Chapter 2 Linux

Linux is a multitasking, multiuser Unix-like computer operating system (OS). Linux can run many different applications (multitasking) and it can be used by many different people (multiuser) on the same computer at the same time.

It is utilised by many programmers, including Bioinformaticians. It is a relatively easy OS to run commands and develop software for. The vast majority of programs and tools for computational analysis of biological data will work in Linux.

There are three parts of the Linux OS:

• The kernel: This is the hub of the operating systems. This is the "behind the scenes" part of the OS which allocates time and memory to programs. This controls the hardware.
• The shell: This acts as the interface between the user and the kernel. When a user runs commands, the shell will interpret these commands for the kernel. The shell can be any program that constitutes the user interface e.g. command line, internet browser, start menu etc.
• Programs: Programs allow the OS to perform specific tasks. Examples of programs include Internet browsers, genome assembly tools, text editors etc.

It is important to learn the Linux language so you can run commands on the command line. This is because:

• Many bioinformatic tools do not have a graphical user interface (gui) and so must be run on the command line.
• There are many powerful commands that can be run on the Linux command line.
• It is quicker and more reproducible to run commands through a shell than through a gui.