Advances in biomedical research require a new generation of researchers having a strong background in both the life and physical sciences and a knowledge of computational, mathematical, and engineering tools for tackling biological problems. The NIH-NSF Bioengineering and Bioinformatics Summer Institute at the University of Pittsburgh (BBSI @ Pitt; www.ccbb.pitt.edu/bbsi) is a multi-institutional 10-week summer program hosted by the University of Pittsburgh, Duquesne University, the Pittsburgh Supercomputing Center, and Carnegie Mellon University, and is one of nine Institutes throughout the nation currently participating in the NIH-NSF program. Each BBSI focuses on a different area; the BBSI @ Pitt, entitled '' Simulation and Computer Visualization of Biological Systems at Multiple Scales '', focuses on computational and mathematical approaches to understanding the complex machinery of molecular-to-cellular systems at three levels, namely, molecular, subcellular (microphysiological), and cellular. We present here an overview of the BBSI @ Pitt, the objectives and focus of the program, and a description of the didactic training activities that distinguish it from other traditional summer research programs. Furthermore, we also report several challenges that have been identified in implementing such an interdisciplinary program that brings together students from diverse academic programs for a limited period of time. These challenges notwithstanding, presenting an integrative view of molecular-to-system analytical models has introduced these students to the field of computational biology and has allowed them to make an informed decision regarding their future career prospects.