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Modeling Biomolecular Site Dynamics: Methods and Protocols

✍ Scribed by William S. Hlavacek

Publisher
Springer New York; Humana
Year
2019
Tongue
English
Leaves
435
Series
Methods in Molecular Biology 1945
Edition
1st ed.
Category
Library
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✦ Synopsis

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

Front Matter ....Pages i-xix
A Pycellerator Tutorial (Bruce E. Shapiro, Eric Mjolsness)....Pages 1-32
Using RuleBuilder to Graphically Define and Visualize BioNetGen-Language Patterns and Reaction Rules (Ryan Suderman, G. Matthew Fricke, William S. Hlavacek)....Pages 33-42
Strategy-Driven Exploration for Rule-Based Models of Biochemical Systems with Porgy (Oana Andrei, Maribel Fernández, Hélène Kirchner, Bruno Pinaud)....Pages 43-70
Using rxncon to Develop Rule-Based Models (Jesper Romers, Sebastian Thieme, Ulrike Münzner, Marcus Krantz)....Pages 71-118
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
Multi-Level Modeling and Simulation of Cellular Systems: An Introduction to ML-Rules (Tobias Helms, Tom Warnke, Adelinde M. Uhrmacher)....Pages 141-160
Using Python for Spatially Resolved Modeling with Simmune (Bastian R. Angermann, Martin Meier-Schellersheim)....Pages 161-177
Rule-Based Modeling Using Wildcards in the Smoldyn Simulator (Steven S. Andrews)....Pages 179-202
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
Spatial Rule-Based Simulations: The SRSim Software (Richard Henze, Gerd Grünert, Bashar Ibrahim, Peter Dittrich)....Pages 231-249
CellOrganizer: Learning and Using Cell Geometries for Spatial Cell Simulations (Timothy D. Majarian, Ivan Cao-Berg, Xiongtao Ruan, Robert F. Murphy)....Pages 251-264
Using Mechanistic Models for Analysis of Proteomic Data (Lily A. Chylek)....Pages 265-270
Annotations for Rule-Based Models (Matteo Cavaliere, Vincent Danos, Ricardo Honorato-Zimmer, William Waites)....Pages 271-296
Markov Chain Aggregation and Its Application to Rule-Based Modelling (Tatjana Petrov)....Pages 297-313
In Silico Evolution of Signaling Networks Using Rule-Based Models: Bistable Response Dynamics (Song Feng, Orkun S. Soyer)....Pages 315-339
Recipes for Analysis of Molecular Networks Using the Data2Dynamics Modeling Environment (Bernhard Steiert, Clemens Kreutz, Andreas Raue, Jens Timmer)....Pages 341-362
RKappa: Software for Analyzing Rule-Based Models (Anatoly Sorokin, Oksana Sorokina, J. Douglas Armstrong)....Pages 363-390
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
Back Matter ....Pages 421-423

✦ Subjects

Life Sciences; Bioinformatics; Biomedical Engineering/Biotechnology

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