Modeling and simulation of molecular biology systems using petri nets: modeling goals of various approaches.
Petri nets are a discrete event simulation approach developed for system representation, in particular for their concurrency and synchronization properties. Various extensions to the original theory of Petri nets have been used for modeling molecular biology systems and metabolic networks. These extensions are stochastic, colored, hybrid and functional. This paper carries out an initial review of the various modeling approaches based on Petri net found in the literature, and of the biological systems that have been successfully modeled with these approaches. Moreover, the modeling goals and possibilities of qualitative analysis and system simulation of each approach are discussed.
Hardy
Simon
S
Computer Engineering Department, Ecole Polytechnique de Montréal, P.B. 6079, succ. Centre-Ville, Montréal, Québec H3C 3A7, Canada. simon.hardy@polymtl.ca
Robillard
Pierre N
PN
D002478:Cells, Cultured; D003198:Computer Simulation; D004912:Erythrocytes / Q000502:physiology*; D005786:Gene Expression Regulation / Q000502:physiology*; D005947:Glucose / Q000378:metabolism; D019344:Lactic Acid / Q000378:metabolism; D008954:Models, Biological; D015233:Models, Statistical; D008967:Molecular Biology / Q000379:methods*; D009097:Multienzyme Complexes / Q000378:metabolism; D016571:Neural Networks, Computer; D015398:Signal Transduction / Q000502:physiology*; D013269:Stochastic Processes
D009097:Multienzyme Complexes; D019344:Lactic Acid; D005947:Glucose