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2010

RuleMonkey: software for stochastic simulation of rule-based models

10 years 1 months ago
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...
Joshua Colvin, Michael I. Monine, Ryan N. Gutenkun
Added 09 Dec 2010
Updated 09 Dec 2010
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
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