Operating systems for bioinformaticians

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Picture yourself, a freshman with a laptop but without an idea on how you will be using it. Picture now, your laptop as a book full of empty pages ready to hold inside the best of the stories; your path on the way to becoming a bioinformatician.

As in every good story, we must provide some context, some place where all the events are going to take place; the operating system. The operating system is the bridge between your computer and you; it will store all your programs and coordinate all your actions within it. As bioinformaticians use the shell as a good writer the ink, Ubuntu – one of the several, and the more user-friendly operating systems Linux has – will be installed into your laptop on the first day. Afterwards, you will spend three more days only installing software you don’t know in order to do unknown things; consider then the several chapters your book has.

The first chapter is named Statistics, statistics and more statistics. Statistical processes are one of the bases of bioinformatics. Rstudio is the first character of your story. Using R as a programming language, this software will help you on all the data processing from the statistical point of view. It is supplied with a collection of functions that will make the work easier for you. Besides the statistical computing, this program also helps with the visual analysis and graphic display of the results you have obtained after the hard work. You can think of Rstudio as the white knight that helps you through the battle. Furthermore, this software has a package named knitr that lets you create Markdown documents. Markdown – that uses plain-text – lets you create documents and reports integrating different languages and engines such as LaTeX.

Programming with different editors is the second chapter and where all the magic takes place. There are loads of code editors; Geany, Kate, Vim or Visual Code among others. In this epic story, these software are some of the wise men that will help you solve the puzzles you will have to face. Each of these programs has unique characteristics that differentiate them and makes it easier for you to work with the programming languages Python or C++. Which one is the best? Which one fits your needs? Which one will be the chosen one to go along with you in this journey? That depends exclusively on you and your evolution as a programmer. For instance, Visual Code will guide you as you create your program by showing your mistakes or by suggesting you what to write whereas on Vim you don’t get any help. In addition, Visual Code has its own interface while in order to work with Vim you need to do it through the terminal. In between these two programs we can find Geany, which will show you the mistakes you are making but won’t make any suggestions.

The final chapter is called Take a closer look. In this chapter the main character is PyMOL.  Think of PyMOL as an alchemist; a software that will let you visualize the 3D structures of different proteins, nucleic acids, small molecules, electron densities and much more. Its power does not end on the visualization but it extends to the edition of these molecules you are using letting you comprehend how it works and becomes very useful when trying to design drugs; but not being satisfied with all these features, it also enables you to make animations of the whole workflow and more.

These are just a few of the several programs you will be using, not only while studying but during your whole life as a bioinformatician. And now that you know a little bit more about the tools you have in your computer and what they are used for, you must recall that as in every good story it does not end here, this is just a “to be continued”.

Disclaimer: Everything above is thought to be used in Linux, but it can also be done with a macOS.