern modules.
Administration¹	Display the Server Settings page.
Server settings¹	Modify settings that affect the GenePattern server.
Help	Display the GenePattern home page.
Tutorial	Display the Tutorial, which provides a comprehensive hands-on tour of GenePattern.
Video Tutorials	Display the list of GenePattern training videos.
User Guide	Display this guide, which describes how to use GenePattern.
Programmers Guide	Display the Programmers Guide, which provides guidelines for writing modules and instructions for accessing GenePattern from the Java, MATLAB, and R programming environments.
Module Documentation	Display a list of the modules and pipelines installed on your server, with brief descriptions and links to the module/pipeline documentation.
File Formats	Display the File Formats Guide, which describes all file formats and provides instructions for creating input files.
Release Notes	Display the Release Notes, which describes new features and known issues in this release.
FAQ	Display the GenePattern list of Frequently Asked Questions.
About	Display the release date and build number of the GenePattern server.
GenomeSpace	Display the GenomeSpace menu options: Login (to GenomeSpace), GenomeSpace UI, and About (GenomeSpace). A GenomeSpace-enabled GenePattern installation includes several elements that help move data files from GenomeSpace and analysis results to GenomeSpace. For more information, see www.genomespace.org.

¹Not available on the public GenePattern server.

Job Menu

When you run an analysis, GenePattern displays the job results in the Recent Jobs tab:

Click the icon next to the job name to display a menu of commands for working with that job. For more information, see Working with Analysis Results.

Download	Download a zip file containing all analysis result files for this job.
Terminate	Stop the job. This menu item appears only while the job is running.
Reload	Display the analysis and its parameters in the center pane, with the parameters set to the values used for this analysis job.
Delete	Delete the analysis job and its analysis result files from the GenePattern server.
Info	Display the parameter values and the analysis result files for this job.
View Java Code View MATLAB Code View R Code	Display the command line that you would use to run this job in the Java, MATLAB, or R programming environments. These commands are useful for programmers who want to access GenePattern from one of these programming environments or from their own applications.

File Menu

When you run an analysis, GenePattern displays the job results in the Recent Jobs tab:

Click the icon next to the file name to display a menu of commands for working with that file. For more information, see Working with Analysis Results.

Delete	Delete the file from the GenePattern server.
Save	Download the file from the GenePattern server.
Send to <input-file-parameter>	Specify this file as the input file parameter.
Create Pipeline	Create a GenePattern pipeline that includes the modules and parameters necessary to reproduce this result file.
List of modules	List of modules that accept this type of file as an input parameter. Select an analysis to display its parameters in the center pane. This result file is specified as the first input parameter.

Upload Menu

The Uploads pane lists files that you have uploaded to the GenePattern server:

Click the icon next to the uploads directory, or a subdirectory or file in that directory, to display a menu of commands for working with that directory or file. For more information, see Running Modules and Pipelines.

Upload Files	Upload a file to the uploads directory on the GenePattern server.
Create Subdirectory	Create a subdirectory under the uploads directory on the GenePattern server.
Delete	Delete the file/directory from the uploads directory on the GenePattern server.
Save	Download the file from the uploads directory on the GenePattern server.
Send to <input-file-parameter>	Specify this file as the input file parameter.
Send Batch to <input-file-parameter>	Specify this directory as the input file parameter. This creates a batch job to analyze each file in the directory.
List of modules	List of modules that accept this type of file as an input parameter. Select an analysis to display its parameters in the center pane. This file is specified as the first input parameter.

Suites Menu

Click Suites>Manage to display the currently installed suites:

Click the icon next to the suite name to display a menu of commands for working with that suite. For more information, see Working with Suites.

Edit	Available only for suites that you have created. Display the Edit GenePattern Suite page, which you can use to modify your suite.
Delete	Delete the suite from the GenePattern server.
Export excluding dependents	Create a ZIP file that contains the definition of the suite, but not the modules or pipelines in the suite. The ZIP file can be used to install the suite on another GenePattern server (see Exporting and Installing Suites Using ZIP Files). Installing the suite from this ZIP file will not install any modules or pipelines in the suite; they must already be installed on the GenePattern server or be installed separately.
Export including dependents	Create a ZIP file that contains the definition of the suite, as well as the modules and/or pipelines in the suite. The ZIP file can be used to install the suite on another GenePattern server (see Exporting and Installing Suites Using ZIP Files). Installing the suite from this ZIP file will also install the modules and pipelines in the suite (unless they are already installed on the GenePattern server).

My Settings

Use My Settings to change your GenePattern account information:

Click My Settings (in the GenePattern title bar). GenePattern displays the Account Information page.
From the left pane, select the information that you want to modify. GenePattern displays the related page.
Modify and save your account information.
Optionally, return to step 2 to make additional changes.

My Settings

Change Email: Change the email address for your GenePattern account on this server. The GenePattern server uses your email address for the following:
- When you run a module or pipeline, GenePattern sends the job to the GenePattern client and displays the Job Status page. On that page, you can click the email notification check box to have GenePattern send you email when the job completes.
- If you forget your password and request a new password, GenePattern sends your new password to this email address.
Change Password: Change the password for your GenePattern account on this server. Note: By default, GenePattern servers are installed without password protection. For information about enabling password protection, see Securing the Server.
History: Use this option to specify the number of recent analyses listed in the Recent Jobs pane on the GenePattern home page.
Visualizer Memory: Specify the Java virtual machine configuration parameters (such as VM memory settings) to be used when running visualization modules. By default, this option is used to specify the amount of memory to allocate when running visualization modules (-Xmx512M).

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