Linux

The Linux operating systems are fundamental to the world of scientific computing. Almost all major scientific tools across all scientific disciplines are developed and maintained in Linux. Scientists routinely execute their tools and analyses in a Linux environment. Part of this is because Linux is a solidly engineered operating system, is robust, and free. At Salis Lab we always adhere to the most cutting edge tools, and thus must conform to the Linux philosophy or open-source software and wide-spread collaboration.

In this part of the book, we introduce you how to install a Linux OS and how to use the BASH (Bourne-Again Shell) to perform basic tasks. These will include creating (C), reading (R), updating (U) and deleting (D) (collecively termed as CRUD operations) files and directories and navigating the file system. We will also demonstrate how to install some basic programs that will be immediately useful to you in your lab-work (for example, a modern text-editor). Finally, most of the open-sourced (or closed-sourced) software and analyses are usually stored in websites like GitHub that use the git protocol. For example, all of our code including this gitbook is hosted on GitHub. So, we will demonstrate how to use the git version control system to download a git repository and keep it updated from using our Private-Code hosted on GitHub as an example.