A new program, ECEP2D, for simulating the one-dimensional (1D) and two-dimensional (2D) patterns of the gel electrophoresis of a protein after it has been digested by one or more enzymes is introduced. With ECEP2D, students can gain deeper insights into gel electrophoresis by performing hands-on simulations. For example, students can visualize how 2D gel electrophoresis can improve resolution over 1D by comparing them side-by-side. Students can watch how different enzymes cut a protein into different fragments, giving rise to different gel patterns; some patterns are less congested than the others. Students can recognize how enzyme digestion can enhance gel electrophoresis to distinguish proteins. For students not having the chance to take biochemistry laboratories, ECEP2D provides a useful simulated learning environment. Instructors can also complement wet-lab experiments with simulations by ECEP2D to introduce more concepts with fewer laboratory hours. ECEP2D is available for free at http://www.umsl.edu/~wongch/software.html.