TY - GEN
T1 - Stochastic simulation of the coagulation cascade
T2 - Parallel Processing Workshops, Euro-Par 2012: BDMC 2012, CGWS 2012, HeteroPar 2012, HiBB 2012, OMHI 2012, Paraphrase 2012, PROPER 2012, Resilience 2012, UCHPC 2012, VHPC 2012
AU - Castaldi, Davide
AU - Maccagnola, Daniele
AU - Mari, Daniela
AU - Archetti, Francesco
PY - 2013
Y1 - 2013
N2 - In this paper we developed a Stochastic Petri Net (SPN) based model to introduce uncertainty to capture the variability of biological systems. The coagulation cascade, one of the most complex biochemical networks, has been widely analyzed in literature mostly with ordinary differential equations, outlining the general behavior but without pointing out the intrinsic variability of the system. Moreover, the computer simulation allows the assessment of the reactions over a broad range of conditions and provides a useful tool for the development and management of several observational studies, potentially customizable for each patient. We describe the SPN model for the Tissue Factor induced coagulation cascade, more intuitive and suitable than models hitherto appeared in the literature in terms of bioclinical manageability. The SPN has been simulated using Tau-Leaping Stochastic Simulation Algorithm, and in order to simulate a large number of models, to test different scenarios, we perform them using High Performance Computing. We analyze different settings for model representing the cases of "healthy" and "unhealthy" subjects, comparing their average behavior, their inter- and intra-variability in order to gain valuable biological insights.
AB - In this paper we developed a Stochastic Petri Net (SPN) based model to introduce uncertainty to capture the variability of biological systems. The coagulation cascade, one of the most complex biochemical networks, has been widely analyzed in literature mostly with ordinary differential equations, outlining the general behavior but without pointing out the intrinsic variability of the system. Moreover, the computer simulation allows the assessment of the reactions over a broad range of conditions and provides a useful tool for the development and management of several observational studies, potentially customizable for each patient. We describe the SPN model for the Tissue Factor induced coagulation cascade, more intuitive and suitable than models hitherto appeared in the literature in terms of bioclinical manageability. The SPN has been simulated using Tau-Leaping Stochastic Simulation Algorithm, and in order to simulate a large number of models, to test different scenarios, we perform them using High Performance Computing. We analyze different settings for model representing the cases of "healthy" and "unhealthy" subjects, comparing their average behavior, their inter- and intra-variability in order to gain valuable biological insights.
KW - Coagulation
KW - Petri Nets
KW - Stochastic Simulation
KW - Systems Biology
UR - http://www.scopus.com/inward/record.url?scp=84874424244&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=84874424244&partnerID=8YFLogxK
U2 - 10.1007/978-3-642-36949-0_28
DO - 10.1007/978-3-642-36949-0_28
M3 - Conference contribution
AN - SCOPUS:84874424244
SN - 9783642369483
VL - 7640 LNCS
T3 - Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
SP - 248
EP - 262
BT - Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Y2 - 27 August 2012 through 31 August 2012
ER -