The theoretical grounding for this article is provided by prior research in three areas of study: (1) students’ difficulties of learning authentic science via complex inquiry, (2) software design principles to support inquiry-learning and (2) prior theories about how teachers’ organize their knowledge for teaching. Research from these areas is examined below in order to set the stage for the analysis of instructional design decisions illustrated by a worked-out-example focusing on gel-electrophoresis and the use of a virtual laboratory.