Nearly every area of modern research in biology and biomedical science is targeted in one way or another on gaining quantitative understanding of the behavior of biochemical systems. Cellular metabolic pathways, genetic regulatory systems, and protein interaction networks represent different examples of biochemical systems that obey a common set of physicochemical laws, and may be analyzed and simulated based on a common set of principles derived from such laws. It is the purpose of this book to introduce and make use of the methods for the analysis and simulation of biochemical systems that lie at the foundation of current and future research in biological and biomedical science.

Computational biology

Since the time of Newton, a key scientific strategy has been to understand physical systems based on their representation in terms of the smallest possible subsystem (i.e., model) that captures the important mechanistic interactions. The influence of gravity in maintaining the earth's orbit about the sun is satisfactorily explained by analyzing the equations of motion representing a universe consisting of two massive bodies; a complete mathematical analysis of the three-body problem remains out of reach. Living biological systems consist of not two, or even two hundred interacting components. Analysis, prediction, and rational manipulation of cellular function requires a mechanistic understanding of physical systems of unimaginable complexity. Thus the computer is an essential tool in helping us to analyze and simulate living systems.