Meta-models are made available to clinical trial protocol designers. A meta-model includes a list of preliminary patient eligibility attributes appropriate for a particular disease category. The protocol designer chooses the appropriate meta-model, and encodes the clinical trial protocol, including eligibility and patient workflow, within the selected meta-model in a protocol database. The resulting protocol database is stored together with databases of other protocols in a library of protocol databases. Sponsors and individual clinical sites have controlled access to the protocols. Study sites make reference to the protocol database in order to perform patient eligibility screening. Once a patient is enrolled into a study, the protocol database indicates to the clinician what workflow tasks are to be performed at each patient visit.