Grid computing for sensitivity analysis of stochastic biological models

Ivan Merelli, Dario Pescini, Ettore Mosca, Paolo Cazzaniga, Carlo Maj, Giancarlo Mauri, Luciano Milanesi

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

Abstract

Systems biology is a multidisciplinary research area aimed at investigating biological systems by developing mathematical models that approach the study and the analysis of both the structure and behaviour of a biological phenomenon from a system perspective. The dynamics described by such mathematical models can be deeply affected by many parameters, and an extensive exploration of the parameters space in order to find crucial factors is most of the time prohibitive since it requires the execution of a huge number of computer simulations. Sensitivity analysis techniques can help in understanding how much the uncertainty in the model outcome is determined by the uncertainties, or by the variations, of the model input factors (components, reactions and respective parameters). In this work we exploit the European Grid Infrastructure to manage the calculations required to perform the SA on a stochastic model of bacterial chemotaxis, using an improved version of the first order screening method of Morris. According to the results achieved in our exploratory analysis, the European Grid Infrastructure is a useful solution for distributing the stochastic simulations required to carry out the SA of a stochastic model. Considering that the more intensive the computation the more scalable the infrastructure, grid computing can be a suitable technology for large scale biological models analysis.

Original languageEnglish
Title of host publicationLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Pages62-73
Number of pages12
Volume6873 LNCS
DOIs
Publication statusPublished - 2011
Event11th International Conference on Parallel Computing Technologies, PaCT 2011 - Kazan, Russian Federation
Duration: Sep 19 2011Sep 23 2011

Publication series

NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume6873 LNCS
ISSN (Print)03029743
ISSN (Electronic)16113349

Other

Other11th International Conference on Parallel Computing Technologies, PaCT 2011
CountryRussian Federation
CityKazan
Period9/19/119/23/11

ASJC Scopus subject areas

  • Computer Science(all)
  • Theoretical Computer Science

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    Merelli, I., Pescini, D., Mosca, E., Cazzaniga, P., Maj, C., Mauri, G., & Milanesi, L. (2011). Grid computing for sensitivity analysis of stochastic biological models. In Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) (Vol. 6873 LNCS, pp. 62-73). (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 6873 LNCS). https://doi.org/10.1007/978-3-642-23178-0_6