Modeling Biomolecular Site Dynamics

Methods and Protocols

Buch | Hardcover

423 Seiten

2019 | 1st ed. 2019
Humana Press Inc. (Verlag)
978-1-4939-9100-6 (ISBN)

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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.

A Pycellerator Tutorial.- Using RuleBuilder to Graphically Define and Visualize BioNetGen-Language Patterns and Reaction Rules.- Strategy-Driven Exploration for Rule-Based Models of Biochemical Systems with PORGY.- Using rxncon to Develop Rule-Based Models.- Efficiently Encoding Complex Biochemical Models with the Multistate Model Builder (MSMB).- Multi-Level Modeling and Simulation of Cellular Systems: An Introduction to ML-Rules.- Using Python for Spatially Resolved Modeling with Simmune.- Rule-Based Modeling using Wildcards in the Smoldyn Simulator.- MCell-R: A Particle-Resolution Network-Free Spatial Modeling Framework.- Spatial Rule-Based Simulations: the SRSim Software.- CellOrganizer: Learning and Using Cell Geometries for Spatial Cell Simulations.- Using Mechanistic Models for Analysis of Proteomic Data.- Annotations for Rule-Based Models.- Markov Chain Aggregation and Its Application to Rule-Based Modelling.- In Silico Evolution of Signaling Networks Using Rule-Based Models: Bistable Response Dynamics.- Recipes for Analysis of Molecular Networks Using the Data2Dynamics Modeling Environment.- RKappa: Software for Analyzing Rule-Based Models.- A Step-by-Step Guide to Using BioNetFit.

Erscheinungsdatum	19.04.2019
Reihe/Serie	Methods in Molecular Biology ; 1945
Zusatzinfo	108 Illustrations, color; 80 Illustrations, black and white; XIX, 423 p. 188 illus., 108 illus. in color. With online files/update.
Verlagsort	Totowa, NJ
Sprache	englisch
Maße	178 x 254 mm
Themenwelt	Mathematik / Informatik ► Informatik ► Theorie / Studium
	Informatik ► Weitere Themen ► Bioinformatik
	Medizin / Pharmazie ► Physiotherapie / Ergotherapie ► Orthopädie
	Naturwissenschaften ► Biologie ► Genetik / Molekularbiologie
	Technik ► Medizintechnik
	Technik ► Umwelttechnik / Biotechnologie
Schlagworte	cellular regulatory systems • compartmental modeling • genetic programming • Markov chain aggregation • Mathematical Models • Model Parameters • Proteomics • rule-based modeling • spatial modeling
ISBN-10	1-4939-9100-0 / 1493991000
ISBN-13	978-1-4939-9100-6 / 9781493991006
Zustand	Neuware