Bioinformatics, Vol 14, 869-883, Copyright © 1998 by Oxford University Press
P Mendes and D Kell
MOTIVATION: The simulation of biochemical kinetic systems is a powerful
approach that can be used for: (i) checking the consistency of a postulated
model with a set of experimental measurements, (ii) answering 'what if?'
questions and (iii) exploring possible behaviours of a model. Here we
describe a generic approach to combine numerical optimization methods with
biochemical kinetic simulations, which is suitable for use in the rational
design of improved metabolic pathways with industrial significance
(metabolic engineering) and for solving the inverse problem of metabolic
pathways, i.e. the estimation of parameters from measured variables.
RESULTS: We discuss the suitability of various optimization methods,
focusing especially on their ability or otherwise to find global optima. We
recommend that a suite of diverse optimization methods should be available
in simulation software as no single one performs best for all problems. We
describe how we have implemented such a simulation-optimization strategy in
the biochemical kinetics simulator Gepasi and present examples of its
application. AVAILABILITY: The new version of Gepasi (3.20), incorporating
the methodology described here, is available on the Internet at
http://gepasi.dbs.aber.ac.uk/softw/Gepasi. html. CONTACT: prm@aber.ac.uk
ARTICLES
Non-linear optimization of biochemical pathways: applications to metabolic engineering and parameter estimation
Institute of Biological Sciences, University of Wales Aberystwyth, Aberystwyth, Ceredigion SY23 3DD, UK. prm@aber.ac.uk
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