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Modeling Biomolecular Site Dynamics

Methods and Protocols

  • Book
  • © 2019

Overview

Editors:
  1. William S. Hlavacek

    1. Theoretical Biology and Biophysics Group, Theoretical Division, Los Alamos National Laboratory, Los Alamos, USA

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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

Part of the book series: Methods in Molecular Biology (MIMB, volume 1945)

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Table of contents (18 protocols)

  1. Front Matter

    Pages i-xix
    Download chapter PDF

  2. A Pycellerator Tutorial

    • Bruce E. Shapiro, Eric Mjolsness
    Pages 1-32

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

    • Ryan Suderman, G. Matthew Fricke, William S. Hlavacek
    Pages 33-42

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

    • Oana Andrei, Maribel Fernández, Hélène Kirchner, Bruno Pinaud
    Pages 43-70

  5. Using rxncon to Develop Rule-Based Models

    • Jesper Romers, Sebastian Thieme, Ulrike Münzner, Marcus Krantz
    Pages 71-118

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

    • Alida Palmisano, Stefan Hoops, Layne T. Watson, Thomas C. Jones Jr, John J. Tyson, Clifford A. Shaffer
    Pages 119-139

  7. Multi-Level Modeling and Simulation of Cellular Systems: An Introduction to ML-Rules

    • Tobias Helms, Tom Warnke, Adelinde M. Uhrmacher
    Pages 141-160

  8. Using Python for Spatially Resolved Modeling with Simmune

    • Bastian R. Angermann, Martin Meier-Schellersheim
    Pages 161-177

  9. Rule-Based Modeling Using Wildcards in the Smoldyn Simulator

    • Steven S. Andrews
    Pages 179-202

  10. MCell-R: A Particle-Resolution Network-Free Spatial Modeling Framework

    • Jose-Juan Tapia, Ali Sinan Saglam, Jacob Czech, Robert Kuczewski, Thomas M. Bartol, Terrence J. Sejnowski et al.
    Pages 203-229

  11. Spatial Rule-Based Simulations: The SRSim Software

    • Richard Henze, Gerd Grünert, Bashar Ibrahim, Peter Dittrich
    Pages 231-249

  12. CellOrganizer: Learning and Using Cell Geometries for Spatial Cell Simulations

    • Timothy D. Majarian, Ivan Cao-Berg, Xiongtao Ruan, Robert F. Murphy
    Pages 251-264

  13. Using Mechanistic Models for Analysis of Proteomic Data

    • Lily A. Chylek
    Pages 265-270

  14. Annotations for Rule-Based Models

    • Matteo Cavaliere, Vincent Danos, Ricardo Honorato-Zimmer, William Waites
    Pages 271-296

  15. Markov Chain Aggregation and Its Application to Rule-Based Modelling

    • Tatjana Petrov
    Pages 297-313

  16. In Silico Evolution of Signaling Networks Using Rule-Based Models: Bistable Response Dynamics

    • Song Feng, Orkun S. Soyer
    Pages 315-339

  17. Recipes for Analysis of Molecular Networks Using the Data2Dynamics Modeling Environment

    • Bernhard Steiert, Clemens Kreutz, Andreas Raue, Jens Timmer
    Pages 341-362

  18. RKappa: Software for Analyzing Rule-Based Models

    • Anatoly Sorokin, Oksana Sorokina, J. Douglas Armstrong
    Pages 363-390

  19. A Step-by-Step Guide to Using BioNetFit

    • William S. Hlavacek, Jennifer A. Csicsery-Ronay, Lewis R. Baker, María del Carmen Ramos Álamo, Alexander Ionkov, Eshan D. Mitra et al.
    Pages 391-419

  20. Back Matter

    Pages 421-423
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Keywords

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.


Editors and Affiliations

  • Theoretical Biology and Biophysics Group, Theoretical Division, Los Alamos National Laboratory, Los Alamos, USA

    William S. Hlavacek

Bibliographic Information

  • Book Title: Modeling Biomolecular Site Dynamics

  • Book Subtitle: Methods and Protocols

  • Editors: William S. Hlavacek

  • Series Title: Methods in Molecular Biology

  • DOI: https://doi.org/10.1007/978-1-4939-9102-0

  • Publisher: Humana New York, NY

  • eBook Packages: Springer Protocols

  • Copyright Information: Springer Science+Business Media, LLC, part of Springer Nature 2019

  • Hardcover ISBN: 978-1-4939-9100-6Published: 04 April 2019

  • eBook ISBN: 978-1-4939-9102-0Published: 03 April 2019

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 1

  • Number of Pages: XIX, 423

  • Number of Illustrations: 80 b/w illustrations, 108 illustrations in colour

  • Topics: Bioinformatics, Biomedical Engineering/Biotechnology

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