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.
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.
GenePattern modules and external applications use GenePattern libraries (see Programmer's Guide) and services (see http://genepattern.broadinstitute.org/gp/services) 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.
The latest release of GenePattern is Version 3.2.1.
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:
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.
OS X 10.4, OS X 10.5, OS X 10.6
Ubuntu 8.04, 8.10, 9.04
Users are also running GenePattern on the Red Hat, Debian, Gentoo, Mandrake and Fedora distributions of Linux.
The GenePattern Web Client has been tested on the following browsers:
Firefox 3.0 and 3.5, MS Internet Explorer 7.0 and 8.0
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.
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.