Modelling in Systems Biotechnology
System bioteknik - modellering

KET080F, 7.5 credits

Valid from: Autumn 2013
Decided by: FN2/Eva Nordberg Karlsson
Date of establishment: 2013-09-06

General Information

Division: Chemical Engineering
Course type: Third-cycle course
Teaching language: English

Aim

A quantitative description of microbial metabolism is the basis for development of new fermentation products and improvement of production strains. The integration of analysis at different levels of microbial metabolism (substrate fluxes, enzyme catalytic systems, regulatory systems, affectors) is the field of System Biology – or with a more applied focus - Systems Biotechnology. This course aims at the quantative understanding of microbial processes, primarily in terms of analyzing carbon flux distributions, and the (mathematical) tools available.

Goals

Knowledge and Understanding

For a passing grade the doctoral student must

• Course participants are expected to attain knowledge on:
• - The various types of networks that exist in a cell
• - The mathematical foundation required for stoichimetric modelling
• - The concepts of network balancing for determined systems and linear programming for underdetermined systems
• - Mathematical terminology and principles for dynamic modelling of reacting systems
• - The structure of enzyme kinetic models

Competences and Skills

For a passing grade the doctoral student must

• Course participants are expected to be able to:
• - Set up and mathematically analyze the stoichiometrix matrix S, including finding null spaces and interpreting their meaning in a stoichiometric network
• - Dynamically simulate a reaction system, decompose response time scale and work with pooled variables
• - Work with one or two software for network analysis, e.g. COBRA or OptFlux

Judgement and Approach

For a passing grade the doctoral student must

• Course participants are expected to be able to
• - Critically assess the usefulness of systems biotechnology in their own research projects.

Course Contents

The focus of the course is the stoichiometric modeling of metabolic network (flux analysis), but to some extent also dynamic network analysis will be looked at.

Course Literature

• Palsson, B.: Systems Biology – Properties of Reconstructed Networks. Cambridge University Press, 2006.
• Palsson, B.: Systems Biology – Simulation of Dynamic Network States. Cambridge University Press, 2011.

The course will be based on the seminal books by Bernhard Palsson on Systems Biology (Systems Biology – Properties of Reconstructed Networks, Cambridge University Press, 2006 and Systems Biology – Simulation of Dynamic Network States, Cambridge University Press, 2011) with most focus on the first book

Instruction Details

Types of instruction: Seminars, laboratory exercises, project. Hands-on experience on simulation tools, like FluxOpt and COBRA, will be included to illustrate simulations tools available.

Examination Details

Examination format: Seminars given by participants. Regular seminars will be arranged in which the course participants will prepare and present course topics and simulation problems. Each participant will be assigned a specific modeling and simulation problem to be treated in a written report. The report and the seminar participation constitute the examination in the course.
Grading scale: Failed, pass
Examiner:

Admission Details

Admission requirements: The course is open to PhD students in the fields of biotechnology,microbiology, chemical engineering, automatic control or chemistry.
Assumed prior knowledge: The course assumes some familiarity with linear algebra and differential equations as well as basic knowledge in biochemistry.

Further Information

The course is given in the Spring 2013 Gunnar Lidén (046 – 222 0862) gunnar.liden@chemeng.lth.se

Course Occasion Information

Contact and Other Information

Course coordinators: