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 web interface (most of the time, the first choice of biologists), many operations can be more efficiently handled with command-line programs and utilities.

Audience

This course is addressed to beginners wanting to become familiar with the UNIX environment and master the most common commands, which could be useful to run software dedicated to high-throughput data management.

Learning objectives

At the end of the course you should:

• be able to execute most basic UNIX commands
• be able to build complex and combined commands using various parameters
• be sufficiently skilled for further courses requiring basics of UNIX, like HPC or NGS courses

Prerequisites

Knowledge / competencies
As it is a course for beginners, no background in UNIX or any programming language is required.
Technical
A laptop with terminal installed on it prior to the course. Terminal applications are installed by default on Mac and Linux machines. For windows users, we recommend you to install Mobaxterm. Download link to the free Home Edition: https://mobaxterm.mobatek.net/download.html

Application

Registration fees are 50 CHF for academics and 250 CHF for for-profit companies. This includes course content material and coffee breaks.

Deadline for registration and free-of-charge cancellation is set is set to 06/02/2018. 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

University of Lausanne, Génopode building, classroom 2020 (Metro M1 line, Sorge station).

Schedule

Morning session (9:00 - 12:45)

• What is UNIX and why should biologists use it?
• UNIX filesystem
• Processes & Jobs

Afternoon session (13:45 - 17:00 / 17:30)

• Working with directories and files
• Working with file content
• Optional exam

Additional information

Coordination: Diana Marek

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.

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