Modeling Biomolecular Site Dynamics : Methods and Protocols - Hlavacek, William S.; SpringerLink (Online service) (New York, NY : Springer New York : Imprint: Humana, 2019)
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. .
Keywords: Bioinformatics; Biomedical engineering; Bioinformatics; Biomedical Engineering/Biotechnology.