In this chapter, we discuss how to set up a workstation running the Linux operating system. Linux is a free, open source version of Unix that makes it possible to turn an ordinary PC into a powerful workstation. By configuring your system with Linux and other open source software, you can have access to a lot of powerful computational biology and bioinformatics tools at a low cost.
In writing this chapter, we encountered a bit of a paradox—in order to get around in Unix you need to have your computer set up, but in order to set up your computer you need to know a few things about Unix. If you don't have much experience with Unix, we strongly suggest that you look through Chapter 4 and Chapter 5 before you set up a Linux workstation of your own. If you're already familiar with the ins and outs of Unix, feel free to skip ahead to Chapter 6.
You are probably accustomed to working with personal computers; you may be familiar with windows interfaces, word processors, and even some data-analysis packages. But if you want to use computers as a serious component in your research, you need to work on computer systems that run under Unix or related multiuser operating systems.
Computer hardware without an operating system is like a dead animal. It isn't going to react, it isn't going to function; it's just going to sit there and look at you with glassy eyes until it rots (or rusts). The operating ...