Highlighting modeling, analysis, and design methods for systems biology, this book discusses how to examine experimental data to learn about mathematical models, develop efficient abstraction and simulation methods to analyze these models, and use analytical methods to design new circuits. It reviews basic molecular biology and biochemistry principles, covers several methods for modeling and analyzing genetic circuits, and uses phage lambda as an example throughout. It also explores the emerging area of synthetic biology. iBioSim software, lecture slides, and a password-protected solutions manual are available on the author’s website.