GenePattern Team Blog

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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Updates to Job Runtime Settings for Public GenePattern server hosted at the Broad Institute

Posted on Tuesday, May 08, 2018 at 02:23PM by GenePattern Team

To help alleviate some of the heavy traffic we have seen in recent months on the public GenePattern server hosted at the Broad Institute, we have implemented a job.walltime limit of 36 hours

  • This means that, by default, jobs will be limited to running for 36 hours. After that, jobs will be terminated by the server. 

Feel free to contact us if you have any questions or comments about any of these updates.

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