[IPython-dev] ANN: GenePattern Notebook released

Thorin Tabor thorin at broadinstitute.org
Mon Aug 15 19:43:27 EDT 2016


I didn't think to post there. Thanks for the suggestion!

Thorin


On 8/9/16 19:07, Fernando Perez wrote:
> Congrats, and thanks for letting us know!
>
> BTW, I didn't see your post on the general Jupyter list:
>
> https://groups.google.com/forum/#!forum/jupyter 
> <https://groups.google.com/forum/#%21forum/jupyter>
>
> 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.
>
> Best
>
> f
>
> On Fri, Aug 5, 2016 at 1:16 PM, Thorin Tabor 
> <thorin at broadinstitute.org <mailto:thorin at broadinstitute.org>> wrote:
>
>     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
>     <http://genepattern.org/genepattern-notebooks>
>     https://github.com/genepattern/genepattern-notebook
>     <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
>     <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 <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
>
>
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>     <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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