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Bioinformatics Advance Access published online on January 31, 2007
Bioinformatics, doi:10.1093/bioinformatics/btm004
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© The Author (2007). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

SGN Sim, a Stochastic Genetic Networks Simulator

Andre S. Ribeiro a,b,* and Jason Lloyd-Price a

aInstitute for Biocomplexity and Informatics, University of Calgary, Canada, bCentre for Computational Physics, University of Coimbra, P-3004-516 Coimbra, Portugal

*to whom correspondence should be addressed.Andre Ribeiro, E-mail: ARibeiro{at}ucalgary.ca


  Abstract

Summary: We present SGNSim, "Stochastic Gene Networks Simulator", a tool to model gene regulatory networks (GRN) where transcription and translation are modelled as multiple time delayed events and its dynamics is driven by a stochastic simulation algorithm (SSA) able to deal with multiple time delayed events. The delays can be drawn from several distributions and the reaction rates from complex functions or from physical parameters. SGNSim can generate ensembles of GRNs, within a set of user-defined parameters, such as topology. It can also be used to model specific GRNs and systems of chemical reactions. Perturbations, e.g. gene deletion, over-expression, copy and mutation, can be modelled as well. As examples, we present a model of a toggle switch without cooperative binding subject to perturbations, a system of reactions within a compartmentalized environment where membrane crossing is controlled by a negative feedback mechanism and a simulation based on the yeast transcriptional network.

Availability: The SGNSim program, instructions and examples are available at www.ucalgary.ca/~aribeiro/SGNtheSim/SGNtheSim.html.

Associate Editor: Chris Stoeckert

Received on November 5, 2006; revised on January 4, 2007; accepted on January 10, 2007

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