Modeling biological systems using Dynetica--a simulator of dynamic networks

Lingchong You; Apirak Hoonlor; John Yin

doi:10.1093/bioinformatics/btg009

Modeling biological systems using Dynetica--a simulator of dynamic networks

Bioinformatics. 2003 Feb 12;19(3):435-6. doi: 10.1093/bioinformatics/btg009.

Authors

Lingchong You¹, Apirak Hoonlor, John Yin

Affiliation

¹ Division of Chemistry and Chemical Engineering, California Institute of Technology, USA.

PMID: 12584138
DOI: 10.1093/bioinformatics/btg009

Abstract

We present Dynetica, a user-friendly simulator of dynamic networks for constructing, visualizing, and analyzing kinetic models of biological systems. In addition to generic reaction networks, Dynetica facilitates construction of models of genetic networks, where many reactions are gene expression and interactions among gene products. Further, it integrates the capability of conducting both deterministic and stochastic simulations.

Availability and supplementary information: Dynetica 1.0, example models, and the user's guide are available at http://www.its.caltech.edu/~you/Dynetica/Dynetica_page.htm

Publication types

Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

Algorithms*
Computer Simulation*
Kinetics
Models, Biological*
Models, Chemical*
Models, Genetic
Software*
Stochastic Processes