ANN: GenePattern Notebook released

[Thorin Tabor]

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.

    http://genepattern.org/genepattern-notebooks
    https://github.com/genepattern/genepattern-notebook

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:

     http://genepattern.org/using-the-genepattern-notebook-environment

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

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

    pip install genepattern-notebook

or

    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.

Cheers!
The GenePattern Team

[Alain Domissy]

Nice!

conda install -c genepattern genepattern-notebook   only works for osx-64

I am not sure what would be needed to make it work for linux... 

[Thorin Tabor]

That was an oversight. I'll get it deployed to conda for linux ASAP.

Thorin Tabor

GenePattern Team

[Brad Reisfeld]

This looks very cool, Thorin. 

Do you have the ability to deploy for win-64 as well?

Thanks.

-brad

[Thorin Tabor]

Deployed win-64, win-32, linux-32 and linux-64 last night.

Thorin