SGN Sim, a Stochastic Genetic Networks Simulator

• Published in: Bioinformatics Vol. 23; no. 6; pp. 777 - 779
• Main Authors: Ribeiro, Andre S., Lloyd-Price, Jason
• Format: Journal Article
• Language: English
• Published: Oxford Oxford University Press 15.03.2007; Oxford Publishing Limited (England)
• Subjects: Algorithms; Biological and medical sciences; Chemical reactions; Computer Simulation; Fundamental and applied biological sciences. Psychology; Gene Expression Regulation - genetics; General aspects; Mathematics in biology. Statistical analysis. Models. Metrology. Data processing in biology (general aspects); Models, Genetic; Models, Statistical; Protein Biosynthesis - genetics; Proteome - genetics; Signal Transduction - genetics; Stochastic Processes; Topology; Transcription, Genetic - genetics; Yeasts; Compartmentalization; Yeast; Stochastic simulation; Perturbation; Gene expression; Scope note; Regulation(control); Chemical reaction; Physical parameter; Network; Genetics; Models; Bioinformatics
• ISSN: 1367-4803; 1367-4811; 1367-4811; 1460-2059
• DOI: 10.1093/bioinformatics/btm004

We present SGNSim, 'Stochastic Gene Networks Simulator', a tool to model gene regulatory networks (GRN) where transcription and translation are modeled 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 modeled 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: SGNSim program, instructions and examples available at www.ucalgary.ca/~aribeiro/SGNtheSim/SGNtheSim.html. Contact: ARibeiro@ucalgary.ca