Getting Started  

GenePattern provides access to a broad array of computational methods used to analyze genomic data. Its extendable architecture makes it easy for computational biologists to add analysis and visualization modules. This ensures that GenePattern users have access to a continuously growing repository of new computational methods.

If you are new to GenePattern, begin with the basics:

• Concepts provides a brief overview of GenePattern, introducing you to its fundamental principles and primary components. All other GenePattern documentation assumes that you are familiar with the basic information provided by Concepts.
• Quick Start provides a 10-minute tutorial on how to run an analysis and review results. Many users find that this is all they need to begin using GenePattern.

Using a GenePattern Server

To use GenePattern, you open a web browser and enter a URL. The URL that you enter is the address of a GenePattern server. For example:

For example, to use the GenePattern public server:

1. Open a web browser, such as Firefox, Chrome, or Safari.
2. Enter the URL of the GenePattern public server: http://genepattern.broadinstitute.org/gp/
   

   GenePattern prompts you to login:

   

3. Enter your user name and password. If you do not have a GenePattern account, select Click to Register.

   Whether a GenePattern server requires passwords depends on how it is configured. The GenePattern public server requires passwords. By default, a local server does not.

4. Click Sign In. The GenePattern home page appears.

Cannot connect to server: If the web browser cannot connect to the server, it displays a message such as “Unable to connect” or “Cannot display the webpage.”

• If you are using the GenePattern public server hosted at the Broad Institute, wait a minute and try again.
• If you are using another networked GenePattern server, wait a minute and try again. If the problem persists, contact the GenePattern administrator.
• If you are using your own local server, start the server (see Starting Your Own GenePattern Server) and try again.

Exiting from GenePattern

To exit from GenePattern, click Sign Out in the top right corner of the title bar.

Getting Help

The GenePattern web site provides an overview of GenePattern and its analysis modules, as well as links to the GenePattern software and documentation. Click Documentation/Tutorials for a list of GenePattern tutorials and documentation, including:

• Concepts. A brief overview of GenePattern, introducing you to its fundamental principles and primary components.
• Quick Start (10 minutes). A quick hands-on introduction to GenePattern and the GenePattern public server.
• Video Tutorials. A frequently updated series of training videos.
• User Guide (this guide). Detailed instructions for using GenePattern.
• Programmers Guide. Guidelines for writing modules and instructions for accessing GenePattern from the Java, MATLAB, and R programming environments.
• Administrators Guide. Information on how to configure and secure a local or networked GenePattern server.
• File Formats Guide. Descriptions of all file formats and instructions for creating input files.
• In-Depth Articles. Brief articles and tutorials written in response to questions from our users or to share information about new GenePattern features, modules or pipelines.

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