Modeling and simulation: tools for metabolic engineering.
Mathematical modeling is one of the key methodologies of metabolic engineering. Based on a given metabolic model different computational tools for the simulation, data evaluation, systems analysis, prediction, design and optimization of metabolic systems have been developed. The currently used metabolic modeling approaches can be subdivided into structural models, stoichiometric models, carbon flux models, stationary and nonstationary mechanistic models and models with gene regulation. However, the power of a model strongly depends on its basic modeling assumptions, the simplifications made and the data sources used. Model validation turns out to be particularly difficult for metabolic systems. The different modeling approaches are critically reviewed with respect to their potential and benefits for the metabolic engineering cycle. Several tools that have emerged from the different modeling approaches including structural pathway synthesis, stoichiometric pathway analysis, metabolic flux analysis, metabolic control analysis, optimization of regulatory architectures and the evaluation of rapid sampling experiments are discussed.
Wiechert
Wolfgang
W
Department of Simulation and Computer Science, Institute of Mechanical and Control Engineering, University of Siegen, Paul-Bonatz-Str. 9-11, D-57068 Siegen, Germany. wiechert@simtec.mb.uni-siegen.de
D001698:Biomedical Engineering; D001709:Biotechnology; D002244:Carbon / Q000378:metabolism; D003198:Computer Simulation; D016208:Databases, Factual; D005786:Gene Expression Regulation; D007700:Kinetics; D008660:Metabolism; D008954:Models, Biological; D013816:Thermodynamics
D002244:Carbon