Unix is an operating system primarily used on servers, but is also the basis for the vast array of Linux distributions and Mac OSX. To manipulate anything (not covered in a graphical program) in a Unix-based operating system, one types commands in the terminal that are interpreted by the shell, and then executed by the kernel. The kernel is the core of a Unix-based OS, and assigns tasks and allocates resources. The shell is the interface between the user and the kernel; it interprets user input.
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