GenePattern 3.4 Release Notes  Print-icon

View release notes for all GenePattern versions:
1.0     1.1     1.2     1.2.1     1.3     1.3.1     1.4     1.4.1     2.0     2.0.1     2.0.2     3.0     3.1     3.1.1     3.2     3.2.1     3.2.2     3.2.3     3.3     3.3.2     3.3.3     3.4     3.5     3.6     3.6.1     3.7.0     3.8.0     3.8.1     3.8.2     3.9.0     3.9.1    

Also see the FAQ for more information about new functionality

Released September 2012

GenePattern 3.4 contains several new features and fixes.

New Features

New and Improved Module Integrator

The module integrator has been redesigned for ease of use.  Updates include:

For more information about the new module integrator, see this tutorial.

New and Improved Pipeline Designer

The pipeline designer has been redesigned for ease of use. Updates include:

For more information about the new pipeline designer, see this video tutorial.

High Speed File Uploader

This release includes a new method for adding large (>2 GB) data files to the Uploads tab for users of the public GenePattern Server. It is integrated with an Aspera server to enable high speed upload of data files.  This uploader can significantly improve file transfer times.  Contact us at gp-help at broadinstitute dot org for more details.

Parallel Execution of Pipeline Steps

The pipeline engine has been updated to enable parallel execution of steps in a pipeline. This allows scatter-gather pipelines to be built with the pipeline editor and executed on the server. For best performance, these pipelines should be run on a server that is integrated with a queuing system such as LSF or SGE. For more information, contact us at gp-help at broadinstitute dot org.

GenePattern in the Cloud

This version of GenePattern has been updated to allow users to install and run their own GenePattern server in the cloud by installing the server as an Amazon Machine Instance (AMI).  For more information about how to run GenePattern in the cloud, see this article.

GenomeSpace Support

Users of GenomeSpace can send files to the cloud-based storage in GenomeSpace and use GenomeSpace files as inputs to GenePattern modules, using the new GenomeSpace tab in GenomeSpace-enabled installations of GenePattern.  GenePattern 3.4 is integrated and compatible with the public beta release of  GenomeSpace (beta 6), including GenomeSpace OpenID login, a GenomeSpace landing page within GenePattern, support for GenomeSpace file conversion, and error messages associated with GenomeSpace. For more information about GenomeSpace, see the GenomeSpace User Guide.  GenomeSpace requires Java 6.


The 3.4 release fixes issues in GenePattern, including:

Known Issues

Known issues in GenePattern 3.4 include:

1. On the 3.4.0 server, select your pipeline and click edit to open it in the Pipeline Designer.
2. Click Save. You don't need to make any other changes to your pipeline.

1. Move Folder:              Destination: /Library/Frameworks/R.framework/Versions
WARNING - There was a problem copying /Library/Frameworks/R.framework/Versions/2.5

you may need to install R2.5 separately.  Download R2.5 from CRAN and follow the instruction in this section of the Administrators Guide.

Hardware Requirements and Software Compatibility

Hardware requirements: GenePattern's hardware requirements are found on almost all currently available machines:

Supported operating systems: GenePattern installers are available for Windows, Mac OS X, and Linux. GenePattern should work with any operating system that has a Java 5 or 6 virtual machine installed. We have tested it on the following OS platforms:

Supported browsers: GenePattern has been tested on the following browsers:

Current technology versions: Following are the technology versions used in GenePattern 3.4.

Updated on April 17, 2013 10:59