Stochastic simulation of the coagulation cascade: A Petri Net based approach

Davide Castaldi, Daniele Maccagnola, Daniela Mari, Francesco Archetti

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Abstract

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.

Original languageEnglish
Title of host publicationLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Pages248-262
Number of pages15
Volume7640 LNCS
DOIs
Publication statusPublished - 2013
EventParallel 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 - Rhodes Island, Greece
Duration: Aug 27 2012Aug 31 2012

Publication series

NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume7640 LNCS
ISSN (Print)03029743
ISSN (Electronic)16113349

Other

OtherParallel 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
CountryGreece
CityRhodes Island
Period8/27/128/31/12

Keywords

  • Coagulation
  • Petri Nets
  • Stochastic Simulation
  • Systems Biology

ASJC Scopus subject areas

  • Computer Science(all)
  • Theoretical Computer Science

Fingerprint Dive into the research topics of 'Stochastic simulation of the coagulation cascade: A Petri Net based approach'. Together they form a unique fingerprint.

Cite this