Open Online Data Meetup (OODM)

Jupyter Notebooks in Jupyter Lab, VSCode, GitHub, Papermill and Jupytext - a good ensemble - a scientific use case
jupytext is a lightweight tool to keep scripts either as notebooks (.ipynb) or simpler text based file formats. For example, as a markdown files (.md) which can be easily rendered on GitHub or python files (.py), which can be executed in VSCode’s interactive shell and are better for version control. But some tools still need ipynb to work, e.g. papermill. Therefore, it is handy to keep different version of a script in sync.

In this OODM, I will give you an overview over my stack and practices working in life sciences. You will learn about some interesting tools and the many possibilities around jupyter, which can be compared to quarto or rmarkdown.

Why do I use more than one file version for the same document?
- jupyter kernels allow live exploration of attributes,
- jupyter lab has a great scratch cell for exploration, while keeping the general structure of a notebook,
- VSCode is great for applying changes in many places (”refactoring”),
- VSCode allows the search over many files.

Bio
I am a PhD student at the Novo Nordisk Foundation Center for Protein Research and work on analyzing data and working on methodological questions. I’ll code using - and package code into -python packages, but I can read and adapt R code if I need to.