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Design and Analysis of Biomolecular Circuits

Engineering Approaches to Systems and Synthetic Biology

  • Book
  • © 2011

Overview

Editors:
  1. Heinz Koeppl

    1. , Automatic Control Laboratory, ETH Zurich, Zurich, Switzerland

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  2. Gianluca Setti

    1. ARCES, Università di Bologna, Bologna, Italy

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  3. Mario di Bernardo

    1. Università di Napoli Federico II, Napoli, Italy

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  4. Douglas Densmore

    1. , Department of Electrical and Computer En, Boston University, Boston, USA

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  • Provides thorough overview of state-of-the-art in synthetic and systems biology
  • Applies to biological systems the formal abstraction methods used to cope with complexity of today’s electronic devices
  • First book to discuss the enabling CAD technologies in terms of data acquisition and DNA synthesis
  • Includes supplementary material: sn.pub/extras

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Table of contents (17 chapters)

  1. Front Matter

    Pages i-xiii
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  2. Analysis and Simulation

    1. Front Matter

      Pages 1-1
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  3. Analysis and simulation

    1. Continuous Time Markov Chain Models for Chemical Reaction Networks

      • David F. Anderson, Thomas G. Kurtz
      Pages 3-42

    2. Stochastic Simulation for Spatial Modelling of Dynamic Processes in a Living Cell

      • Kevin Burrage, Pamela M. Burrage, André Leier, Tatiana Marquez-Lago, Dan V. Nicolau Jr
      Pages 43-62

    3. Graph-Theoretic Analysis of Multistability and Monotonicity for Biochemical Reaction Networks

      • Gheorghe Craciun, Casian Pantea, Eduardo D. Sontag
      Pages 63-72

    4. From Structure to Dynamics in Biological Networks

      • Murad Banaji
      Pages 73-92

    5. Contraction Theory for Systems Biology

      • Giovanni Russo, Mario di Bernardo, Jean Jacques Slotine
      Pages 93-114

  4. Modularity and Abstraction

    1. Front Matter

      Pages 115-115
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  5. Modularity and abstraction

    1. Toward Modularity in Synthetic Biology: Design Patterns and Fan-out

      • Kyung Hyuk Kim, Deepak Chandran, Herbert M. Sauro
      Pages 117-138

    2. Retroactivity as a Criterion to Define Modules in Signaling Networks

      • Julio Saez-Rodriguez, Holger Conzelmann, Michael Ederer, Ernst Dieter Gilles
      Pages 139-159

    3. The Impact of Retroactivity on the Behavior of Biomolecular Systems

      • Domitilla Del Vecchio
      Pages 161-181

    4. Modularity, Retroactivity, and Structural Identification

      • Eduardo D. Sontag
      Pages 183-200

  6. Design and Standardization

    1. Front Matter

      Pages 201-201
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  7. Design and standardization

    1. Computer-Aided Design for Synthetic Biology

      • Deepak Chandran, Frank T. Bergmann, Herbert M. Sauro, Douglas Densmore
      Pages 203-224

    2. High-Level Programming Languages for Biomolecular Systems

      • Jacob Beal, Andrew Phillips, Douglas Densmore, Yizhi Cai
      Pages 225-252

    3. Rational Design of Robust Biomolecular Circuits: from Specification to Parameters

      • Marc Hafner, Tatjana Petrov, James Lu, Heinz Koeppl
      Pages 253-279

    4. Data Model Standardization for Synthetic Biomolecular Circuits and Systems

      • Michal Galdzicki, Deepak Chandran, John H. Gennari, Herbert M. Sauro
      Pages 281-293

    5. DNA Assembly Method Standardization for Synthetic Biomolecular Circuits and Systems

      • Nathan J. Hillson
      Pages 295-314

  8. Enabling Technologies

    1. Front Matter

      Pages 315-315
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  9. Enabling technologies

    1. Gene Synthesis – Enabling Technologies for Synthetic Biology

      • Michael Liss, Ralf Wagner
      Pages 317-335
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Keywords

About this book

The book deals with engineering aspects of the two emerging and intertwined fields of synthetic and systems biology. Both fields hold promise to revolutionize the way molecular biology research is done, the way today’s drug discovery works and the way bio-engineering is done. Both fields stress the importance of building and characterizing small bio-molecular networks in order to synthesize incrementally and understand large complex networks inside living cells. Reminiscent of computer-aided design (CAD) of electronic circuits, abstraction is believed to be the key concept to achieve this goal. It allows hiding the overwhelming complexity of cellular processes by encapsulating network parts into abstract modules. This book provides a unique perspective on how concepts and methods from CAD of electronic circuits can be leveraged to overcome complexity barrier perceived in synthetic and systems biology.

Reviews

From the reviews:

“This collection of papers is an excellent reference for anyone who would like to learn more about the engineering and computing side of systems and synthetic biology. … this clear and detailed volume will help to introduce mathematicians, engineers, and computer scientists to an application of their fields in biology. It will also serve biologists who want to know more about how in silico technologies can be an important part of the arsenal used to understand and create biological systems.” (Sara Kalvala, ACM Computing Reviews, June, 2012)

Editors and Affiliations

  • , Automatic Control Laboratory, ETH Zurich, Zurich, Switzerland

    Heinz Koeppl

  • ARCES, Università di Bologna, Bologna, Italy

    Gianluca Setti

  • Università di Napoli Federico II, Napoli, Italy

    Mario di Bernardo

  • , Department of Electrical and Computer En, Boston University, Boston, USA

    Douglas Densmore

Bibliographic Information

  • Book Title: Design and Analysis of Biomolecular Circuits

  • Book Subtitle: Engineering Approaches to Systems and Synthetic Biology

  • Editors: Heinz Koeppl, Gianluca Setti, Mario di Bernardo, Douglas Densmore

  • DOI: https://doi.org/10.1007/978-1-4419-6766-4

  • Publisher: Springer New York, NY

  • eBook Packages: Engineering, Engineering (R0)

  • Copyright Information: Springer Science+Business Media, LLC 2011

  • Hardcover ISBN: 978-1-4419-6765-7

  • Softcover ISBN: 978-1-4899-9505-6

  • eBook ISBN: 978-1-4419-6766-4

  • Edition Number: 1

  • Number of Pages: XIII, 402

  • Topics: Circuits and Systems, Computer-Aided Engineering (CAD, CAE) and Design

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