Abstract: A protocol record database is used in conjunction with operating a centrifuge device. Each protocol record includes information relevant to the centrifugation of a certain specimen. The user can search the database for a protocol on the basis of the specimen and/or the type of separation desired. The database has an interface to one or more centrifuges via a controller. The controller, operates a centrifuge in accordance with the run program of a selected protocol record. In a preferred embodiment, the protocol records have links to additional files which supplement the information contained in the protocol records. These supplemental files include information related to the availability and compatibility of the various hardware needed to perform a centrifugation. The supplemental files can also be used to provide general information to assist the user in setting up a centrifuge for an experiment.