Every single notebook or desktop or web server is run by an Operating System - the low-level software that communicates with the hardware equipment, including peripherals such as a mouse and a printer, along with any applications that are installed on the system. Any program input using a command line or a Graphical User Interface (GUI) is processed by sending an Application Program Interface (API) request to the Operating System. On a server, every single application runs within the parameters specified by the OS as well - priority, physical memory, processing time, etcetera. This goes for both standard website scripts and server-side software such as a media server. If a virtual server is set up on a physical one, there can be two independent Operating Systems, called guest OS and host OS, so you'll be able to set up a different software environment on a single machine.