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Computational Methods in Synthetic Biology

  • Book
  • © 2015

Overview

Editors:
  1. Mario Andrea Marchisio

    1. School of Life Science and Technology, Harbin Institute of Technology, Harbin, China

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  • Gives complete coverage of the computational approaches currently used in Synthetic Biology
  • Provides step-by-step detail essential for reproducible results
  • Contains key notes and implementation advice from the experts

Part of the book series: Methods in Molecular Biology (MIMB, volume 1244)

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Table of contents (17 protocols)

  1. Front Matter

    Pages i-xi
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  2. Component Design

    1. Front Matter

      Pages 1-1
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    2. Computational Protein Design Methods for Synthetic Biology

      • Pablo Carbonell, Jean-Yves Trosset
      Pages 3-21

    3. Computer-Aided Design of DNA Origami Structures

      • Denis Selnihhin, Ebbe Sloth Andersen
      Pages 23-44

    4. Computational Design of RNA Parts, Devices, and Transcripts with Kinetic Folding Algorithms Implemented on Multiprocessor Clusters

      • Tim Thimmaiah, William E. Voje Jr., James M. Carothers
      Pages 45-61

    5. Regulatory RNA Design Through Evolutionary Computation and Strand Displacement

      • William Rostain, Thomas E. Landrain, Guillermo Rodrigo, Alfonso Jaramillo
      Pages 63-78

  3. Circuit Design

    1. Front Matter

      Pages 79-79
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    2. Programming Languages for Circuit Design

      • Michael Pedersen, Boyan Yordanov
      Pages 81-104

    3. Kappa Rule-Based Modeling in Synthetic Biology

      • John Wilson-Kanamori, Vincent Danos, Ty Thomson, Ricardo Honorato-Zimmer
      Pages 105-135

    4. Modular Design of Synthetic Gene Circuits with Biological Parts and Pools

      • Mario Andrea Marchisio
      Pages 137-165

    5. Computationally Guided Design of Robust Gene Circuits

      • Najaf A. Shah, Casim A. Sarkar
      Pages 167-178

    6. Chemical Master Equation Closure for Computer-Aided Synthetic Biology

      • Patrick Smadbeck, Yiannis N. Kaznessis
      Pages 179-191

    7. Feedback Loops in Biological Networks

      • Elisa Franco, Kate E. Galloway
      Pages 193-214

  4. Circuit Analysis and Simulations

    1. Front Matter

      Pages 215-215
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    2. Efficient Analysis Methods in Synthetic Biology

      • Curtis Madsen, Chris Myers, Nicholas Roehner, Chris Winstead, Zhen Zhang
      Pages 217-257

    3. Using Computational Modeling and Experimental Synthetic Perturbations to Probe Biological Circuits

      • Joshua R. Porter, Eric Batchelor
      Pages 259-276

    4. In Silico Control of Biomolecular Processes

      • Jannis Uhlendorf, Agnès Miermont, Thierry Delaveau, Gilles Charvin, François Fages, Samuel Bottani et al.
      Pages 277-285

    5. Stochastic Modular Analysis for Gene Circuits: Interplay Among Retroactivity, Nonlinearity, and Stochasticity

      • Kyung Hyuk Kim, Herbert M. Sauro
      Pages 287-297

  5. Distributed Systems and Automation

    1. Front Matter

      Pages 299-299
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    2. Distributed Model Construction with Virtual Parts

      • Michael T. Cooling, Tommy Yu
      Pages 301-322
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Keywords

About this book

This volume provides complete coverage of the computational approaches currently used in Synthetic Biology.  Chapters focus on computational methods and algorithms for the design of bio-components, insight on CAD programs, analysis techniques, and distributed systems. Written in the highly successful Methods in Molecular Biology series format, the chapters include the kind of detailed description and implementation advice that is crucial for getting optimal results in the laboratory.

 

Authoritative and practical, Computational Methods in Synthetic Biology serves as a guide to plan in silico the in vivo or in vitro construction of a variety of synthetic bio-circuits.

Editors and Affiliations

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

    Mario Andrea Marchisio

Bibliographic Information

  • Book Title: Computational Methods in Synthetic Biology

  • Editors: Mario Andrea Marchisio

  • Series Title: Methods in Molecular Biology

  • DOI: https://doi.org/10.1007/978-1-4939-1878-2

  • Publisher: Humana New York, NY

  • eBook Packages: Springer Protocols

  • Copyright Information: Springer Science+Business Media New York 2015

  • Hardcover ISBN: 978-1-4939-1877-5Published: 09 December 2014

  • Softcover ISBN: 978-1-4939-5380-6Published: 22 September 2016

  • eBook ISBN: 978-1-4939-1878-2Published: 08 December 2014

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 1

  • Number of Pages: XI, 358

  • Number of Illustrations: 93 b/w illustrations, 43 illustrations in colour

  • Topics: Bioinformatics

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