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.

Please do not use a public GenePattern server to analyze protected health information.

GenePattern in the Amazon Cloud

This publicly available server makes use of Amazon’s elastic compute resources and batch processing, allowing for greater compute capacity, both in terms of numbers and intensity of jobs.

  • The job purge for the Amazon Cloud server is set to 14 days.
  • There is a 30 GB quota on jobs and uploaded data.
  • As of Nov 4, 2019, there will be a limit of 20 concurrent jobs per user.
  • We are in the process of verifying that all of our public modules are available on this server. If you find that something is missing, just let us know and we'll resolve the issue as soon as possible.
  • This server has a 1 hour maintenance window on the first Monday of each month from 2pm - 3pm UTC-8


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.
  • 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 second Sunday each month. Typically, GenePattern will be unavailable from 5pm the Saturday before until 9am the Monday after, 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, administrators 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)



Protected Health Information: By registering for GenePattern/GenePattern Notebook, you agree that you will upload only information that can be made available for public consumption and for which you have specific permission.  Do not upload information that identifies specific individuals or that can be associated with them, known as Personally Identifiable Information (PII).  If you have any doubts as to whether specific information can be uploaded, please consult the Compliance Office in your institution. The Regents of the University of California do not accept any responsibility or liability for any information that you upload that is prohibited above.