Non-linear optimization of biochemical pathways: applications to metabolic engineering and parameter estimation.

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