[IPython-dev] ANN: GenePattern Notebook released

Fernando Perez fperez.net at gmail.com
Tue Aug 9 22:07:53 EDT 2016

Congrats, and thanks for letting us know!

BTW, I didn't see your post on the general Jupyter list:


I'd recommend reposting there, as most of Jupyter-general discussion has
moved over to that forum, leaving the IPython list for topics that are more
specific to that kernel and terminal shell.  Obviously it's quite OK to
post there too, I'm just thinking of having better reach for your message.



On Fri, Aug 5, 2016 at 1:16 PM, Thorin Tabor <thorin at broadinstitute.org>

> 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
> _______________________________________________
> IPython-dev mailing list
> IPython-dev at scipy.org
> https://mail.scipy.org/mailman/listinfo/ipython-dev

Fernando Perez (@fperez_org; http://fperez.org)
fperez.net-at-gmail: mailing lists only (I ignore this when swamped!)
fernando.perez-at-berkeley: contact me here for any direct mail
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