SGN Sim / SGNS2 2.1.170
SGNSim (Stochastic Gene Networks Simulator) is 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.
SGNS2 (Simulator of delayed stochastic genetic circuits. Version 2, which includes transient compartmentalization of reactions)
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Lloyd-Price J, Gupta A, Ribeiro AS.
SGNS2: a compartmentalized stochastic chemical kinetics simulator for dynamic cell populations.
Bioinformatics. 2012 Nov 15;28(22):3004-5. doi: 10.1093/bioinformatics/bts556. Epub 2012 Sep 26. PMID: 23014631.
Andre S. Ribeiro; Jason Lloyd-Price, (2007)
SGN Sim, a Stochastic Genetic Networks Simulator
Bioinformatics, 23(6):777-779. doi:10.1093/bioinformatics/btm004.