This book provides a broad, integrative overview of systems biology, giving particular attention to functional modeling, analysis, and experimental testing of protein circuits. It begins at the fundamental building blocks of a cell, introducing the underpinnings from thermodynamics and statistical mechanics, and then addresses biochemical networks. The author focuses on giving students the practical toolkit necessary for work in this field, from model estimation to predictive modeling and beyond. Among the key topics discussed in depth are gene transcription, signal transduction, metabolism, synthetic biology, and systems physiology.