[IPython-dev] ANN: GenePattern Notebook released
thorin at broadinstitute.org
Mon Aug 15 19:43:27 EDT 2016
I didn't think to post there. Thanks for the suggestion!
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:
> 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 <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.
> 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
> IPython-dev mailing list
> IPython-dev at scipy.org <mailto:IPython-dev at scipy.org>
> 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
> IPython-dev mailing list
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