AbstractCancer is a complex disease that involves multiple types of biological interactions across diverse physical, temporal, and biological scales. This complexity presents substantial challenges for the characterization of cancer biology, and motivates the study of cancer in the context of molecular, cellular, and physiological systems. Computational models of cancer are being developed to aid both biological discovery and clinical medicine. The development of these in silico models is facilitated by rapidly advancing experimental and analytical tools that generate information‐rich, high‐throughput biological data. Statistical models of cancer at the genomic, transcriptomic, and pathway levels have proven effective in developing diagnostic and prognostic molecular signatures, as well as in identifying perturbed pathways. Statistically inferred network models can prove useful in settings where data overfitting can be avoided, and provide an important means for biological discovery. Mechanistically based signaling and metabolic models that apply a priori knowledge of biochemical processes derived from experiments can also be reconstructed where data are available, and can provide insight and predictive ability regarding the behavior of these systems. At longer length scales, continuum and agent‐based models of the tumor microenvironment and other tissue‐level interactions enable modeling of cancer cell populations and tumor progression. Even though cancer has been among the most‐studied human diseases using systems approaches, significant challenges remain before the enormous potential of in silico cancer biology can be fully realized. Copyright © 2009 John Wiley & Sons, Inc.This article is categorized under: Models of Systems Properties and Processes > Cellular Models