Modeling Metabolism

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The eight-weeks course is divided into two main parts, covering (i) kinetic modeling of physiological and biochemical systems using ordinary differential equations and (ii) structural genome-scale metabolic modelling of intracellular metabolism using flux balance analysis, constraint-based analysis, and topological approaches. In the first part, students will learn to build kinetic models of biochemical reactions using mass-action and enzyme kinetics as well as to build whole-body physiological models (e.g. for plasma glucose control). Furthermore, a focus will be on model fitting, parameter estimation, and sensitivity analysis. The second part of the course covers the reconstruction of genome-scale metabolic models (GEMs), as well as the use of the reconstructed models for estimation of steady state intracellular reaction fluxes. Furthermore, students will learn about omics data integration into GEMs for building tissue-specific models and for estimating differential fluxes related to disease. The hands-on part of the course will focus on the implementation of the acquired theoretical knowledge in Matlab, including the use of ODE solvers, optimization methods, and the COBRA toolbox for constraint- based reconstruction and analysis of genome-scale metabolic models.