{
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        "author": "Thorin Tabor",
        "author_email": "tmtabor@cloud.ucsd.edu",
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        "classifiers": [
            "Development Status :: 5 - Production/Stable",
            "Framework :: Jupyter",
            "Intended Audience :: Developers",
            "Intended Audience :: Science/Research",
            "License :: OSI Approved :: BSD License",
            "Programming Language :: Python :: 3.6",
            "Programming Language :: Python :: 3.7",
            "Topic :: Scientific/Engineering :: Bio-Informatics"
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        "description": "[![Version](https://img.shields.io/pypi/v/genepattern-notebook.svg)](https://pypi.python.org/pypi/genepattern-notebook)\n[![Build](https://travis-ci.org/genepattern/genepattern-notebook.svg?branch=master)](https://travis-ci.org/genepattern/genepattern-notebook)\n[![Documentation Status](https://img.shields.io/badge/docs-latest-brightgreen.svg?style=flat)](http://genepattern-notebook.org/programmatic/)\n[![Docker Pulls](https://img.shields.io/docker/pulls/genepattern/genepattern-notebook.svg)](https://hub.docker.com/r/genepattern/genepattern-notebook/)\n[![Join the chat at https://gitter.im/genepattern](https://badges.gitter.im/Join%20Chat.svg)](https://gitter.im/genepattern/genepattern-notebook?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge)\n\nGenePattern Notebook\n====================\n\nThe [GenePattern Notebook](http://www.genepattern-notebook.org) \nenvironment gives GenePattern users the ability to interleave text, graphics, and code with \ntheir GenePattern analyses to create \"notebooks\" that can be edited, shared, and published. \nGenePattern Notebooks are built on the [Jupyter](https://jupyter.org/) environment \nand extend it so that users can take advantage of its ease of use and ability to encapsulate \nan entire scientific research narrative, without the need to write code.\n\n# Installation\n\nFull installation instructions for casual use are detailed on the \n[GenePattern Notebook website](http://www.genepattern-notebook.org/install/). Users should \nalso consider the [GenePattern Notebook Repository](https://notebook.genepattern.org), which \nprovides an install-free cloud deployment of the GenePattern Notebook environment.\n\n## Development Install\n\nThe installation instructions below are intended for developers who want to install the \nproject from PIP or GitHub for the purposes of software development.\n\n### Install Python\n\nIn order to get the GenePattern Notebook working you will first need to install a compatible \nversion of Python. This means you will need Python 3.4+. We recommend using the \n[Anaconda](https://www.anaconda.com/download/#macos) Python distribution. This is \na scientific version of Python that ships with many of the most popular Python packages for \nscience, math and data analysis (ex: NumPy, SciPy, Pandas, Matplotlib, IPython, etc.).\n\n**Note for Mac Users:** Mac comes with Python, but you will need to install a newer version, \nas OSX ships with Python 2.\n\n### Install GenePattern Notebook from GitHub\n\nCopy the contents of genepattern-notebook/extension to your development computer and ensure \nthat the resulting directory if on your Python path. To test this, open Python and try to \n*import genepattern*. If this is successful, you have a copy of the extension available.\n\nIf you don't already have Jupyter installed, you can install it from PIP by running:\n\n> pip install jupyter\n\nFrom here go to the \"Load the GenePattern extension\" step below.\n\n### Install GenePattern Notebook from PIP or Conda\n\nThe easiest way to install GenePattern Notebook is through either PIP or conda. It can be installed by \nexecuting one of the following commands:\n\n> pip install genepattern-notebook\n\n*or*\n\n> conda install -c genepattern genepattern-notebook\n\n### Load the GenePattern extension\n\nIn Jupyter 5.2 and earlier, before you can use the GenePattern extension for the very first time, \nyou need to enable it by running command lines below. \n\nIn Jupyter 5.3 and later this is automatic and there is no need to run these commands.\n\n> jupyter nbextension enable --py widgetsnbextension\n>\n> jupyter nbextension install --py nbtools\n>\n> jupyter nbextension enable --py nbtools\n>\n> jupyter nbextension install --py genepattern\n>\n> jupyter nbextension enable --py genepattern\n>\n> jupyter serverextension enable --py genepattern\n\n### Launch Jupyter\n\nFinally, you may launch Jupyter Notebook by issuing the following command at the terminal:\n\n> jupyter notebook\n\nThis will start up the notebook kernel and launch your web browser pointing to the Notebook.\n\n### Updating GenePattern Notebook\n\nIf you want to update GenePattern Notebook to a more recent version on PIP, run the following \ncommand:\n\n> pip install --upgrade --no-deps genepattern-notebook\n\n# Related Repositories\n\nThe following GitHub repositories contain code or other data related to the GenePattern \nNotebook environment.\n\n* [genepattern-python](https://github.com/genepattern/genepattern-python): The GenePattern \n    Library allows for programmatic access to GenePattern from Python, and is used by \n    GenePattern Notebook behind the scenes.\n* [nbtool-manager](https://github.com/genepattern/nbtool-manager): The Notebook Tool Manager \n    is a tool-agnostic interface and registry for searching, browsing and launching available \n    notebook tools in a Jupyter environment.\n* [jupyter-wysiwyg](https://github.com/genepattern/jupyter-wysiwyg): A WYSIWYG editor for \n    markdown cells.\n* [example-notebooks](https://github.com/genepattern/): A repository of example notebooks that \n    demonstrate functionality or analysis techniques in the GenePattern Notebook environment. \n* [notebook-docker](https://github.com/genepattern/notebook-docker): A collection of Dockerfiles \n    which are used to build containers encapsulating the GenePattern Notebook environment.\n* [notebook-repository](https://github.com/genepattern/notebook-repository): Scripts, services \n    and other infrastructure used in the operation of the GenePattern Notebook Repository.\n\n# Known Issues\n\n**The current version of the code only works with GenePattern 3.9.3 and up!**\n\nUsers using the GenePattern Notebook with an older version of GenePattern (3.9.3 or 3.9.4) may\nneed to log into the GenePattern UI before making use of the notebook. The server status \nmessage and child jobs will also be unavailable. If you are using one of these older versions,\nwe recommend that you upgrade to the latest version of GenePattern.\n\n# Feature Support\n\nMost common GenePattern features are supported in the GenePattern Notebook environment. A few, \nhowever, have yet to be implemented. GenePattern features that are not yet supported include:\n\n* Batch job submission\n* GenomeSpace integration\n\n# Code of Conduct\n\nWe are dedicated to providing a harassment-free experience for all members of the GenePattern community, regardless of gender, gender identity and expression, sexual orientation, disability, physical appearance, body size, age, race, or religion. We do not tolerate harassment of participants in any form. This code of conduct applies to all GenePattern spaces, including the Google Group, our Git repositories, and our social media accounts, both online and off. 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