Performance evaluation comes to life: quantitative methods applied to biological systems
ACM SIGMETRICS Performance Evaluation Review
Petri nets for modelling metabolic pathways: a survey
Natural Computing: an international journal
Hybrid Petri net based modeling for biological pathway simulation
Natural Computing: an international journal
Stochastic Petri net models of Ca2+ signaling complexes and their analysis
Natural Computing: an international journal
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Motivation: Cellular signaling networks are dynamic systems that propagate and process information, and, ultimately, cause phenotypical responses. Understanding the circuitry of the information flow in cells is one of the keys to understanding complex cellular processes. The development of computational quantitative models is a promising avenue for attaining this goal. Not only does the analysis of the simulation data based on the concentration variations of biological compounds yields information about systemic state changes, but it is also very helpful for obtaining information about the dynamics of signal propagation. Results: This article introduces a new method for analyzing the dynamics of signal propagation in signaling pathways using Petri net theory. The method is demonstrated with the Ca2+/calmodulin-dependent protein kinase II (CaMKII) regulation network. The results constitute temporal information about signal propagation in the network, a simplified graphical representation of the network and of the signal propagation dynamics and a characterization of some signaling routes as regulation motifs. Contact: simon.hardy@polymtl.ca Supplementary information: Complete data of the Petri net model of the CaMKII regulation pathway available at http://www.polymtl.ca/rgl/Downloads.php