GenePattern 3.9.3 Release Notes

Released June 23, 2015

GenePattern 3.9.3 requires Java 7. Click on the links below for details on the updates.

System requirements and known issues are detailed on the following pages. 

New User Features

Expand the main panel over the left panel by clicking the toggle button. (outlined in red below)


Display the left panel again by clicking the toggle bar. (outlined in red)


Download multiple job results simultaneously from the Job Results Summary page by (1) checking the desired jobs and (2) clicking the Download button. Each job downloads in a separate zip file named by job number.

Bug Fixes and Enhancements

  • Fixed issue with file list parameters not working with server file paths that contain spaces in their names. (This was discovered in AffySTExpressionFileCreator, will apply to any module that makes use of file lists via server file path)
  • Fixed issue where upgrading GenePattern over an existing installation clobbers and config YAML.

Admin Support

  • The Windows installer is now deprecated. The last available version is for GenePattern 3.9.2.
    • Because of the number of new bioinformatics analysis tools that run only on Unix-based platforms (Linux and Mac), and the additional effort required to support Windows architecture, we have discontinued providing Windows-based installers for v3.9.3 and for future versions of GenePattern. The Windows installer for GenePattern v3.9.2 will continue to be available on GitHub. Future versions of GenePattern may run on Windows but will not be tested. If you are concerned about this change and what it might mean for you, please contact us and we will be happy to discuss this with you.
  • Added a Python programming library 
  • Updated the HSQLDB database to version 2.3.2 for improved performance, so that we know ship with a database which can be used in a production environment.
  • Added prototype support for the PostgreSQL database

Please contact us with any questions or comments.