4 min to read

Why biologists need to learn BASH?

Unlocking the Full Potential of Bioinformatics with Command Line

In this series, we’ll be exploring the power of Bash commands and most importantly why learning Bash is crucial for Biologists to enter in the realm of Bioinformatics?

What is Bash?

If you’ve seen any movies about hacking, you’re probably familiar with black scenes with green text. The hacker sits at the computer, fingers flying across the keyboard, as lines of code and text scroll rapidly across the screen.

But what exactly is the hacker doing? What is this mysterious text-based interface that they're using?

This interface is known as a Command Line Interface, or CLI for short. It’s a way of interacting with a computer using text commands, rather than a graphical user interface (GUI) like you might be used to. One of the most common types of CLI is Bash.

Why BASH for Biologists?

Well there are so many reasons but I will give you 2 most important reasons.

  1. As biologists, we work with a lot of data - whether it’s genetic sequences, protein structures, or experimental results. And while there are some software tools available to help us analyse this data, however if you want to use the latest and greatest cutting edge open source Bioinformatics tools then learning the basics of BASH can come in handy because most of the latest Bioinformatics tools dont come with Graphical User Interface.
  2. When we are working with big data you have to use supercomputers and it is rather difficult to buy and maintain a supercomputer in your home. So, those super computers are present in specific locations where they can be kept cool and maintained they way they are supposed to be maintained. The good thing is that you can access those supercomputers and run your Bioinformatics Pipelines from the comfort of your laptop just by using BASH. Those supercomputers are generally known as HPC’s.

What and why is HPC?

You might have heard this term HPC. These are known as high-performance computing (HPC) clusters. These clusters are essential for processing large-scale bioinformatics datasets, but they require a solid understanding of Bash commands to navigate and interact with the system because usually they don’t come with a GUI so you have to do all the things by using bash commands. From opening a folder to copying files and running scripts.

Things you can do with BASH

With Bash, you can automate common tasks, manipulate and filter data, and even create your own custom scripts to streamline your workflow. Whether you’re just getting started in bioinformatics or you’re an experienced researcher, understanding Bash commands is a valuable skill that can take your data analysis to the next level.

Next, we’ll learn how you can access bach ot terminal on your machine, be it mac, linux or windows. All different operating systems will be covered. Thanks for your time and will see you next time ;)