The Shell For Scientists

Written by   on October 05, 2014

I’ve posted a half-day “The Shell for Scientists” tutorial that I’ve given variants on a number of times; the motivating problem, provided by Greg Wilson for a two-day set of of tutorials at the University of Toronto, was cleaning up a bunch of auditory lab data on people’s cochlear implants.

The focus is on productivity and automation; PDF slides are available here (although I really should translate them into a markdown-based format to make them more re-usable).

Covered are a number of basic shell commands

  • echo
  • pwd
  • cd
  • ls
  • man
  • file
  • cat
  • more
  • wc
  • mv
  • cp
  • rm
  • head
  • tail
  • sort
  • mkdir
  • rmdir
  • grep

As well as simple script writing. There is some optional material on make (again, for automation) and ssh/scp (because that was frequently necessary for tutorials at SciNet). There are a number of hands-on exercises sprinkled throughout.