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.
Publication types
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Evaluation Study
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Research Support, N.I.H., Extramural
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Research Support, U.S. Gov't, P.H.S.
MeSH terms
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Algorithms
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Cell Physiological Phenomena*
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Computer Simulation*
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Gene Expression Regulation / physiology*
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Kinetics
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Models, Biological*
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Models, Statistical
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Multienzyme Complexes / metabolism
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Proteins / metabolism*
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Signal Transduction / physiology*
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Software*
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Stochastic Processes
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User-Computer Interface
Substances
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Multienzyme Complexes
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Proteins