GenePattern Team Blog

GenePattern is Moving to the Cloud!

Posted on Thursday, October 25, 2018 at 06:00PM by GenePattern Team

GenePattern is Moving to the Cloud

At the end of December 2018, the public GenePattern server hosted by the GenePattern team will be running on the Amazon cloud: This migration will allow us to provide more flexible compute power and support the growing analysis needs of the genomics research community, while still maintaining our free service to the community.


What this means for GenePattern users

  • We created a new account for you on the Amazon cloud GenePattern server,, with the same username, password, and email address you had on the Broad-hosted server. 
  • Please note that we have not migrated your job results or pipelines to the new server. If you would like to save your job results and pipelines, please see the instructions below.
  • We encourage you to sign in and use the new server right away, as the Broad-hosted server will be shut down on January 1, 2019
  • On November 1, 2018, we will end new...

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Come and work with us! New position open for bioinformatics programmer on our Jupyter Notebooks team!

Posted on Tuesday, August 14, 2018 at 04:43PM by GenePattern Team



We in the Mesirov Lab at UCSD are looking for a bioinformatics programmer to develop methods for the multi-omic analysis of cancer and other diseases, and to disseminate those methods via Jupyter notebooks and GenePattern


to the worldwide genomics community. 

Apply today!



The Department of Medicine is responsible for fulfilling the teaching, research, and clinical missions of the University of California, San Diego and employs 500+ full-time salaried faculty members and 150+ academic appointees. Staff personnel include 800+ staff in 9 bargaining units, students, and volunteers.

There are over 250 clinical faculties practicing at multiple sites and hospitals. Professional fee billings for the department exceed $50 million with collections of over $19 million per year. The total annual budget is approximately $170 million, which includes contract and grant revenues, clinical practice and medical center funds, and other state and...

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Final Update to CentOS 5 Compute Node Availability for Broad-hosted Servers

Posted on Wednesday, July 18, 2018 at 03:01PM by Barbara Hill

On June 22, 2018, there was a fire at the main data center for the Broad Institute, resulting in an end of service for the last remaining CentOS 5 node, which enabled the running of the following legacy modules on our Broad-hosted servers:

  • ApplyGatingML
  • CopyNumberInferencePipeline (SNPFileCreator_SNP6, Birdseed, CopyNumberInference, CopyNumberNoise, RemoveCopyNumberOutliers, TangentNormalization, ParallelCBS, SegmentationCount)
  • ESPPredictor
  • FCMSinglePanelQC
  • FLAMEChooseOptimalClusterNumber
  • FLAMEMetacluster
  • FLAMEMixtureModel
  • FlowMeansCluster
  • FlowMergeCluster
  • GLAD
  • IlluminaDASLPipeline (IlluminaScanExtractor, IlluminaNormalizer, IlluminaConcatenate)
  • IlluminaNormalizer
  • ImmPortFCSConvLogicleTrans
  • ImmPort_FLOCK_CrossSample (ImmPortFCSConvLogicleTrans, ImmPortColSelection, ImmPortFLOCK, ImmPortCrossSample)
  • ImmPort_FLOCK_Individual_FCS (ImmPortFCSConvLogicleTrans, ImmPortColSelection, ImmPortFLOCK)
  • MultiplotPreprocess (and thus Multiplot)
  • RemoveCopyNumberOutliers
  • ...

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