Abstract: A system and method of operating a centrifuge is disclosed. The operational parameters of the centrifuge are determined on the basis of the experimental protocol selected by the user. Parameters relevant to the particular experimental protocol are supplied by the user, while the run-time operating parameters of the centrifuge are automatically computed by the system. The centrifugal protocols contemplated in the present invention include pelleting, rate-zonal and isopycnic experiments. Depending upon the specific experimental protocol, the user must provide certain minimum information such as sedimentation rate and gradient concentrations used in the experiment. The user also must identify the rotor to be used, unless the centrifuge device is capable of identifying the rotor automatically. For unusual situations, the user may set the specific operating parameters of a centrifugal run in order to provide for customized experiments.