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PMID: 15852513 Published · ppublish English Evaluation Study Journal Article Research Support, N.I.H., Extramural Research Support, U.S. Gov't, P.H.S.

Dizzy: stochastic simulation of large-scale genetic regulatory networks.

Journal of bioinformatics and computational biology ·Vol. 3 ·No. 2 ·2005-04-00 ·Pages 415-36

Ramsey S, Orrell D, Bolouri H

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.

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

Chemicals

Multienzyme Complexes Proteins

Authors & Affiliations

3 authors, click to expand affiliations / ORCID

Ramsey Stephen

Institute for Systems Biology, 1441 North 34th Street, Seattle, Washington 98103-8904, USA.

Orrell David

Bolouri Hamid

Article Info

Journal

Journal of bioinformatics and computational biology

Abbr.

J Bioinform Comput Biol

ISSN

0219-7200

DOI

10.1142/s0219720005001132

Published

2005-04-00

Pages

415-36

Language

English

Region

Singapore

NLM ID

101187344

Subset

Grants

PHS HHS · 10830302 · United States

External Links

PubMed source DOI: 10.1142/s0219720005001132 View journal details

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