Mathematical Biology:
Metabolic Network Analysis - 2019

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. 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. CellNetAnalyzer). The concepts are applied to the problem of optimal metabolite production for a model organism. If time permits, parametric sensitivity is discussed.

The course targeted at students in the Life Sciences, Mathematics and Bioinformatics. The topics will be dicsussed in a well-balanced mixture of biology, biochemistry, mathematics and computer science. Examination will be by means of assignments that students need to make individually, and final team assignments in which in a small interdisciplinary team specially selected research papers on applications of metabolic network analysis are studied. The results are presented to the other students. The team presentation and a written report of the study are evaluated. The results of individual assignments, team presentation and team reports are combined to obtain the final grade.

Literature (facultative):
The course was initially based on: 'Systems Biology: properties of reconstructed networks', Bernhard O. Palsson, Cambridge University Press, 2006 (ISBN-13 978-0-521-85903-5)
This book may still be helpful, but not essential for following the course.

However, in its latest version the course is based on various papers from the scientific literature instead. References will be provided during the lectures and in the lecture notes of the course. These will come available piece by piece on this website.


Course material

Slides of lectures:

Lecture Notes (subject to updates):

An updated version of the Lecture Notes becomes available section-wise during the course. 


Assignments (30%):
Assignments are sent to the students by email and become available
on this website too during the course. Individually written essay on selected research papers (30%):
Students will be alllocated to small teams of 2-3 students that study a collection of research papers. Each team member will write an essay individually (max. 10 pages A4) on a specific research question related to the collection of papers.
The deadline for this essay will be announced.

Team presentations (10%):
The teams mentioned above will present togerther, in a joint presentation, for all course attendees their interpretation of the results presented in the collection of papers assigned to the team. A date for a final presentation session of team presentations on various topics on Metabolic Network Analysis will be agreed upon by the participants  during the lecture.
The most convenient date and time of the final presentation session will be determined with the students during the course.

Written exam (30%):
The date, time and location of the written exam still needs to be determined. It will be annouced as soon as possible. The final grade for the course is computed as the weighted average of the various parts of the examination, with weighting as indicated above. 

Final presentation topics and papers:
Will be announced.

Individual essays:
Details will be announced.  

This page was last updated: 11th February 2019