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Mathematical Biology, The Virtual Cell

Vak 2013-2014

Admission requirements

Elementary calculus and linear algebra (and an interest in biology/biochemistry)

Description

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 currents, extreme pathways, elementary modes and the relationships among them. 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.

Course objectives

The course aims to provide the students a concise overview of the state-of-the-art in stoichiometry-based metabolic network analysis, such that they are able to understand and discuss recent research papers in the field, at the end of the course. They know then the mathematical principles that underly the algorithms for computing the fundamental ‘elementary modes’ associated to a metabolic network and their attributes. They can perform these computations and apply the resulting modes in network analysis. That is, computing network statistics, interpret such statistics and compare them among different organisms. Moreover they can use these concepts in discussing the functioning of metabolic networks and changes therein due to genetic engineering. In the course they get accustomed to working in an interdisciplinary team, in these lectures with mathematicians and/or biologist.

Timetable

The most recent timetable can be found at the LIACS website

Mode of instruction

Lectures

Assessment method

Individual assignments and small-team projects with written report and presentation

Reading list

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.

Registration

You have to sign up for classes and examinations (including resits) in uSis. Check this link for more information and activity codes.

Registration

You have to sign up for classes and examinations (including resits) in uSis. Check this link for more information and activity codes.

There is a limited capacity for students from outside the master Computer Science programme. Please contact the study advisor.

Contact information

Study coordinator Computer Science, Riet Derogee

Website

Mathematical Biology, Virtual Cell