TitleDizzy: stochastic simulation of large-scale genetic regulatory networks.
Publication TypeJournal Article
Year of Publication2005
AuthorsRamsey, SA, Orrell, D, Bolouri, H
JournalJ Bioinform Comput Biol
Volume3
Issue2
Pagination415-36
Date Published2005 Apr
ISSN0219-7200
KeywordsAlgorithms, Cell Physiological Phenomena, Computer Simulation, Gene Expression Regulation, Kinetics, Models, Biological, Models, Statistical, Multienzyme Complexes, Proteins, Signal Transduction, Software, Stochastic Processes, User-Computer Interface
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.
DOI10.1142/s0219720005001132
Alternate JournalJ Bioinform Comput Biol
PubMed ID15852513
Grant List10830302 / / PHS HHS / United States