GenePattern 3.2.1 Release Notes

Released November 1, 2009

New in this Release

Java 1.6 Support

As of Release 3.2.1, the GenePattern server can be configured to run under Java 1.5 or Java 1.6. When installed on Mac OS X 10.6 (Snow Leopard), the GenePattern server is configured for Java 1.6 by default. When installed on any other platform, the GenePattern server is configured for Java 1.5 by default. For instructions on how to change the server configuration, see Setting the Java Version.

Corrections to Known Issues

This release also corrects the following known issues:

  • Usernames: GenePattern now fully supports usernames that include space (' ') characters.
  • Custom settings: GenePattern server restart now preserves custom settings.
  • Libraries and services: GenePattern 3.2.1 programming libraries and services now preserve backward compatibility.

Upgrade Recommended

The GenePattern team strongly recommends upgrading from GenePattern 3.2.0 to GenePattern 3.2.1:

  • If you have installed a GenePattern 3.2.0 server, upgrade the server to GenePattern 3.2.1.
  • If you have used GenePattern 3.2.0 programming libraries or services, upgrade them to GenePattern 3.2.1.


Compatibility Details

GenePattern modules and external applications use GenePattern libraries (see Programmer's Guide) and services (see to interact with GenePattern servers. The GenePattern libraries and services from any release should be compatible with GenePattern servers from any release. However, GenePattern 3.2.0 libraries and services are compatible only with GenePattern 3.2.0 servers.

To prevent compatibility issues, upgrade GenePattern 3.2.0 installations to GenePattern 3.2.1. GenePattern 3.2.1 libraries and services are compatible with GenePattern servers from any release except GenePattern 3.2.0. Libraries and services for releases prior to GenePattern 3.2.0 are also compatible with GenePattern servers from any release except GenePattern 3.2.0.

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Hardware requirements and software compatibility

  • GenePattern components: The latest release of GenePattern is Version 3.2.1.
  • Hardware requirements: GenePattern's hardware requirements are found on almost all currently available machines:


    • 256 MB RAM (individual modules may require additional RAM depending on the data being processed)
    • 500 MHz Pentium 3 or equivalent
    • Hard drive space:
      • Server: 252 MB
      • Modules: As of November 2009, installing all GenePattern modules requires approximately 1 GB of hard drive space
  • 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 1.5 virtual machine installed. We have tested it on the following OS platforms:


    Windows XP, Vista On Vista:
    • The StartGenePatternServer and StopGenePatternServer applications must be run as administrator. To start or stop the GenePattern server, right-click the desktop icon and select the Run as administrator option.
    • Operating system timestamps are incorrectly written to the log files. Timestamps recorded in both the webserver and GenePattern logs are likely a few hours ahead or behind the system time.
    Mac OS X 10.4, OS X 10.5, OS X 10.6  
    Linux Ubuntu 8.04, 8.10, 9.04

    Users are also running GenePattern on the Red Hat, Debian, Gentoo, Mandrake and Fedora distributions of Linux.

  • Supported browsers: The GenePattern Web Client has been tested on the following browsers:


    Windows Firefox 3.0 and 3.5,
    MS Internet Explorer 7.0 and 8.0
    Mac Firefox 3.0 and 3.5, Safari On Safari, the default preference is open "safe" files after downloading. This setting prevents GenePattern from correctly exporting and importing zip files. To clear this preference: open Safari, select Safari>Preferences, select General preferences, and clear the Open "safe" files after downloading check box.
    Linux Firefox 3.0 and 3.5  

    Users are also running GenePattern on Chrome and Opera.

  • Current technology versions: Following are the technology versions used in GenePattern 3.2.1.


    • Java 5, Java 6
    • R 2.5.0
    • Perl 5.8.8
    • Tomcat 5.5.* series
    • HSQL 1.8.0

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