AbstractThis article describes three interactive software simulations targeted to key domains of modern molecular genetics: genetics, biochemistry, and molecular biology. These simulations allow students to deepen their understanding of key principles in these domains by setting up crosses, designing proteins, and designing genes; the simulations then apply these principles to produce results that the students can interpret. Using this software, students can confront their misconceptions and connect these disciplines in a way that is difficult if not impossible without an interactive environment. We present lab exercises that guide the students as they use the software in a series of activities that begin by introducing the tools and build towards more open inquiry. Preliminary evaluation shows that students enjoy the software and that it promotes active engagement and application of the material. The open‐source Java software and the relevant lab manuals are available free of charge on line.