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https://github.com/genepattern/genepattern-notebook

Platform for integrating genomic analysis with Jupyter Notebooks.
https://github.com/genepattern/genepattern-notebook

bioinformatics genepattern jupyter nbextension python reproducible-research

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Platform for integrating genomic analysis with Jupyter Notebooks.

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README 

        
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GenePattern Notebook for JupyterLab

====================



The [GenePattern Notebook](https://www.g2nb.org/) 

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](https://jupyter.org/) 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](https://www.g2nb.org/) 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!](https://github.com/genepattern/genepattern-notebook/tree/notebook)**



### **Prerequisites**



* JupyterLab >= 3.6.0

* ipywidgets >= 8.0.0



# Docker



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



```bash

docker pull g2nb/lab

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

```



# Installation



Full installation instructions for casual use are detailed on the 

[GenePattern Notebook website](https://docs.g2nb.org/en/latest/local-installation/). Users should 

also consider the [g2nb Workspace](https://workspace.g2nb.org), which 

provides an install-free cloud deployment of the full suite of g2nb tools, including GenePattern Notebook.



## Development Install



The installation instructions below are intended for developers who want to install the 

project from PIP or GitHub for the purposes of software development.



### Install Python



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](https://www.anaconda.com/download/#macos) 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.).



### Install GenePattern Notebook from GitHub



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.



### Install GenePattern Notebook from PIP or Conda



The easiest way to install GenePattern Notebook is through either PIP or conda. It can be installed by 

executing one of the following commands:



```bash

pip install genepattern-notebook

```



*or*



```bash

conda install -c genepattern genepattern-notebook

```



### Load the nbtools extension



```bash

# Clone the nbtools repository

git clone https://github.com/g2nb/nbtools.git

cd nbtools



# Install the nbtools JupyterLab prototype

pip install .

jupyter labextension install .

```



### Launch Jupyter



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.



# Related Repositories



The following GitHub repositories contain code or other data related to the GenePattern 

Notebook environment.



* [g2nb](https://github.com/g2nb/g2nb): A meta-package which installs all of the g2nb tools and extensions.

* [genepattern-python](https://github.com/genepattern/genepattern-python): The GenePattern 

    Library allows for programmatic access to GenePattern from Python, and is used by 

    GenePattern Notebook behind the scenes.

* [nbtools](https://github.com/g2nb/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](https://github.com/g2nb/jupyter-wysiwyg): A WYSIWYG editor for 

    markdown cells.

* [example-notebooks](https://github.com/g2nb/example-notebooks): A repository of example notebooks that 

    demonstrate functionality or analysis techniques in the GenePattern Notebook environment.

* [workspace](https://github.com/g2nb/workspace): Scripts, services 

    and other infrastructure used in the operation of the GenePattern Notebook Repository.



# Code of Conduct



We 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 our [Code of Conduct](https://github.com/genepattern/genepattern-notebook/blob/master/Code_of_Conduct.md).