Package: genepattern-notebook
GenePattern Notebook for JupyterLabTheGenePattern Notebookenvironment gives GenePattern users the ability to interleave text, graphics, and code with
their GenePattern analyses to create "notebooks" that can be edited, shared, and published.GenePattern Notebooks are built on theJupyterenvironment
and extend it so that users can take advantage of its ease of use and ability to encapsulate
an entire scientific research narrative, without the need to write code. They are a core
component of theg2nbproject.Looking for classic Jupyter Notebook support?Jupyter Notebook support in is available, albeit no longer in active development. You can
find it in its own branch.Just click here!PrerequisitesJupyterLab >= 3.0.0ipywidgets >= 7.0.0DockerA Docker image with nbtools and the full JupyterLab stack is available through DockerHub.dockerpullgenepattern/lab
dockerrun--rm-p8888:8888genepattern/labInstallationFull installation instructions for casual use are detailed on theGenePattern Notebook website. Users should
also consider theg2nb Notebook Repository, which
provides an install-free cloud deployment of the full suite of g2nb tools, including GenePattern Notebook.Development InstallThe installation instructions below are intended for developers who want to install the
project from PIP or GitHub for the purposes of software development.Install PythonIn order to get the GenePattern Notebook working you will first need to install a compatible
version of Python. This means you will need Python 3.6+. We recommend using theAnacondaPython distribution. This is
a scientific version of Python that ships with many of the most popular Python packages for
science, math and data analysis (ex: NumPy, SciPy, Pandas, Matplotlib, IPython, etc.).Note for Mac Users:Mac comes with Python, but if you have an older version of the OS
you will need to install a newer version, as many older versions of MacOS ship with Python 2.Install GenePattern Notebook from GitHubCopy the contents of genepattern-notebook/extension to your development computer and ensure
that the resulting directory if on your Python path. To test this, open Python and try toimport genepattern. If this is successful, you have a copy of the extension available.If you don't already have Jupyter installed, you can install it from PIP by running:pip install jupyterFrom here go to the "Load the GenePattern extension" step below.Install GenePattern Notebook from PIP or CondaThe easiest way to install GenePattern Notebook is through either PIP or conda. It can be installed by
executing one of the following commands:pipinstallgenepattern-notebookorcondainstall-cgenepatterngenepattern-notebookLoad the nbtools extension# Install ipywidgets, if you haven't alreadyjupyternbextensionenable--pywidgetsnbextension
jupyterlabextensioninstall@jupyter-widgets/jupyterlab-manager# Clone the nbtools repositorygitclonehttps://github.com/genepattern/nbtools-lab-prototype.gitcdnbtools-lab-prototype# Install the nbtools JupyterLab prototypepipinstall.
jupyterlabextensioninstall.
jupyternbextensioninstall--pynbtools--sys-prefix
jupyternbextensionenable--pynbtools--sys-prefixLaunch JupyterFinally, you may launch JupyterLab by issuing the following command at the terminal:jupyter labThis will start up the notebook kernel and launch your web browser pointing to the Notebook.Related RepositoriesThe following GitHub repositories contain code or other data related to the GenePattern
Notebook environment.g2nb: A meta-package which installs all of the g2nb tools and extensions.genepattern-python: The GenePattern
Library allows for programmatic access to GenePattern from Python, and is used by
GenePattern Notebook behind the scenes.nbtools: The Notebook Tool Manager
is a tool-agnostic interface and registry for searching, browsing and launching available
notebook tools in a Jupyter environment.jupyter-wysiwyg: A WYSIWYG editor for
markdown cells.example-notebooks: A repository of example notebooks that
demonstrate functionality or analysis techniques in the GenePattern Notebook environment.workspace: Scripts, services
and other infrastructure used in the operation of the GenePattern Notebook Repository.Known IssuesThe current version of the code only works with GenePattern 3.9.3 and up!Users using the GenePattern Notebook with an older version of GenePattern (3.9.3 or 3.9.4) may
need to log into the GenePattern UI before making use of the notebook. The server status
message and child jobs will also be unavailable. If you are using one of these older versions,
we recommend that you upgrade to the latest version of GenePattern.Code of ConductWe 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. Anyone who violates this code of conduct may be sanctioned or expelled from these spaces at the discretion of the GenePattern team.For more details, see ourCode of Conduct.