A method and system for creating a protocol dependent control path for instrument applications. In a representative embodiment, identifications of a client, of an instrument application, of a client specific protocol, and of an application specific protocol are obtained. The client is configured to invoke the application and to communicate using the client specific protocol. The application is configured to communicate using the application specific protocol. Then a control path between the client and the application is automatically created. In another representative embodiment, a system for creating the protocol dependent control path for instrument applications includes a management logic module configured to obtain identification of the client, to obtain identification of the instrument application, to obtain identification of the client specific protocol, to obtain identification of the application specific protocol, and to automatically create the control path between the client and the application.