Methods in Molecular Biology

Metabolic Network Reconstruction and Modeling

Methods and Protocols

Editors: Fondi, Marco (Ed.)

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  • Includes cutting-edge methods and protocols
  • Provides step-by-step detail essential for reproducible results
  • Contains key notes and implementation advice from the experts
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About this book

This volume looks at the latest methodologies used to study cellular metabolism with in silico approaches. The chapters in this book are divided into 3 parts: part I discusses tools and methods used for metabolic reconstructions and basic constraint-based metabolic modeling (CBMM); Part II explores protocols for the generation of experimental data for metabolic reconstruction and modeling, including transcriptomics, proteomics, and mutant generations; and Part III cover advanced techniques for quantitative modeling of cellular metabolism, including dynamic Flux Balance Analysis and multi-objective optimization. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls.

Cutting-edge and thorough, Metabolic Network Reconstruction and Modeling: Methods and Protocols is a valuable resource for qualified investigators studying cellular metabolism, and novice researchers who want to start working with CBMM.

About the authors

Marco Fondi
Department of Biology
University of Florence
Via Madonna del Piano 6, I-50019 Sesto Fiorentino, Italy
Email: marco.fondi@unifi.it

Table of contents (18 chapters)

Table of contents (18 chapters)
  • Reconstructing High-Quality Large-Scale Metabolic Models with merlin

    Pages 1-36

    Dias, Oscar (et al.)

  • Analyzing and Designing Cell Factories with OptFlux

    Pages 37-76

    Vila├ža, Paulo (et al.)

  • The MONGOOSE Rational Arithmetic Toolbox

    Pages 77-99

    Le, Christopher (et al.)

  • The FASTCORE Family: For the Fast Reconstruction of Compact Context-Specific Metabolic Networks Models

    Pages 101-110

    Pacheco, Maria Pires (et al.)

  • Reconstruction and Analysis of Central Metabolism in Microbes

    Pages 111-129

    Edirisinghe, Janaka N. (et al.)

Buy this book

eBook $109.00
price for USA in USD (gross)
  • ISBN 978-1-4939-7528-0
  • Digitally watermarked, DRM-free
  • Included format: PDF, EPUB
  • ebooks can be used on all reading devices
  • Immediate eBook download after purchase
Hardcover $149.99
price for USA in USD
  • ISBN 978-1-4939-7527-3
  • with online files
  • Free shipping for individuals worldwide
  • Usually dispatched within 3 to 5 business days.
Softcover $139.00
price for USA in USD
  • ISBN 978-1-4939-8511-1
  • Free shipping for individuals worldwide
  • Usually dispatched within 3 to 5 business days.
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Bibliographic Information

Bibliographic Information
Book Title
Metabolic Network Reconstruction and Modeling
Book Subtitle
Methods and Protocols
Editors
  • Marco Fondi
Series Title
Methods in Molecular Biology
Series Volume
1716
Copyright
2018
Publisher
Humana Press
Copyright Holder
Springer Science+Business Media, LLC
eBook ISBN
978-1-4939-7528-0
DOI
10.1007/978-1-4939-7528-0
Hardcover ISBN
978-1-4939-7527-3
Softcover ISBN
978-1-4939-8511-1
Series ISSN
1064-3745
Edition Number
1
Number of Pages
XI, 410
Number of Illustrations
11 b/w illustrations, 92 illustrations in colour
Topics