Introduction to Linux and workflows for biologists


31 July-4 August 2017


Course overview

Most high-throughput bioinformatics work these days takes place on the Linux command line. The programs which do the majority of the computational heavy lifting — genome assemblers, read mappers, and annotation tools — are designed to work best when used with a command-line interface. Because the command line can be an intimidating environment, many biologists learn the bare minimum needed to get their analysis tools working. This means that they miss out on the power of Linux to customize their environment and automate many parts of the bioinformatics workflow. This course will introduce the Linux command line environment from scratch and teach students how to make the most of its tools to achieve a high level of productivity when working with biological data.

Intended audience

This workshop is aimed at researchers and technical workers with a background in biology who want to learn to use the Linux operating system and the command line environment. No previous experience of Linux is required.


Monday 31th -Classes from 9:30 to 17:30


Session 1 – The design of Linux


In the first session we briefly cover the design of Linux: how is it different from Windows/OSX and how is it best used? We’ll then jump straight onto the command line and learn about the layout of the Linux filesystem and how to navigate it. We’ll describe Linux’s file permission system (which often trips up beginners), how paths work, and how we actually run programs on the command line. We’ll learn a few tricks for using the command line more efficiently, and how to deal with programs that are misbehaving. We’ll finish this session by looking at the built in help system and how to read and interpret manual pages.



Dr. Martin Jones


Martin started his programming career by learning Perl during the course of his PhD in evolutionary biology, and started teaching other people to program soon after.

Available Packages

Introduction to Linux and workflows for biologists

Course and refreshments


Introduction to Linux and workflows for biologists


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Cancellation Policy:


> 30  days before the start date = 30% cancellation fee

< 30 days before the start date= No Refund.


Physalia-courses cannot be held responsible for any travel fees, accommodation or other expenses incurred to you as a result of the cancellation.