TY - GEN
T1 - iSimBioSys
T2 - 39th Annual Simulation Symposium, 2006
AU - Ghosh, Samik
AU - Ghosh, Preetam
AU - Basu, Kalyan
AU - Das, Sajal K.
AU - Daefler, Simon
PY - 2006
Y1 - 2006
N2 - 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 test-bed 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.
AB - 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 test-bed 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.
UR - http://www.scopus.com/inward/record.url?scp=33750126634&partnerID=8YFLogxK
U2 - 10.1109/ANSS.2006.22
DO - 10.1109/ANSS.2006.22
M3 - Conference contribution
AN - SCOPUS:33750126634
SN - 0769525598
SN - 9780769525594
T3 - Proceedings - Simulation Symposium
SP - 204
EP - 213
BT - Proceedings - 39th Annual Simulation Symposium
Y2 - 2 April 2006 through 6 April 2006
ER -