1. A protocol interface system comprising: a dynamic module that specifies a plurality of stages of a protocol, where a selected stage of the plurality of stages includes an instruction and an associated tool for performing said selected stage; a user interface that enables a user to interact with the protocol specified by the module, where the user interface presents the user with the instruction for the selected stage, and enables the user to utilize the associated tool; and a module manager that administers the module, such that the module manager modifies the module based at least in part upon user input received through the user interface.