Are you a field or bench scientist and always wanted to feel more comfortable with your computing skills? This course was designed for those who have never used the command line, but realize that the responsibilities they have or will soon take on require them to automate tasks. It will teach basic UNIX command-line skills, enable participants to work remotely on more powerful machines, create and run scripts to automate complex workflows, and synchronize your scripts with the larger community with Github.


  • Week 1: Introducing the GEMS Platform
  • Week 2: Introducing JupyterLab
  • Week 3: Demystifying the UNIX command line
    • UNIX in a nutshell (1)
      • file and folder basics
  • Week 4: Demystifying the UNIX command line
    • UNIX in a nutshell (2)
      • intermediate file concepts
  • Week 5: Demystifying the UNIX command line
    • UNIX in a nutshell (3)
      • advanced UNIX concepts
  • Week 6: Demystifying the UNIX command line
    • Shell scripting for task automation
  • Week 7: Working remotely
    • Remote login to the Minnesota Supercomputing Institute (MSI)
    • Customizing your remote experience
    • Scheduling jobs on MSI's queue
  • Week 8: Data transfer to remote sites
    • Globus for high-speed data transfer
    • sep for quick command line copying
    • Command line utilities for bulk remote downloads
  • Week 9: Syncing your work with the community: Source control basics with git
  • Week 10: Review + Final homework due
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