Practical Linux Course

Designed for researchers, including PhD students and postdocs, this course provides attendees with an introduction to the Linux operating system. Linux powers more than 90% of the world’s supercomputers, most internet servers, and more than a billion Android devices. Additionally, bioinformatics depends heavily on Linux since a lot of scientific software is written specifically for it.

This short and concise hands-on course will teach you how to effectively use Linux using the command line interface. You will be able to swiftly start using Linux both on a server, e.g., the LUMC Shark cluster, as well as on your personal computer. Learning outcomes:

  • Understand and navigate through the filesystem structure.
  • Obtain information about files and directories.
  • Manipulate, i.e., create, delete, move, and rename files and directories.
  • Inspect and edit files content.
  • Gather disk storage information.
  • Search for and within files.
  • Manage file and directory access permissions.
  • Connect to other computers.


  • Date: TBA
  • Time: TBA
  • Location: TBA
  • Teachers:
    • Mihai Lefter (
    • Jonathan Vis (
  • Registration via Direct access to the registration form.


Time Activity Contents
13:00 Lecture 1 Introduction: operating systems, linux, course outline.
13:10 Lecture 2 Connecting: basics, PuTTy, MobaXterm, copy.
13:30 Practical 1
13:50 Lecture 3 Core 1: the filesystem, the shell, the command line interface.
14:10 Practical 2
14:30 Break
14:40 Lecture 4 Core 2: basic commands, output redirection.
15:10 Practical 3
15:50 Break
16:00 Lecture 5 User Environment: users, groups, file permissions, and ownership.
16:20 Practical 4
16:50 Final Questions
17:00 Closing


You can find the practical start point files here and the commands cheat sheet here.

Past sessions

You can access the materials for the previous sessions below:



Follow Up

The Practical Linux course is mandatory for the following courses: