Addressing biological circuit simulation accuracy: Reachability for parameter identification and initial conditions

Meeko Oishi, Elebeoba May

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

5 Scopus citations

Abstract

Accurate simulation of biological networks is difficult not only due to the computational cost associated with large-scale systems simulation, but also due to the inherent limitations of mathematical models. We address two components to improve biological circuit simulation accuracy: 1) feasible initial conditions, and 2) identification of critical yet unknown model parameters. For those parameters that may not be available from experimental data, we incorporate reachability analysis to enhance our optimization/simulation framework and estimate those parameters that are capable of creating behaviors consistent with known experimental data. We apply these techniques to a biological circuit model of tryptophan biosynthesis in E. coli, and quantify the improvement in simulation accuracy when reachability analysis is used.

Original languageEnglish (US)
Title of host publication2007 IEEE/NIH Life Science Systems and Applications Workshop, LISA
PublisherInstitute of Electrical and Electronics Engineers Inc.
Pages152-155
Number of pages4
ISBN (Print)9781424418138
DOIs
StatePublished - Jan 1 2007
Event2007 IEEE/NIH Life Science Systems and Applications Workshop, LISA - Bethesda, MD, United States
Duration: Nov 8 2007Nov 9 2007

Other

Other2007 IEEE/NIH Life Science Systems and Applications Workshop, LISA
CountryUnited States
CityBethesda, MD
Period11/8/0711/9/07

Keywords

  • Biological circuits
  • Escherichia coli
  • Hybrid systems
  • Parameter identification
  • Reachability
  • Tryptophan

ASJC Scopus subject areas

  • Computer Science Applications
  • Information Systems

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