autumn 2016

BIO-3010 Modelling in Systems Biology I -Metabolic pathway modelling - 5 stp

Last changed: 08.04.2017

The course is administrated by

Faculty of Biosciences, Fisheries and Economics


Tromsø |

Application deadline

Concerns only admission to singular courses: Applicants from Nordic countries: 1 June for the autumn semester and 1 December for the spring semester. Exchange students and Fulbright students: 1 October for the spring semester and 15 April for the autumn semester.

Type of course

Master course for biology students.The course is available as a singular course. Maximum participants: 10 (minimum 4)

Admission requirements

Local admission, application code 9371 - - Master`s level singular course.
Admission requires a Bachelor`s degree (180 ECTS) or equivalent qualification, with a major in biology of minimum 80 ECTS.

The course will be arranged with a minimum number of  4 students.

Maximum participants: 10

Course contents

Modeling is an important tool in current biology. It is widely used to help experimental design, in drug target prediction and in the prediction of disease related changes. We will focus on the modeling of metabolic pathways in this course especially on the reconstruction of kinetic models and simulation techniques. We will discuss limitation of modeling approaches due to limited parameter availability and perform parameter estimation based on available experimental data. In the practical part students will be introduced to different programs available for stoichiometric and kinetic modeling. The integration of gene expression data into the modeling approach will be an essential part of the course. Furthermore, several related databases such as BioCyc, KEGG, BRENDA and Biomodels will be introduced during the course.

Objective of the course

Basic knowledge on metabolic pathway analysis, biomathematical modelling, sensitivity analysis and parameter estimation. Knowledge of tools available for kinetic modeling and knowledge about related databases. Students will be able to reconstruct small metabolic network models and simple kinetic models and perform time courses simulations as well as parameter estimation from biological data. Students will furthermore be able to perform stoichiometric analysis and simple flux balance analysis with tools available in the internet. The goal is that the students have a general understanding of modeling and its applications to different biological topics. They will furthermore be familiar with available databases and web based tools.

Language of instruction


Teaching methods

Intensive course 1 week, 40 hours combined lectures and computer practicals


Written project work. Grade: Pass/Fail. There will be a re-sit examination for students that did not pass the previous ordinary examination.


Recommended reading/syllabus

Syllabus and reading list will be announced prior to course start.
Lectures Autumn 2016
First attendance: October 26th at 08.15, 3102 (Naturfagbygget)
Lectures prof. Ines Heiland
Computer practicals prof. Ines Heiland