A little bit about the Linux/Unix command line
First of all, let me tell you about the working environment I will use for this data analyis series. I have a laptop with a 4 core Intel processor and 2*4G RAM. I use 64-bit Ubuntu (version 13.04 to be exact).
Several open source bioinformatics tools are Linux/Unix only and if you’re not a Linux user, you can try some Linux terminal-like environments within your current operation system: check out CygWin, if you’re a Windows user. Mac supposedly has a native bash environment, but to tell you the truth, I don’t really have any experience with that.