Introduction in Synthetic Biology

Description

The textbook is based on the lectures of the course “Synthetic Biology” for Master’s students in biology and biotechnology at the Harbin Institute of Technology. The goal of the textbook is to explain how to make mathematical models of synthetic gene circuits that will, later on, drive the circuit implementation in the lab. Concepts such as kinetics, circuit dynamics and equilibria, stochastic and deterministic simulations, parameter analysis and optimization are presented. At the end of the textbook, a chapter contains a description of structural motifs (e.g. positive and negative feedback loops, Boolean gates) that carry out specific functions and can be combined into larger networks. Moreover, several chapters show how to build up (an analyse, where possible) models for synthetic gene circuits with four different open-source software i.e. COPASI, XPPAUT, BioNetGeN, and Parts & Pools-ProMoT. Front Matter ....Pages i-xii Introduction (Mario Andrea Marchisio)....Pages 1-5 Modeling: Choosing a Kinetics (Mario Andrea Marchisio)....Pages 7-28 Modeling at Computer: Getting Started (Mario Andrea Marchisio)....Pages 29-38 Stochastic Modeling (Mario Andrea Marchisio)....Pages 39-52 Stability Analysis: Steady States (Mario Andrea Marchisio)....Pages 53-65 Stability Analysis: Hysteresis and Oscillations (Mario Andrea Marchisio)....Pages 67-83 Toggle Switch: Dynamics and Steady States (Mario Andrea Marchisio)....Pages 85-90 Rule-Based Modeling (Mario Andrea Marchisio)....Pages 91-107 Computational Gene Circuit Design (Mario Andrea Marchisio)....Pages 109-129 Parameter Analysis (Mario Andrea Marchisio)....Pages 131-148 Circuit Analysis with COPASI (Mario Andrea Marchisio)....Pages 149-158 Circuit Motifs (Mario Andrea Marchisio)....Pages 159-183 Back Matter ....Pages 185-187