Title | Dizzy: stochastic simulation of large-scale genetic regulatory networks. |
Publication Type | Journal Article |
Year of Publication | 2005 |
Authors | Ramsey, SA, Orrell, D, Bolouri, H |
Journal | J Bioinform Comput Biol |
Volume | 3 |
Issue | 2 |
Pagination | 415-36 |
Date Published | 2005 Apr |
ISSN | 0219-7200 |
Keywords | Algorithms, 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. |
DOI | 10.1142/s0219720005001132 |
Alternate Journal | J Bioinform Comput Biol |
PubMed ID | 15852513 |
Grant List | 10830302 / / PHS HHS / United States |