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.
mathematical models cellular regulatory systems rule-based modeling spatial modeling genetic programming compartmental modeling spatial modeling proteomics Markov chain aggregation model parameters
Editors and affiliations
- DOI https://doi.org/10.1007/978-1-4939-9102-0
- Copyright Information Springer Science+Business Media, LLC, part of Springer Nature 2019
- Publisher Name Humana Press, New York, NY
- eBook Packages Springer Protocols
- Print ISBN 978-1-4939-9100-6
- Online ISBN 978-1-4939-9102-0
- Series Print ISSN 1064-3745
- Series Online ISSN 1940-6029
- Buy this book on publisher's site