Sharing Jupyter Notebooks

Open science practices furthered through Jupyter Notebook

Jupyter Notebooks offer an excellent avenue for a researcher seeking to expand on their research process. These expansions should not exist in a vacuum, however. Jupyter Notebook offers a great opportunity to engage in open science practices. This can be witnessed ‘in house’ through the expansion of commenting tools via Markdown, as well as additions of option text, images, videos, websites etc. However, none of this matters if no one can actually easily access the Notebook you have created. This short post demonstrates that Jupyter Notebooks are the tool to use if you wish to pursue open science-based practices.

Jupyter Notebooks are written and saved as an .ipynb file. This is a text-based interactive file - it takes its name from the old-school IPython Notebook Style. These .ipynb files have two attractive qualities. The first is that it can be saved/exported as an HTML file - which can then be easily hosted on any website. The second is that it can also be kept as it is - as a .ipybn file - and hosted on a repository site such as GitHub. Github doesn’t simply store the file like a Word document, it displays the entire document as it was last executed and saved. For a demonstration of this, check out the Notebook hosted by Vernon Gayle and Roxanne Connelly here.

The .ipybn file type used by Jupyter Notebook is thus: Human-readable using plain text format (through JSON), has an open standard meaning it is open for anyone to access and use, finally it can be converted to other formats like HTML, PDF etc.