Mathematical Biology:
Metabolic Network Analysis - 2017

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. FluxAnalyzer). 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):
Systems Biology: properties of reconstructed networks, Bernhard O. Palsson, Cambridge University Press, 2006 (ISBN-13 978-0-521-85903-5)

Relevant papers from the scientific literature will be mentioned during the lectures.
Announcements:


Course material

Slides of lectures:

Lecture Notes (subject to updates):

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


Examination

Assignments:
Assignments are sent to the students by email and become available
on this website too during the course. Indiviually written essay on selected research papers:
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 has been extended from Monday, 12th June 2017, 23.59h to Sunday 18th June, 23.59h. A pdf-file of the essay can be sent by email to the lecturer.  

Team presentations:
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 final presentation session is planned for Monday, 29th May 2017, 9.00-13.00h. The detailed schedule is available here

The final grade for the course is computed as the weighted average of the various parts of the examination: (1) the average over the assignments contributes 25%, (2) individual essay contributes 45% and (3) the final team presentation contributes 30%. The criteria for evaluation of the presentations will be annouced on the detailed scheldule for the final presentation session. 

Final presentation topics and papers:
The teams, their allocated topic and papers and some key questions that each team should address in their presentation has been circulated by email on May 10th 2017. The pdf-file can be obtained here. Each team must coordinate which student studies which paper paper in depth, for the essay, and inform the lecturer about the resulting allocation of papers as soon as possible. Note that all team members are supposed to have read all papers allocated to the team! However, one student in the team is 'the specialist' on a paper and has read it in further depth.

Individual essays:
Consult the pdf-file with guidelines with details on the essay.
Deadline for submission of the final version of the essay has been extended from Monday, 12th June 2017, 23.59h to Sunday, 18th June 2017, 23.59h/b>. A pdf-file of the essay can be sent by email to the lecturer.  


This page was last updated: 29th May 2017