This paper describes part of a project called Modeling Across the Curriculum which is a large-scale research study in 15 schools across the United States. The specific data presented and discussed here in this paper is based on BioLogica, a hypermodel, interactive environment for learning genetics, which was implemented in multiple classes in eight high schools. BioLogica activities, data logging, and assessments were refined across this series of implementations. All students took a genetics content knowledge pre- and posttests. Traces of students' actions and responses to computer-based tasks were electronically collected (via a "log file" function) and systematically analyzed. An intensive 3-day field test involving 24 middle school students served to refine methods and create narrative profiles of students' learning experiences, outcomes, and interactions with BioLogica. We report on one high school implementation and the field test as self-contained studies to document the changes and the outcomes at different phases of development. A discussion of design changes concludes this paper.