Methods of optimizing instruction through the use of course knowledge portrayal methods were studied, based on a series of experiments conducted over 6 years. Sixteen university courses in the sciences, social sciences, and humanities were investigated through the application of cognitive theory to instruction. Attention was first focused on portraying the knowledge structures in the courses. Next, these knowledge structures were used as the basis of research into student learning in the course (i.e., to measure gains in student knowledge and to test the degree to which they predicted course achievement). Current analysis of the knowledge structures using feature analysis and network analysis demonstrated the kinds of analytic processes required to understand the main concepts in the course and the degree of concurrence of relationships within and between concepts. The research is based on cognitive theory applied to instruction. The concept was the unit of analysis; the methods were different forms of conceptual analysis. The application of conceptual portrayal to instruction and to learning is illustrated with reference to a university course. In addition, a taxonomy illustrating relationships between concepts is presented. (Author/SW)