On the verification and correction of large-scale kinetic models in systems biology

Attila Gábor, Katalin M. Hangos, Gábor Szederkényi, Julio R. Banga

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

1 Citation (Scopus)

Abstract

In this paper we consider the problem of verification of large dynamic models of biological systems. We present syntactical criteria based on biochemical kinetics to ensure the plausibility of a model and the positivity of its solution. These criteria include the positivity of the rate functions, their kinetic type dependence on the reactant species concentrations, and the absence of the negative cross-effects that together guarantee the nonnegativity of the dynamics. Further, the stoichiometric matrix of the truncated reaction system is checked against conservation using its algebraic properties. Algorithmic procedures are then proposed for checking these criteria with emphasis on good scaling up properties. In addition to these verification procedures, we also provide, for certain typical errors, model correcting methods. The capabilities and usefulness of these procedures are illustrated on biochemical models taken from the Biomodels database. In particular, a set of 11 kinetic models related with E. coli are checked, finding two with deficiencies. Correcting actions for these models are proposed.

Original languageEnglish
Title of host publicationComputational Methods in Systems Biology - 11th International Conference, CMSB 2013, Proceedings
Pages206-219
Number of pages14
DOIs
Publication statusPublished - Oct 28 2013
Event11th International Conference on Computational Methods in Systems Biology, CMSB 2013 - Klosterneuburg, Austria
Duration: Sep 22 2013Sep 24 2013

Publication series

NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume8130 LNBI
ISSN (Print)0302-9743
ISSN (Electronic)1611-3349

Other

Other11th International Conference on Computational Methods in Systems Biology, CMSB 2013
CountryAustria
CityKlosterneuburg
Period9/22/139/24/13

Keywords

  • Kinetic models
  • Model checking
  • Verification

ASJC Scopus subject areas

  • Theoretical Computer Science
  • Computer Science(all)

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    Gábor, A., Hangos, K. M., Szederkényi, G., & Banga, J. R. (2013). On the verification and correction of large-scale kinetic models in systems biology. In Computational Methods in Systems Biology - 11th International Conference, CMSB 2013, Proceedings (pp. 206-219). (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 8130 LNBI). https://doi.org/10.1007/978-3-642-40708-6_16