First Steps with UNIX in Life Sciences

Overview

With a constant evolution of technologies, life scientists (such as laboratory biologists) are faced with an increasing need for bioinformatics skills to deal with high-throughput data storage, retrieval and analysis.

Although several resources developed for such tasks have a graphical user interface, many operations can be more efficiently handled with command-line programs and utilities.

This course provides an introduction to using the Linux / UNIX operating system via the command line interface (CLI), as well as an introduction to the Bash shell and some of the Linux / UNIX core utilities commands.

More specifically, the course covers the following topics:

What is Linux / UNIX and why use it? Navigating the file system. Shell expansions: brace, tilde, and filename expansion. File and directory management: create, move, copy, delete. File access permissions and ownership. Locating files: the find command. Displaying file content. Archiving and compressing data. Standard input/output and pipes. Text processing utilities: wc, tr, sort, uniq, cut, diff, cat, paste. Introduction to grep and regular expressions.

Audience

This course is addressed to beginners wanting to become familiar with the Linux / UNIX environment, its basic commands, and the Bash shell.

Learning objectives

At the end of the course you should:

• Be able to execute most of the basic Linux / UNIX commands.
• Be able to build simple pipelines by combining different UNIX commands.
• Be sufficiently skilled for further courses requiring basics of Linux / UNIX, like HPC or NGS courses.

Prerequisites

Knowledge / competencies

This is a course for beginners, no background in Linux / UNIX or any programming language is required.

Technical

A laptop with a command line terminal and a relatively recent version of Bash (>= 4.0).

Application

Registration fees are 100 CHF for academics and 500 CHF for for-profit companies.

Deadline for registration and free-of-charge cancellation is set to 25/08/2025. Cancellation after this date will not be reimbursed. Please note that participation to SIB courses is subject to our general conditions.

You will be informed by email of your registration confirmation.

Venue and time

The course will take place at the University of Bern. It will start at 9:15 CET and end around 17:15 CET. The participants will get detailed information before the course.

Additional information

Coordination: Grégoire Rossier - SIB Training Group

We will recommend 0.25 ECTS credits for this course (given a passed exam at the end of the course).

You are welcome to register to the SIB courses mailing list to be informed of all future courses and workshops, as well as all important deadlines using the form here.

SIB abides by the ELIXIR Code of Conduct. Participants of SIB courses are also required to abide by the same code.

For more information, please contact training@sib.swiss.