Methods in Molecular Biology

Modeling Biomolecular Site Dynamics

Methods and Protocols

Editors: Hlavacek, William S. (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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eBook $169.00
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  • ISBN 978-1-4939-9102-0
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Hardcover $219.99
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  • ISBN 978-1-4939-9100-6
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About this book

This volume covers a variety of topics related to the practice of rule-based modeling, a type of mathematical modeling useful for studying biomolecular site dynamics. There is an emphasis on software tools and detailed descriptions of techniques. The chapters in this book discuss topics such as software tools and frameworks for compartmental modeling (Pycellerator, RuleBuilder, Prgy, rxncon, MSMB, and ML-Rules); tools for spatial modeling (Simmune, Smoldyn, MCell-R, SRSim, and CellOrganizer); rule-based models to analyze proteomic data; model annotation; Markov chain aggregation; BioJazz; and methods to identify model parameters (Data2Dynamics, RKappa, and BioNetFit). Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary resources, step-by-step, readily reproducible protocols, and tips on troubleshooting and avoiding known pitfalls.

Cutting-edge and thorough, Modeling Biomolecular Site Dynamics: Methods and Protocols is a valuable resource for both the novice and expert rule-based modeler. It will also appeal to systems biologists and help them enhance their studies with easy-to-read and write rule-based models.

Table of contents (18 chapters)

Table of contents (18 chapters)
  • A Pycellerator Tutorial

    Shapiro, Bruce E. (et al.)

    Pages 1-32

  • Using RuleBuilder to Graphically Define and Visualize BioNetGen-Language Patterns and Reaction Rules

    Suderman, Ryan (et al.)

    Pages 33-42

  • Strategy-Driven Exploration for Rule-Based Models of Biochemical Systems with Porgy

    Andrei, Oana (et al.)

    Pages 43-70

  • Using rxncon to Develop Rule-Based Models

    Romers, Jesper (et al.)

    Pages 71-118

  • Efficiently Encoding Complex Biochemical Models with the Multistate Model Builder (MSMB)

    Palmisano, Alida (et al.)

    Pages 119-139

Buy this book

eBook $169.00
price for USA in USD (gross)
  • ISBN 978-1-4939-9102-0
  • Digitally watermarked, DRM-free
  • Included format: EPUB, PDF
  • ebooks can be used on all reading devices
  • Immediate eBook download after purchase
Hardcover $219.99
price for USA in USD
  • ISBN 978-1-4939-9100-6
  • with online files
  • Free shipping for individuals worldwide
  • Usually dispatched within 3 to 5 business days.
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Bibliographic Information

Bibliographic Information
Book Title
Modeling Biomolecular Site Dynamics
Book Subtitle
Methods and Protocols
Editors
  • William S. Hlavacek
Series Title
Methods in Molecular Biology
Series Volume
1945
Copyright
2019
Publisher
Humana Press
Copyright Holder
Springer Science+Business Media, LLC, part of Springer Nature
eBook ISBN
978-1-4939-9102-0
DOI
10.1007/978-1-4939-9102-0
Hardcover ISBN
978-1-4939-9100-6
Series ISSN
1064-3745
Edition Number
1
Number of Pages
XIX, 423
Number of Illustrations
80 b/w illustrations, 108 illustrations in colour
Topics