Abstract: An analysis system utilizes a reagent with a machine-readable label for performing a biological assay on a sample. A scanner reads the label, and generates a scanner signal in response to reading the label. A memory stores a plurality of protocols for the automation of one or more assays performed on one or more samples. A detector generates a detector signal in response to the sample. A controller receives the scanner signal and selecting a corresponding protocol from the plurality of protocols in response to at least the scanner signal. The detector signal is received by the controller and processed into a data set. A user input module facilitates user selection of assay protocol parameters. The user input module is in communication with the controller. A data processing module is in communication with the controller. The data processing module receives the data set and processes the data set according to the protocol.