The course discusses the mathematical modelling of large biochemical networks, metabolic networks in particular, and the subsequent contrained-based analysis of their dynamic properties. Focus will be on the mathematical underpinning and algorithms involved. The necessary biological and biochemical background will be developed during the course. We introduce the fundamental concepts of the stoichiometric matrix and flux vector and show what information can already deduced from the first, e.g. concerning possible steady state flux vectors for the system: extreme pathways, elementary modes and the relationships among the two. Several algorithms will be explained for computing them together with software packages that implement these (e.g. FluxAnalyzer). The concepts are applied to the problem of optimal metabolite production for a model organism. This is of importance in the production of e.g. pharmaceuticals in plant cell cultures or bacteria. If time permits, parametric sensitivity is discussed.
The course forms a good starting point for further specialisation in the master phase towards biomathematics.
Lecture hours
2 per week
Assessment
Individual assignments and small-team projects with written report and presentation
Literature
Handouts of slides, partial lecture notes and research papers will be provided during the course. It is based on the book B.O. Palsson, Systems Biology: properties of reconstructed networks, Cambridge University Press, 2006 (ISBN 0-521-85903-4). Purchasing of the book may be helpful, but is not required.
Prerequisites
Elementary calculus and linear algebra (and an interest in biology/biochemistry)
Remarks
For all material and up to date information about the course see the lecturer’s home page
Links
Lecturer’s home page