The present disclosure provides for modeling a clinical trial study, which may implement a cross-over design. A plurality of treatments is generated for a clinical trial study, based on a first subset of operational parameters. A plurality of sequences is also generated for the clinical trial study, based on a second subset of the operational parameters. Each sequence of the plurality of sequences comprises a combination of ones of the plurality of treatments. A plurality of subject groups is assigned to the plurality of sequences, where one subject group of the plurality of subject groups is respectively assigned to one sequence of the plurality of sequences. The one sequence is administered to subjects of the one subject group during the clinical trial study.