The Linux Command Line: From Basic Commands to Shell Scripting (Online Course)

1st – 3rd November 2023

Nearly all Bioinformatics analyses are best performed using the Linux command line. Many researchers consider this a drawback and choose to learn only the bare minimums required for a certain task or even try to circumvent Linux completely. A common misunderstanding is, that working on the command line is archaic or performed because it is a cheaper alternative to often costly proprietary solutions. However, it is neither antiquated views nor avarice which makes nearly all Bioinformaticians use the command line, but rather its unmatched efficiency and overwhelming power.

This three-day course will introduce the Linux command line from scratch. Participants will learn to work efficiently with its tools and they will also learn to automate tasks and write first bash scripts. The focus is on processing (large) texts and tables. Examples will be from the field of genome informatics, but methods taught will be universally applicable.

Participants will join remotely using their personal computers (mobile phones and tablets are not suitable). Installing Linux locally is not required, other recent operating system should also be fine. We will use the conferencing solution Zoom and work in a virtual Linux environment (de.NBI cloud).

Location: Online / Zoom
Lecturer: Dr. M. Alawi (UKE Bioinformatics Core)
Date and time: 1st – 3rd November 2023 (14:00-17:00)

To register, please send an email to Dr. Ceren Saygi ( with the following information:

  • First and last name
  • Institutional affiliation
  • Workgroup / department
  • Institutional email address
  • Academic degree


Please note:
We do not charge course fees and usually select participants on a first-come, first-served basis.
An application text or motivation letter is not necessary and does not improve the prospect of a course place.
Incorrect or incomplete statements will regularly lead to exclusion from participation.
We use the information provided exclusively for the organization and implementation of the course, as well as for compiling anonymous statistics on the range of participants.
There is no general right to participate.
We reserve the right to change the course program at short notice or to cancel the course completely without giving reasons.