Polynomial algebra of discrete models in systems biology.
BACKGROUND
An increasing number of discrete mathematical models are being published in Systems Biology, ranging from Boolean network models to logical models and Petri nets. They are used to model a variety of biochemical networks, such as metabolic networks, gene regulatory networks and signal transduction networks. There is increasing evidence that such models can capture key dynamic features of biological networks and can be used successfully for hypothesis generation.


RESULTS
This article provides a unified framework that can aid the mathematical analysis of Boolean network models, logical models and Petri nets. They can be represented as polynomial dynamical systems, which allows the use of a variety of mathematical tools from computer algebra for their analysis. Algorithms are presented for the translation into polynomial dynamical systems. Examples are given of how polynomial algebra can be used for the model analysis.


BACKGROUND
alanavc@vt.edu


BACKGROUND
Supplementary data are available at Bioinformatics online.
Veliz-Cuba
Alan
A
Virginia Bioinformatics Institute, Department of Mathematics, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA. alanavc@vt.edu
Jarrah
Abdul Salam
AS
Laubenbacher
Reinhard
R
D000465:Algorithms; D008954:Models, Biological; D015233:Models, Statistical; D049490:Systems Biology