S. Ramsey, D. Orrell, H. Bolouri
tlooto Summary
Dizzy, a software tool for stochastically and deterministically modeling the spatially homogeneous kinetics of integrated large-scale genetic, metabolic, and signaling networks, is described.
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.
Citation format
RAMSEY, S.; ORRELL, D.; BOLOURI, H. Dizzy: Stochastic simulation of large-scale genetic regulatory networks. JOURNAL OF BIOINFORMATICS AND COMPUTATIONAL BIOLOGY, 2005, 3 2: 415–36.