GenePattern 3.3 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 March 2011

GenePattern 3.3 contains several new features and enhancements, as well as bug fixes and beta features.

New Features

Module Search

A search box on the home page allows users to find modules by typing names or parts of names. The results are presented in a dynamic Google search style.

Uploaded Datasets

Users can now view all files they have uploaded and use them in any future analysis via the Uploads tab on the home page.

Job Output Subfolders

Users can now browse files in subfolders on the Job Status page, enabling users to directly use those files as module input. In addition, users can download jobs with the subdirectories preserved.


The 3.3 release fixes issues in several functional areas of GenePattern, including:

Pipeline Execution

GenePattern 3.3 extensively refactors the GenePattern pipeline engine to fix the following issues:

Job Execution

GenePattern 3.3 provides improvements to job execution and configuration:

LSF Integration

GenePattern 3.3 improves the integration between GenePattern and the LSF batch queuing system:

Server Configuration

GenePattern server configuration is improved in this release, allowing server administrators to:

Other Fixes

GenePattern 3.3 includes a number of other bug fixes and improvements:

Beta Features

These features are in development. While they are present in the GenePattern 3.3 code, they are turned off by default. If you would like to help us test them, please contact us at for instructions for turning these features on in your GenePattern server installation.

Advanced Upload for Large Input Files

This feature implements a new file upload system for handling input files larger than 2 GB. This is available in individual modules (select the Advanced Upload radio button) and the Uploads tab, and enables batch execution and the directory input parameter, as described below.

Batch Execution

Users can select multiple files in a folder via the Advanced Upload feature. The module will be run once for each file selected.

New Input Parameter: directory

Module developers can specify an input parameter as a directory. The user can then select a directory of input files for the module, rather than a single input file. All the files in this directory are treated as input for a single run of the module. Using this parameter type invokes the Advanced Upload option.

Upload Files via the Uploads Tab

Users can upload files without running a module by using the Upload Files button in the Uploads tab. Uploaded files can used in any future analysis.

Important Note: When users run a job normally, the job input files are scheduled to be purged 7 days after the job run (on the Broad public server and on servers where the default time is in place). However, when users upload a file directly, the files are not scheduled for deletion at all. Uploaded files must be manually deleted from the server.

Known Issues

Known issues in GenePattern 3.3 include:

back to top

Updated on May 20, 2011 20:00