Before attending, you should be comfortable writing some code in python or R, including basics:

  • Conditionals/if statements.
  • Iteration.
  • Reading from files, writing to files.
  • Taking arguments on the command line.
  • Use of functions.
  • Data types.
  • Data frames/arrays (R) or numpy arrays (python). Indexing into them.

It would also be helpful if you were familiar with:

  • Plotting in ggplot2 or matplotlib.
  • Some experience/use of functional programming, such as lapply in R.


  • If you have a Windows computer, please install Ubuntu through WSL
  • If you have a Mac, and it has an M1 chip, that you either have access to codon or you have set up conda with intel packages
  • Install vscode, and extensions for python.

Session 2

  • Make sure you have an account and can submit jobs on codon (at EBI) or a similar HPC environment at your own institution.

Session 3

Session 4

  • Set up a github account. You can get a pro account for free with an EBI email.
  • Set up ssh key access for your github account.