1. A user configurable instrument comprising: a plurality of analog elements; a plurality of digital elements; a plurality of connection elements between the plurality of analog elements and the plurality of digital elements, wherein a first portion of the plurality of analog elements and the plurality of digital elements receives inputs from one or more sources and wherein a second portion of the plurality of analog elements and the plurality of digital elements generates at least one of output signals for generating control signals and outputs presenting one or more measurements to one or more output receiving elements based on the received inputs; and a configurable graphical user interface system that includes at least one of a processor and a programmable logic device to interface with: a user tree structure that receives one or more input or output functions of the user configurable instrument on one or more graphical user interfaces; and a hidden tree structure that configures at least one of: the plurality of analog elements, a plurality of digital elements, and a plurality of connection elements by connecting elements and defining operating characteristics in response to the one or more functions of the user configurable instrument selected on the one or more graphical user interfaces.