Concepts of object- and agent-oriented simulation
Transactions of the Society for Computer Simulation International - Special issue: multi-agent systems and simulation
CMSB '03 Proceedings of the First International Workshop on Computational Methods in Systems Biology
CSBW '05 Proceedings of the 2005 IEEE Computational Systems Bioinformatics Conference - Workshops
Parametric modeling of protein-DNA binding kinetics: A discrete event based simulation approach
Discrete Applied Mathematics
ISBRA'07 Proceedings of the 3rd international conference on Bioinformatics research and applications
Transactions on computational systems biology VIII
Stochastic modeling of cytoplasmic reactions in complex biological systems
ICCSA'06 Proceedings of the 6th international conference on Computational Science and Its Applications - Volume Part I
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With the availability of huge databases cataloguing the various molecular "parts of complex biological systems, researchers from multiple disciplines have focused on developing modeling and simulation tools for studying the variability of cellular behavior at a system level - encompassing the dynamics arising from many species of interacting molecules. In this work, we present a system engineering approach to model biological processes. In this approach, a biological process is modeled as a collection of interacting functions driven in time by a set of discrete events. We focus on the discrete event simulation platform, called "iSimBioSys, which we have developed for studying the dynamics of cellular processes in silico. As a testbed for studying our approach we model the two component PhoPQ system, responsible for the expression of several virulence genes in Salmonella Typhimurium. We analyzed the effect of extra cellular magnesium on the behavioral dynamics of this pathway using our framework and compared the results with an experimental system. We also analyze the performance of iSimBioSys, based on the model biological system, in terms of system usage and response.