RuleMonkey: software for stochastic simulation of rule-based models

Background: The system-level dynamics of many molecular interactions, particularly protein-protein interactions, can be conveniently represented using reaction rules, which can be specified using model-specification languages, such as the BioNetGen language (BNGL). A set of rules implicitly defines a (bio)chemical reaction network. The reaction network implied by a set of rules is often very large, and as a result, generation of the network implied by rules tends to be computationally expensive. Moreover, the cost of many commonly used methods for simulating network dynamics is a function of network size. Together these factors have limited application of the rule-based modeling approach. Recently, several methods for simulating rule-based models have been developed that avoid the expensive step of network generation. The cost of these "network-free" simulation methods is independent of the number of reactions implied by rules. Software implementing such methods is now neede...

• Type: Journal
• Year: 2010
• Where: BMCBI
• Authors: Joshua Colvin, Michael I. Monine, Ryan N. Gutenkunst, William S. Hlavacek, Daniel D. Von Hoff, Richard G. Posner
• Keywords: BMCBI 2010, Reaction Network, Rule-based Models, Simulation