Title :
Constraint-Based Simulation of Biological Systems Described by Molecular Interaction Maps
Author :
Bortolussi, Luca ; Fonda, Simone ; Policriti, Alberto
Author_Institution :
Univ. of Trieste, Trieste
Abstract :
We present a method to simulate biochemical networks described by the graphical notation of Molecular Interaction Maps within stochastic Concurrent Constraint Programming. Such maps are compact, as they represent implicitly a wide set of reactions, and therefore not easy to simulate with standard tools. The encoding we propose is capable to stochastically simulate these maps implicitly, without generating the full list of reactions.
Keywords :
biochemistry; biology computing; constraint handling; encoding; molecular biophysics; stochastic programming; biochemical networks; biological systems; constraint-based simulation; encoding; molecular interaction maps; stochastic concurrent constraint programming; Analytical models; Biological information theory; Biological system modeling; Biological systems; Computational modeling; Computer science; Computer simulation; Encoding; Stochastic processes; Stochastic systems;
Conference_Titel :
Bioinformatics and Biomedicine, 2007. BIBM 2007. IEEE International Conference on
Conference_Location :
Fremont, CA
Print_ISBN :
978-0-7695-3031-4
DOI :
10.1109/BIBM.2007.31
