We're upgrading the GitLab server on Monday April 3 starting at ~ 8:00 in the morning. This will include a longer then normal downtime around 4hrs, Gitlab will be updated from 8.12 to 8.17 this will include a new version of Ruby on the server. Please let us know if you notice anything broken afterwards. -- Michel



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.
  • Connect to other computers.
  • 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.


In 2017 the course will be given on the following dates: 6 April (9-12 AM), 3 May (2-5 PM) , 12 June (2-5 PM), 12 July (2-5 PM), 9 August (2-5 PM), 6 September (2-5 PM), 11 October (2-5 PM), 1 November (2-5 PM), 6 December (2-5 PM).

Details regarding the next session:

  • Date: April 6th, 2017
  • Time: 09:00 - 12:00 AM
  • Location: 01-J-01-082
  • Teachers:
    • Jeroen Laros (J.F.J.Laros@lumc.nl)
    • Mihai Lefter (M.Lefter@lumc.nl)
  • Registration via www.medgencentre.nl. Direct access to the registration form.


Time Activity Contents
09:00 Lecture 1 Introduction: operating systems, linux, course outline.
09:05 Lecture 2 Connecting: basics, PuTTy, MobaXterm, copy.
09:25 Practical 1
09:40 Break
09:50 Lecture 3 Core: the filesystem, the shell, the command line interface, basic commands, output redirection.
10:30 Practical 2
11:00 Break
11:10 Lecture 4 User Environment: users, groups, file permissions, and ownership.
11:30 Practical 3
11:50 Final Questions
12:00 Closing



Follow Up

The Practical Linux course is mandatory for the following:

  • Shark course
  • Git course
  • Advanced scripting course