Dizzy: stochastic simulation of large-scale genetic regulatory networks |
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Authors: | Ramsey Stephen Orrell David Bolouri Hamid |
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Affiliation: | Institute for Systems Biology, 1441 North 34th Street, Seattle, Washington 98103-8904, USA. |
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Abstract: | We describe Dizzy, a software tool for stochastically and deterministically modeling the spatially homogeneous kinetics of integrated large-scale genetic, metabolic, and signaling networks. Notable features include a modular simulation framework, reusable modeling elements, complex kinetic rate laws, multi-step reaction processes, steady-state noise estimation, and spatial compartmentalization. |
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