Modeling Biomolecular Site Dynamics by William S. Hlavacek
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Modeling Biomolecular Site Dynamics

Modeling Biomolecular Site Dynamics


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About the Book

Preface...Foreword...Table of Contents...Contributing Authors...
1. A Pycellerator TutorialBruce E. Shapiro and Eric Mjolsness
2. Using RuleBuilder to Graphically Define and Visualize BioNetGen-Language Patterns and Reaction RulesRyan Suderman, G. Matthew Fricke, and William S. Hlavacek
3. Strategy-Driven Exploration for Rule-Based Models of Biochemical Systems with PORGYOana Andrei, Maribel Fernández, Hélène Kirchner, and Bruno Pinaud
4. Using rxncon to Develop Rule-Based ModelsJesper Romers, Sebastian Thieme, Ulrike Münzner, and Marcus Krantz
5. 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 and Clifford A. Shaffer
6. Multi-Level Modeling and Simulation of Cellular Systems: An Introduction to ML-RulesTobias Helms, Tom Warnke, and Adelinde M. Uhrmacher
7. Using Python for Spatially Resolved Modeling with SimmuneBastian R. Angermann and Martin Meier-Schellersheim
8. Rule-Based Modeling using Wildcards in the Smoldyn SimulatorSteven S. Andrews
9. MCell-R: A Particle-Resolution Network-Free Spatial Modeling FrameworkJose-Juan Tapia, Ali Sinan Saglam, Jacob Czech, Robert Kuczewski, Thomas M. Bartol, Terrence J. Sejnowski, and James R. Faeder
10. Spatial Rule-Based Simulations: the SRSim SoftwareRichard Henze, Gerd Grünert, Bashar Ibrahim, and Peter Dittrich
11. CellOrganizer: Learning and Using Cell Geometries for Spatial Cell SimulationsTimothy D. Majarian, Ivan Cao-Berg, Xiongtao Ruan, and Robert F. Murphy
12. Using Mechanistic Models for Analysis of Proteomic DataLily A. Chylek
13. Annotations for Rule-Based ModelsMatteo Cavaliere, Vincent Danos, Ricardo Honorato-Zimmer, and William Waites
14. Markov Chain Aggregation and Its Application to Rule-Based ModellingTatjana Petrov
15. In Silico Evolution of Signaling Networks Using Rule-Based Models: Bistable Response DynamicsSong Feng and Orkun S. Soyer
16. Recipes for Analysis of Molecular Networks Using the Data2Dynamics Modeling EnvironmentBernhard Steiert, Clemens Kreutz, Andreas Raue, and Jens Timmer
17. RKappa: Software for Analyzing Rule-Based Models
Anatoly Sorokin, Oksana Sorokina, and J. Douglas Armstrong
18. A Step-by-Step Guide to Using BioNetFitWilliam S. Hlavacek, Jennifer Longo, Lewis R. Baker, María del Carmen Ramos Álamo, Alexander Ionkov, Eshan D. Mitra, Ryan Suderman, Keesha E. Erickson, Raquel Dias, Joshua Colvin, Brandon R. Thomas, and Richard G. Posner


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Product Details
  • ISBN-13: 9781493991006
  • Publisher: Humana Press
  • Publisher Imprint: Humana Press
  • Height: 254 mm
  • No of Pages: 423
  • Series Title: Methods in Molecular Biology
  • Sub Title: Methods and Protocols
  • Width: 178 mm
  • ISBN-10: 1493991000
  • Publisher Date: 04 Apr 2019
  • Binding: Hardback
  • Language: English
  • Returnable: Y
  • Spine Width: 25 mm
  • Weight: 1033 gr


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