During the past decade, we have witnessed the emergence of a new era in biology. Driven largely by advances in high-throughput technologies and computational power, biologists today can collect data and measurements on a scale and complexity level unimaginable until recently. With the new era, biology is now becoming an information and engineering science that will rely not only on the fundamental organizational principles, but also on predictive modeling. Previous efforts to attract students with diverse training backgrounds were successful, creating a multidisciplinary environment. However, the complexity of the challenges ahead will require that students integrate perspectives from different disciplines to synthesize completely new approaches, rather than working within their own silos. This process of achieving true interdisciplinary training, where the boundaries of traditional disciplines are blurred, or removed altogether, requires a new approach to graduate education. To meet this challenge, we have developed a comprehensive interdisciplinary program for training students in the understanding and engineering of complex biological systems. The Integrative Program in Complex Biological Systems (ipCBS) departs significantly from a traditional curriculum. Built on an entirely new foundation focused on the observation, modeling, and manipulation of complex biological systems, the ipCBS represents a novel approach to solve the critical sociological and linguistic problems associated with training scientists to be simultaneously conversant in the languages of biology, mathematics, physics, and engineering.