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Computational notebooks for biomedical research

The slides are available as a notebook on GitHub Overview.ipynb. Complimentary (opinionated) slides are available in other notebooks.

Run the notebooks with examples online:

  • For Jupyter notebook: Examples_Jupyter_notebook.ipynb Binder (JupyterLab)
  • For R Markdown: Examples_R_Markdown.Rmd Binder (RStudio)

The online environments may take some time (>10 minutes) to boot up if they are run after a fresh commit or for a first time in a while.

Widgets screencast

For your convenience sreencasts of widgets which may be of use for biomedical researchers are embedded below:






This talk was given during an NGSeminar on the use of Jupyter and R notebooks in biomedical research, available to watch on YouTube and later, in an improved version for the Big Data Institute training session.


The Python packages used in the seminar and demonstration are listed in the environment.yml file. You can install them with conda, or install specific Python requirements with pip.

The JupyterLab extensions used are listed in the postBuild file. You can install them by copy-pasting the line which starts with jupyter labextension install. In this file you will also find the instructions on downloading the example datasets used in the presentation.