RuleMonkey

Software for stochastic simulation of rule-based models

Joshua Colvin, Michael I. Monine, Ryan N. Gutenkunst, William S. Hlavacek, Daniel D. Von Hoff, Richard G Posner

Research output: Contribution to journalArticle

43 Citations (Scopus)

Abstract

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 needed for the simulation and analysis of rule-based models of biochemical systems.Results: Here, we present a software tool called RuleMonkey, which implements a network-free method for simulation of rule-based models that is similar to Gillespie's method. The method is suitable for rule-based models that can be encoded in BNGL, including models with rules that have global application conditions, such as rules for intramolecular association reactions. In addition, the method is rejection free, unlike other network-free methods that introduce null events, i.e., steps in the simulation procedure that do not change the state of the reaction system being simulated. We verify that RuleMonkey produces correct simulation results, and we compare its performance against DYNSTOC, another BNGL-compliant tool for network-free simulation of rule-based models. We also compare RuleMonkey against problem-specific codes implementing network-free simulation methods.Conclusions: RuleMonkey enables the simulation of rule-based models for which the underlying reaction networks are large. It is typically faster than DYNSTOC for benchmark problems that we have examined. RuleMonkey is freely available as a stand-alone application http://public.tgen.org/rulemonkey. It is also available as a simulation engine within GetBonNie, a web-based environment for building, analyzing and sharing rule-based models.

Original languageEnglish (US)
Article number404
JournalBMC Bioinformatics
Volume11
DOIs
StatePublished - Jul 30 2010

Fingerprint

Stochastic Simulation
Software
Language
Model
Simulation
Reaction Network
Proteins
Specification languages
Molecular interactions
Simulation Methods
Costs and Cost Analysis
Benchmarking
Costs
Molecular Dynamics Simulation
Chemical reactions
Chemical Reaction Networks
Association reactions
Network Dynamics
Model Specification
Engines

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Biology
  • Computer Science Applications
  • Structural Biology
  • Applied Mathematics

Cite this

Colvin, J., Monine, M. I., Gutenkunst, R. N., Hlavacek, W. S., Von Hoff, D. D., & Posner, R. G. (2010). RuleMonkey: Software for stochastic simulation of rule-based models. BMC Bioinformatics, 11, [404]. https://doi.org/10.1186/1471-2105-11-404

RuleMonkey : Software for stochastic simulation of rule-based models. / Colvin, Joshua; Monine, Michael I.; Gutenkunst, Ryan N.; Hlavacek, William S.; Von Hoff, Daniel D.; Posner, Richard G.

In: BMC Bioinformatics, Vol. 11, 404, 30.07.2010.

Research output: Contribution to journalArticle

Colvin, J, Monine, MI, Gutenkunst, RN, Hlavacek, WS, Von Hoff, DD & Posner, RG 2010, 'RuleMonkey: Software for stochastic simulation of rule-based models', BMC Bioinformatics, vol. 11, 404. https://doi.org/10.1186/1471-2105-11-404
Colvin, Joshua ; Monine, Michael I. ; Gutenkunst, Ryan N. ; Hlavacek, William S. ; Von Hoff, Daniel D. ; Posner, Richard G. / RuleMonkey : Software for stochastic simulation of rule-based models. In: BMC Bioinformatics. 2010 ; Vol. 11.
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