The GenePattern Notebook environment 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 the Jupyter environment 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 the g2nb project.

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!

• JupyterLab >= 3.6.0
• ipywidgets >= 8.0.0

A Docker image with nbtools and the full JupyterLab stack is available through DockerHub.

docker pull g2nb/lab
docker run --rm -p 8888:8888 g2nb/lab

Full installation instructions for casual use are detailed on the GenePattern Notebook website. Users should also consider the g2nb Workspace, which provides an install-free cloud deployment of the full suite of g2nb tools, including GenePattern Notebook.

The installation instructions below are intended for developers who want to install the project from PIP or GitHub for the purposes of software development.

In 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 the Anaconda Python 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.).

Copy 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 to import 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 jupyter

From here go to the "Load the GenePattern extension" step below.

The easiest way to install GenePattern Notebook is through either PIP or conda. It can be installed by executing one of the following commands:

pip install genepattern-notebook

or

conda install -c genepattern genepattern-notebook

# Clone the nbtools repository
git clone https://github.com/g2nb/nbtools.git
cd nbtools

# Install the nbtools JupyterLab prototype
pip install .
jupyter labextension install .

Finally, you may launch JupyterLab by issuing the following command at the terminal:

jupyter lab

This will start up the notebook kernel and launch your web browser pointing to the Notebook.

The 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.

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For more details, see our Code of Conduct.