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  • Textbook
  • © 2018

Introduction to Synthetic Biology

About Modeling, Computation, and Circuit Design

  • Explains how to make mathematical models of synthetic gene circuits
  • Presents concepts such as kinetics, circuit dynamics and equilibria, stochastic and deterministic simulations, parameter analysis and optimization
  • Shows how to build up models for synthetic gene circuits with four different open-source software

Part of the book series: Learning Materials in Biosciences (LMB)

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Table of contents (13 chapters)

  1. Front Matter

    Pages i-xii
  2. Introduction

    • Mario Andrea Marchisio
    Pages 1-5
  3. Modeling: Choosing a Kinetics

    • Mario Andrea Marchisio
    Pages 7-28
  4. Modeling at Computer: Getting Started

    • Mario Andrea Marchisio
    Pages 29-38
  5. Stochastic Modeling

    • Mario Andrea Marchisio
    Pages 39-52
  6. Stability Analysis: Steady States

    • Mario Andrea Marchisio
    Pages 53-65
  7. Stability Analysis: Hysteresis and Oscillations

    • Mario Andrea Marchisio
    Pages 67-83
  8. Toggle Switch: Dynamics and Steady States

    • Mario Andrea Marchisio
    Pages 85-90
  9. Rule-Based Modeling

    • Mario Andrea Marchisio
    Pages 91-107
  10. Computational Gene Circuit Design

    • Mario Andrea Marchisio
    Pages 109-129
  11. Parameter Analysis

    • Mario Andrea Marchisio
    Pages 131-148
  12. Circuit Analysis with COPASI

    • Mario Andrea Marchisio
    Pages 149-158
  13. Circuit Motifs

    • Mario Andrea Marchisio
    Pages 159-183
  14. Correction to: Introduction to Synthetic Biology

    • Mario Andrea Marchisio
    Pages E1-E1
  15. Back Matter

    Pages 185-187

About this book

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.

Authors and Affiliations

  • School of Life Science and Technology, Harbin Institute of Technology, Harbin, China

    Mario Andrea Marchisio

About the author

Mario Andrea Marchisio has obtained his PhD in Physics at the University of Trento, Italy in 2002. After working for four years at the CILEA computing center in Milan, Italy, he spent six years as a Post Doc at the ETH Zurich, Switzerland. Since September 2013, he is working as an Associate Professor in Synthetic Biology at the Harbin Institute of Technology, China.

Bibliographic Information

Buy it now

Buying options

eBook USD 79.99
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book USD 99.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Other ways to access