The present invention provides a bar-code driven, completely automated, microplate-based analyzer system for performing chemical, biochemical or biological assays. The analyzer is a modular, bench-top instrument that compactly integrates subsystems for sample dispensing, liquid handling, microplate transport, thermal incubation, vortexing, solid phase separation and optical reading. An internal processor is included for automating the instrument, and a user interface to facilitate communication with the operator via a touch-sensitive liquid-crystal display (LCD), and communicating with a remote network via multiple protocols. The analyzer includes firmware resident within the processing system and the user interface allows the operator to select pre-defined assay batch protocols and the user interface is configured in such as way so as to restrict an operator from programming the firmware.