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Introduction to UNIX for Biologists

20-22 November 2017, Lund

 

Course description

Introductory course to using the UNIX environment and to using the UNIX-terminal for processing biological data. This course is organized by Geneco and PlantLink.

The terminal interface in UNIX, the environment on which the operating systems Linux and Mac are built, is a central tool for processing and managing biological data. It inherently provides a variety of programs and commands for performing text-file manipulation, and is frequently the main platform for more advanced bioinformatic tools. Large processing clusters like UPPMAX are also often based on a UNIX environment.

Basic knowledge of how to navigate, manage data and perform data processing in UNIX is a highly useful and versatile skill for anyone working with biological data. It is also a crucial skill to have when working with command-line based bioinformatic software.

To apply for the course you are required to fill in a basic application form at Google forms (https://goo.gl/forms/4NqKDn4zn4eLccMs2). This course allows for a limited number of participants, and places will be filled primarily on a first-come-first-serve basis. Researchers on all levels (PhD students, post-docs, PIs) are welcome to attend.

Time period and venue

November 20 - 22, 2017. 9:00 - 16:00 daily. The course will be held in the Biology building, Sölvegatan 35, Lund. Room: Will be announced.

Prerequisites

No previous knowledge in UNIX is required. The target audience is biologists with no previous background in working with UNIX. If you have limited experience with UNIX and have worked occasionally with the UNIX terminal, the course will likely still be useful for you as it includes more challenging non-mandatory exercises.

Course Content

The course will cover the following topics:

Background and introduction to UNIX

Navigation and file management in the UNIX file system

Working with bioinformatic file formats (FASTA, FASTQ, GFF) using UNIX commands

Linking multiple UNIX commands together using streams and pipes

Processing multiple files in a single command

Proper handling of file permissions and project structure in a UNIX environment

Automate tasks in UNIX using Bash scripting

 

Goal of the Course

This course both aims to provide a fundamental understanding of the UNIX environment, what it can do and how to use it, as well as providing a basis for more advanced courses using UNIX-based tools. After the course, the student should feel comfortable navigating in the UNIX environment and should be able to perform basic processing and to extract information from biological data.

Preliminary schedule

Note that this schedule only is the planned outline, and might be subject to change both before and during the course.

Day 1: Introduction to UNIX, the file system, how to manage files and basic processing commands

Day 2: Using streams, linking commands through pipes, pattern matching and more processing commands

Day 3: Variables, loops and introduction to scripting
 

Literature
Custom tutorials written for this course.


Course Organizers

Jakob Willforss, Lund University

Dag Ahrén, Geneco, Lund University

Alexander Koc, PlantLink, Swedish University of Agricultural Sciences


Application
A first come, first serve, principle applies. The course will take a limited number of participants. Deadline for application: November 6, 2017

Please apply for the course using this Google form (https://goo.gl/forms/4NqKDn4zn4eLccMs2).

Course Fee
The course will be free for researchers associated to either Geneco or PlantLink. Other participants are welcome for a fee of 1200 SEK  + VAT (approximately 130 € + VAT).

If you have any question please email to: jakob [dot] willforss [at] immun [dot] lth [dot] se

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