ABSTRACT

This text presents the modeling, analysis, and design methods for systems biology. It 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. The author reviews basic molecular biology and biochemistry principles, covers several methods for modeling and analyzing genetic circuits, and uses phage lambda as an example throughout to help illustrate the methods. He 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.

chapter 1|50 pages

An Engineer’s Guide to Genetic Circuits

chapter 2|34 pages

Learning Models

chapter 3|18 pages

Differential Equation Analysis

chapter 4|28 pages

Stochastic Analysis

chapter 5|30 pages

Reaction-Based Abstraction

chapter 6|26 pages

Logical Abstraction

chapter 7|28 pages

Genetic Circuit Design