This book describes the theoretical modeling of a wide variety of biological problems, with the common thread being how to quantitatively describe the intrinsic fluctuations in these systems. Strongly pedagogical in style, the book introduces both analytical and computational methods in biological systems and then applies these methods on three different biological scales - ecological, biochemical, and cellular/developmental. Traditional theoretical biology has tended to ignore fluctuations, using, instead, deterministic models to describe biology. Such models have proven to be useful; however, it is becoming increasingly clear that fluctuations and noise are fundamental in many biological systems. Unlike most other books in the field, this book presents a coherent discussion on how to formulate biological problems in such a way that fluctuations can be quantitatively assessed.