Jupyter Notebooks for Performing and Sharing Bioinformatics Analyses

I was asked to do a half-day tutorial at the Great Lakes Bioinformatics conference Workshop session. The focus was mainly on R, with some python as well. We covered:

  • The basics of Jupyter notebooks - what they are and how they work
  • How to install and run Jupyter notebooks on their laptop, in R and Python
  • How to perform interactive analyses in a web browser using Jupyter
  • Using markdown and latex to
  • How to “Port” an R bioinformatics workflow from some scripts into a Jupyter notebook
  • How to share a Jupyter notebook online, using three different approaches
    • SageMathCloud
    • GitHub and
    • mybinder.org

I think it went prety well; the materials are available On GitHub. It was largely hands-on, so apart from some introductory slides, it was mainly about giving a tour of the notebook and how use Jupyter to share analyses; the “scripts” that I went through in presenting the material were aimed at having the students produce the notebooks here.