A recent paper of mine has just appeared in the latest issue of
Bioinformatics (abstract below). This paper describes the use of
non-linear optimisation methods in metabolic modelling and also
covers its implementation in the GEPASI biochemical kinetics software.
GEPASI's web site has now two additional tutorials that serve to
illustrate the use of the "optimisation" and "fitting" modules.
GEPASI's home page is at:
http://gepasi.dbs.aber.ac.uk/softw/gepasi.html
ABSTRACT OF PAPER:
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"Non-linear optimization of biochemical pathways: applications to metabolic
engineering and parameter estimation."
P. Mendes & D. B. Kell
Institute of Biological Sciences, University of Wales Aberystwyth,
Aberystwyth, Ceredigion SY23 3DD, UK.
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 at aber. ac.uk
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Pedro Mendes
IMPORTANT NOTE
>From March onwards my new email address will be:
pjm at ncgr.org
(this is already working, please update your records)
NCGR, 1800-A, Old Pecos Trail, Santa Fe, NM 87505, USA
