Preface. Foreword. Table of Contents. Contributing Authors. 1. A Pycellerator Tutorial Bruce E. Shapiro and Eric Mjolsness 2. Using RuleBuilder to Graphically Define and Visualize BioNetGen-Language Patterns and Reaction Rules Ryan Suderman, G.
Matthew Fricke, and William S. Hlavacek 3. Strategy-Driven Exploration for Rule-Based Models of Biochemical Systems with PORGY Oana Andrei, Maribel Fernández, Hélène Kirchner, and Bruno Pinaud 4. Using rxncon to Develop Rule-Based Models Jesper 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-Rules Tobias Helms, Tom Warnke, and Adelinde M. Uhrmacher 7. Using Python for Spatially Resolved Modeling with Simmune Bastian R. Angermann and Martin Meier-Schellersheim 8. Rule-Based Modeling using Wildcards in the Smoldyn Simulator Steven S. Andrews 9.
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, and James R. Faeder 10. Spatial Rule-Based Simulations: the SRSim Software Richard Henze, Gerd Grünert, Bashar Ibrahim, and Peter Dittrich 11. CellOrganizer: Learning and Using Cell Geometries for Spatial Cell Simulations Timothy D. Majarian, Ivan Cao-Berg, Xiongtao Ruan, and Robert F. Murphy 12.
Using Mechanistic Models for Analysis of Proteomic Data Lily A. Chylek 13. Annotations for Rule-Based Models Matteo Cavaliere, Vincent Danos, Ricardo Honorato-Zimmer, and William Waites 14. Markov Chain Aggregation and Its Application to Rule-Based Modelling Tatjana Petrov 15. In Silico Evolution of Signaling Networks Using Rule-Based Models: Bistable Response Dynamics Song Feng and Orkun S. Soyer 16. Recipes for Analysis of Molecular Networks Using the Data2Dynamics Modeling Environment Bernhard 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 BioNetFit William 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.