Identification of biochemical reaction networks: an observer based approach

E. Bullinger, D. Fey, M. Farina, R. Findeisen

Research output: Contribution to journalArticle

4 Citations (Scopus)

Abstract

Dynamic models present a fundamental tool in systems biology, but rely on kinetic parameters, such as association and dissociation constants. Their direct estimation from studies on isolated reactions is usually expensive, time-consuming or even infeasible for large models. As a consequence, they must be estimated from indirect measurements, usually in the form of time-series data. We describe an observer-based parameter estimation approach taking the specific structure of biochemical reaction networks into account. Considering reaction kinetics described by polynomial or rational functions, we propose a three step approach. In a first step, the estimation of not directly measured states is decoupled from the estimation of the parameters using a suitable model extension. In a second step, a specially suited nonlinear observer estimates the extended state. Based on the obtained state estimates, the parameter estimates are calculated in a straightforward way in the final step. The applicability of the approach is exemplified considering a simplified model of the circadian rhythm.
LanguageEnglish
Pages269-279
Number of pages10
JournalAt-automatisierungstechnik
Volume56
Issue number5
DOIs
Publication statusPublished - 2008

Fingerprint

Rational functions
Kinetic parameters
Reaction kinetics
Parameter estimation
Time series
Dynamic models
Association reactions
Polynomials
Systems Biology

Keywords

  • parameter identification
  • identifiability
  • observer
  • observability
  • systems biology
  • parameter-estimation
  • global identifiability
  • model identification
  • gene-expression
  • systems
  • optimization
  • equations

Cite this

Bullinger, E. ; Fey, D. ; Farina, M. ; Findeisen, R. / Identification of biochemical reaction networks: an observer based approach. In: At-automatisierungstechnik. 2008 ; Vol. 56, No. 5. pp. 269-279.
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Identification of biochemical reaction networks: an observer based approach. / Bullinger, E.; Fey, D.; Farina, M.; Findeisen, R.

In: At-automatisierungstechnik, Vol. 56, No. 5, 2008, p. 269-279.

Research output: Contribution to journalArticle

TY - JOUR

T1 - Identification of biochemical reaction networks: an observer based approach

AU - Bullinger, E.

AU - Fey, D.

AU - Farina, M.

AU - Findeisen, R.

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KW - parameter identification

KW - identifiability

KW - observer

KW - observability

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KW - parameter-estimation

KW - global identifiability

KW - model identification

KW - gene-expression

KW - systems

KW - optimization

KW - equations

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