Genomics to Notebook (g2nb)

g2nb combines the accessibility and research narrative capabilities of Jupyter⁠ with the genomics tools available in Galaxy⁠, GenePattern⁠, and other popular bioinformatics platforms, adding many features for ease of use by non-programming scientists.

Using the Image

This image is based on Jupyter Stacks. To use it, first pull the image and then run it, mapping port 8888 to an outside port. To preserve your files between runs, map /home/jovyan to a directory on the host

Features

• GenePattern Notebook⁠: 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.
• GiN⁠: Support for Galaxy analyses in Jupyter notebooks.
• igv-jupyter⁠: An extension for Jupyter which wraps igv.js, the javascript version of the Integrative Genomics Viewer.
• jupyter-wysiwyg⁠: A rich test editor for markdown cells.
• **cywidget⁠: Visualize Cytoscape networks in a notebook
• nbtools⁠: A framework for creating user-friendly Jupyter notebooks that are accessible to both programming and non-programming users.

Source Code

This project is open source under the BSD-3-Clause⁠ license. You can find the complete code under our GitHub organization⁠.