The book is devoted to the design and analysis of biomolecular circuits as considered in systems biology and synthetic biology – two very dynamic and promising fields of research. Combining expertise and know-how from the biological and physical sciences with computer science, mathematics and engineering, their potential to impact society is only limited by the imagination of those working in the fields. Synthetic biology promises to introduce new bio-therapeutic, bio-remediation, and bio-sensing applications. For example, synthesizing bacteria to seek out and destroy cancer cells, grass that glows red if planted on top of a land mine, cells that perform arithmetic operations, and small organisms that detect and remove heavy metals from the world’s most dangerous drinking water. These systems are all possible by introducing key concepts in the way we abstract and standardize the process by which biological systems are developed. The book is organized around four general thematic areas: A. Analysis and Simulation B. Modularity and Abstraction C. Design and Standardization D. Enabling Technologies Drawing parallels to electronic circuit design the chosen organization of the book indicate are the important necessary steps to build complex synthetic circuits. Based on an appropriate mathematical formalism of how to describe, analyze and simulate basic cellular processes one can start to abstract away part of this overwhelming complexity (Part A). Abstraction and the clear definition of functional entities or modules that can be composed is the crucial step toward large-scale integration (Part B). If well-defined building blocks with well defined interfaces are in place, standards can be created and the in silico design process can be automated (Part C). The concluding theme of the book discusses the experimental feasibility of the corresponding in vivo design and analysis process (Part D).