Use GenePattern

The GenePattern team and collaborating organizations maintain several servers that can be used without installing any software. All that is needed is to register (Note that each server must be registered for separately). More information about the servers is provided below.

GenePattern @ Broad

The Broad Institute hosts a publicly available GenePattern server.

  • The job purge for the public Broad-hosted server is set to 7 days.
  • There is a 30 GB quota on jobs and uploaded data.
  • Most of the modules and pipelines available from the Broad Institute (see the Modules page of the GenePattern web site) are available on the Broad-hosted server. Several modules are available only on the Broad-hosted server because they require customized server configuration. (If you are interested in these modules, contact us for more information). A small number of modules are not available on the Broad-hosted server because they run only on the Windows platform; the Broad-hosted server runs under Unix.


GenePattern @ Indiana University

The GenePattern team in collaboration with Indiana University’s (IU) National Center for Genome Analysis Support (NCGAS) hosts a public server on IU’s high performance computing system. This server has more capacity to better accommodate next generation sequencing analysis and other compute intensive analyses. 

  • The job purge for the IU server is currently set to 30 days, as opposed to 7 days on the Broad server, so your jobs will remain on the server longer.
  • There is currently no quota on the IU server, with regard to jobs or data upload. This may change in the future.
  • The server is unavailable on the first Tuesday of every month for planned maintenance. We will communicate any other planned downtime as far in advance as possible.


GenePattern @ Broad (Internal) (must be connected to the Broad internal network or VPN)

The Broad Institute hosts an internal GenePattern server, available only to Broad Institute members and collaborators. All of the features outlined above for the public Broad-hosted server are available with some differences listed below.

  • The job purge for the internal Broad-hosted server is set to 90 days.
  • There is a 20 GB quota on jobs and uploaded data.
  • Data available on the Broad filesystem can be accessed directly without having to upload.
  • Module creation privileges are available.  Contact us for more information.


Running your own GenePattern server

For those who wish to install and maintain their own GenePattern Server, the installer can be downloaded here.

We suggest that you first familiarize yourself with our concepts, adminstrators and user guides before installing your own server.

Please note that it is not required to install GenePattern in order to use it. (see the above sections for more information on selecting a server to use)