GenePattern v3.9.11-rc.5 b234 Release Notes

Released October 21, 2019

Release Notes - GenePattern - Version v3.9.11-rc.5 b234

The public GenePattern server hosted by the GenePattern team was officially migrated to the Amazon cloud: on January 1, 2019. To support this migration, GenePattern now requires that all modules be run in a Docker container.
More information about our use of Docker and the administration of GenePattern in the cloud can be found in our wiki on GitHub.

Please note that GenePattern releases are now hosted on GitHub along with our source code.

New Features and Improvements

  • [GP-7828] - New 'Files' tab uploader for files >2GB (using resumable.js) - this replaces the former uploader which no longer worked in modern browsers.
  • [GP-7909] - New throttle to limit the number of concurrent analyses a user can have in pending/running state. This is set by a parameter, max_simultaneous_jobs, in the config_custom.yaml which can be set for the entire server or per user as with other parameters. Default is 100 concurrent jobs if not otherwise specified.
  • [GP-7248] - Updated the URL for the module repositories in the following configuration files: repo.yaml and More information about how to configure this change in your server can be found in our blog.

Modules Released or Updated Since July 5, 2019

MutPanning - New - MutPanning identifies driver genes based on their abundance of nonsynonymous mutations and their increased number of mutations in unusual nucleotide contexts that deviate from the background mutational process.

Kallisto - New- Running Kallisto with basic parameters to perfomr pseudoalignment using a human transcriptome index (GRCh 38 from the Ensembl Archive Release 95)

CellFie - New - Metabolic task modeling with CellFie

MethylationCNVAnalysis - New - Methylation array preprocessing with the minfi R package and copy-number variation analysis with the conumee R package. Compatible with both 450k or EPIC array data.

GSEAPreranked - Updated to use the GSEA v4.0.2 code base. Updated to give access to MSigDB v7.0. OpenJDK 11 port. Java code moved into the GSEA Desktop code base.

GSEA - Updated to use the GSEA v4.0.2 code base. Updated to give access to MSigDB v7.0. OpenJDK 11 port. Java code moved into the GSEA Desktop code base.

ssGSEAProjection - Updated to give access to MSigDB v7.0. Unified the Gene Set DB selector parameters and better downloading of MSigDB files. Removed Java dependency. Added a no-normalize option as the default.

ConstellationMap - Updated for MSigDB v7.0

DESeq2 - Updated to output a counts table file

Other Tools and Resources Released or Updated Since July 5, 2019

HCA Notebook Workspace & GenePattern Notebook Workspace:

New Feature and Update Highlights:

  • Updated to Plotly 4.0 in the Python 3.7 kernel.
  • R kernel added to the Docker image 
  • New GenePattern theme added
  • Added support for HTML in module, widget, and parameter descriptions
  • Added better support for defining and importing UI Builder widgets from a Python module
  • Implemented support for large file uploads in the UI Builder
  • Added r_build_ui magic (UI Builder support for R cells)
  • Upgraded the rich text widget to TinyMCE 5

Full release notes can be found on the GenePattern Notebook website.