The first dogma in bioinformatics that I learned is:
“A bioinformatician uses Linux”
and therefore it is necessary to know how to use and move in this operating system.
The most naive of you (as I was at the beginning) will say: “Simple, there is a graphical interface and I move with the mouse. Like Windows on the other hand”.
Well yes, but actually no, it’s more complicated than that. When you want to use Linux you can certainly use the intuitive graphical interface that every OS offers but the most appropriate, quick and fun way to use Linux is through the textual Shell, that is an interface where we can write commands in order to drive the computer to perform actions.
Let me give you a practical example.
Let’s say you are on your Desktop and you want to create a new folder called “Photo”. Well, the novice user presses (even by intuition) the right button of the mouse and a menu appears in which he finds the item “New Folder” and proceeds in this way. But there is a more inclusive way to use Linux. Just right click and open the terminal (“Open new terminal”) and write in the text shell the command mkdir with the argument “Photo” and our new folder is created.
Beyond the fun of directly controlling the computer from the terminal, it is necessary to understand what is the real reason why a data scientist or bioinformatician often uses the terminal for his work. The answer is simple. Many bioinformatics tools that are used during the analyzes are performed thanks to the use of commands that are given directly from the terminal. For example, if I want to align reads obtained by sequencing a genome on a referance genome using the BWA tool, it is necessary to use a command line as follows:
The BWA bioinformatics tool does not have a graphical interface and cannot be operated with a simple mouse click. We must interact with the computer through the terminal and therefore we must know how to use it in the best way.
Unfortunately, work calls me and I don’t have the time to make a course on the basic commands that you need to know to move, orient yourself and use the textual Shell but as usual I leave you below several sources that I also used to study and that can help you to understand these fundamental concepts for a bioinformatician.
In any case, I hope I have made you understand, with this short post, how the use of the terminal and the typical commands of the Shell is a fundamental skill to work in the fantastic world of bioinformatics and more generally of data science.
Bye and see you soon.
- Linux Phrasebook (Scott Granneman) (anche in Italiano)
- The Linux Command Line, 2nd Edition: A Complete Introduction (William Shotts)
- Linux Bible (Christopher Negus)