Educators:
Malik Alawi, Ceren Saygi (UKE Bioinformatics Core) (External Training Partner)

Date:
24th - 26th June 2021 (14:00-17:00)

Location:
Online

Contents:
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.

Topics:

• Basic file operations
• Working with (large) text files
• Using the shell efficiently
• Data compression
• Working with tables
• Regular expressions
• Variables and loops
• Bash scripting
• Common application scenarios of command line usage in a bioinformatics context

Learning goals:
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.

Prerequisites:
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).

Keywords:
Linux, Bash, Shell, Scripting, Command line

Tools:
Linux, Command line