Dizzy: stochastic simulation of large-scale genetic regulatory networks

J Bioinform Comput Biol. 2005 Apr;3(2):415-36. doi: 10.1142/s0219720005001132.

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

  • Evaluation Study
  • Research Support, N.I.H., Extramural
  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Algorithms
  • Cell Physiological Phenomena*
  • Computer Simulation*
  • Gene Expression Regulation / physiology*
  • Kinetics
  • Models, Biological*
  • Models, Statistical
  • Multienzyme Complexes / metabolism
  • Proteins / metabolism*
  • Signal Transduction / physiology*
  • Software*
  • Stochastic Processes
  • User-Computer Interface

Substances

  • Multienzyme Complexes
  • Proteins