Much of the time the science applications you'll need to use are going to be, to some degree or another, terminal based. You'll type commands in and programs will run, just like computers from the 1970s. The command interpreter which manages this is called a shell, and we use the default Linux shell, bash. We don't expect you to become a shell wizard but you're going to need to gain some degree of familiarity with bash to work efficiently - you will want to review some of these links, or do some Googling of your own:
You should not try to read these in isolation - read them while using a shell alongside to practice!
Other command shells are available - one called tcsh is commonly used within solar physics for historical reasons. Normally if you were going to be using Solarsoft (SSW) you'd be using tcsh but as you'll read in the notes below that's not necessary on our systems.
The Terminal application works much like any other program, and is tabbed so you can have multiple shells running within the same window. The main 'gotcha' in using it is that the usual keyboard commands for things like copy, paste, and new tab (ctrl-c, ctrl-v, ctrl-t) don't apply - they have to be passed to the shell itself since they have special meanings (eg. ctrl-c means 'kill this task' to the shell). Instead you use shift-ctrl-c, shift-ctrl-v, etc. This can be a little jarring at first.