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Bash

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Bash is the most common programming language in a Unix-like environment these days. More importantly, bash is very likely the most foundational skillset you can learn for bioinformatics (and much more). Below is a table of some quick terminology for some help in what is meant by terms like “bash” and “Unix”. An introduction to bash can be found here. And if you would like some help getting a bash environment up and running on your computer, check out this page 🙂

Some terminology

Here are some terms that are often used interchangeably – not because it’s important to remember them or any differences (it’s not for most of us), but just to have them laid out somewhere.

Term What it is
shell what we use to talk to the computer; anything where you are pointing and clicking with a mouse is a Graphical User Interface (GUI) shell; something with text only is a Command Line Interface (CLI) shell
command line a text-based environment capable of taking input and providing output
Unix a family of operating systems
bash the most common programming language used at a Unix command-line




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