Full course description
The eight-week course is divided into two main parts, covering (i) kinetic modelling of physiological and biochemical systems using ordinary differential equations and (ii) genome-scale metabolic modelling of intracellular metabolism using constraint-based modelling methods such as flux balance analysis.
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 different approaches to study steady-state reaction flux distributions through these networks; with an emphasis on applications to human metabolism.
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.
During this course, students will learn theoretical concepts of and gain practical experience with metabolic modelling approaches using Matlab. The focus will be both on kinetic and constraint-based (genome-scale) metabolic models. Furthermore, students will learn to understand and interpret recent research articles in the field.
- Klipp, Liebermeister, Wierling, Kowald: ‘Systems Biology’, Wiley-VCH, 2016, ISBN: 9783527336364;
- Palsson: ‘Systems Biology: Constraint-based Reconstruction and Analysis’, Cambridge University Press, 2015, ISBN: 9781107038851
In addition, several papers of recent research topics in metabolic modelling will be discussed in dedicated journal club sessions