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Inherent Dynamics Visualizer, an Interactive Application for Evaluating and Visualizing Outputs from a Gene Regulatory Network Inference Pipeline
Published on: December 7, 2021
Dizzy: stochastic simulation of large-scale genetic regulatory networks
Stephen Ramsey1, David Orrell, Hamid Bolouri
1Institute for Systems Biology, 1441 North 34th Street, Seattle, Washington 98103-8904, USA.
Journal of Bioinformatics and Computational Biology
|April 27, 2005
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.
