[IPython-dev] ANN: GenePattern Notebook released

Thorin Tabor thorin at broadinstitute.org
Fri Aug 5 16:16:10 EDT 2016

We are pleased to announce the release of GenePattern Notebook, an 
extension for Jupyter which provides access to hundreds of different 
bioinformatic analyses through the GenePattern web service.


Supported analyses include machine learning algorithms (clustering, 
classification, dimension reduction), tools for working with gene 
expression data (both RNA-seq and microarray), sequence variation and 
copy number analysis, proteomics, flow cytometry and network analysis.

Included in the extension are visual widgets for running analyses, tools 
for sending results to downstream steps in a bioinformatic workflow, 
Jupyter magics for creating GenePattern widgets and a Python library for 
programmatically working with your results.

To get started after installing the extension, just open a notebook and 
change a cell to the new GenePattern cell type. A full walk-through of 
using the extension is available on our website:


An early version of the GenePattern Notebook Repository, a service 
providing access to GenePattern Notebook functionality as well as a 
variety of example notebooks, is available at the address below.

https://notebook.genepattern.org <https://notebook.genepattern.org>

The GenePattern Notebook extension can also be easily installed from pip 
or conda:

     pip install genepattern-notebook


     conda install -c genepattern genepattern-notebook

Once installed, you will need to install and enable the accompanying 
server and nbextensions. The ipywidgets nbextension must also be enabled:

     jupyter nbextension enable --py widgetsnbextension
     jupyter nbextension install --py genepattern
     jupyter nbextension enable --py genepattern
     jupyter serverextension enable --py genepattern

The GenePattern Notebook extension supports both Python 3.3+ and Python 2.7.

The GenePattern Team

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