Course Syllabus for

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


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.


Knowledge and Understanding

For a passing grade the doctoral student must

Competences and Skills

For a passing grade the doctoral student must

Judgement and Approach

For a passing grade the doctoral student must

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

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

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)

Course Occasion Information

Contact and Other Information

Course coordinators:

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