Title :
A symbolic approach to the simulation of biochemical models: application to circadian rhythms
Author :
Fontana, Federico ; Bianco, Luca ; Manca, Vincenzo
Author_Institution :
Dept. of Comput. Sci., Univ. of Verona, Italy
Abstract :
Symbolic rewriting systems are gaining interest as tools for simulating biochemical dynamics. Compared to traditional methods based on differential equations, the symbolic approach allows a straightforward translation of a signal transduction network into a system of rewriting rules capable of describing the network dynamics by means of a proper application of these rules. Coherently with this design approach, our algorithm applies rewriting rules proportionally to the values assumed by specific reaction maps. Such maps are nonlinear functions of the state of the system. Preliminary results obtained using this algorithm in the simulation of a known model of circadian rhythms in Drosophila envision its potential applicability in reproducing complex biochemical networks, such as that presented here.
Keywords :
biochemistry; biology computing; differential equations; molecular biophysics; rewriting systems; simulation; stochastic processes; Drosophila circadian rhythms; biochemical dynamics simulation; biochemical model simulation; complex biochemical networks reproduction; differential equations; network dynamics; nonlinear state functions; rewriting rules system; signal transduction network translation; specific reaction maps; stochastic processes; symbolic approach; symbolic rewriting systems; Algorithm design and analysis; Application software; Biological system modeling; Circadian rhythm; Computational modeling; Computer science; Computer simulation; Differential equations; Evolution (biology); Nonlinear dynamical systems;
Conference_Titel :
Computational Systems Bioinformatics Conference, 2005. Workshops and Poster Abstracts. IEEE
Print_ISBN :
0-7695-2442-7
DOI :
10.1109/CSBW.2005.17
