autumn 2016

BIO-8011 Modelling in Systems Biology I -Metabolic pathway modelling - 5 stp

Last changed: 06.04.2017

The course is administrated by

Faculty of Biosciences, Fisheries and Economics

Campus

Tromsø |

Application deadline

Apply in Søknadsweb (application code 9303) by June 1st

PhD students at UiT The Arctic University of Norway apply for admission by registering for class in Studentweb by September 1st. Registrations for the autumn semester starts in the middle of June.

Type of course

Single course PhD, master students can participate if sufficient places are available.

Admission requirements

PhD students or holders of a Norwegian master´s degree of five years or 3+ 2 years (or equivalent) may be admitted. Valid documentation is a statement from your institution that you are a registered PhD student, or a Master´s Diploma with Diploma Supplement / English translation of the diploma. PhD students are exempt from semester fee.

Maximum participants 10, minimum 4.

If more than 10 applicants, priority will be given as follows:

  • Participants admitted to the PhD programme at UiT
  • Participants in the Associate Professor programme (Førstelektorprogrammet)
  • PhD candidates from other universities
  • People with a minimum of a Masters degree (or equivalent), who have not been admitted to a PhD programme

PhD students at UiT register for the course through StudentWeb

Other applicants apply for admission through SøknadsWeb.Application code 9303.

Contact Ingjerd Gauslaa Nilsen at the BFE-faculty if you have troubles or questions regarding registration to the course.

Course contents

Modelling 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 modelling of metabolic pathways in this course, especially on the reconstruction of kinetic models and simulation techniques. We will discuss limitation of modelling 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 modelling. The integration of gene expression data into the modelling 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 modelling 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 modelling and its applications to different biological topics. They will furthermore be familiar with available databases and web based tools.

Language of instruction

English

Teaching methods

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

Course will take place end of October/beginning of November. Exact dates will be determined after course registration has been closed in September.

Assessment

Written project work. Pass/Fail.

Schedule

Recommended reading/syllabus

Available on request.


Contact

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Ines Heiland


Professor for Molecular Biology and Bioinformatics
Phone: +4777646889 ines.heiland@uit.no

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Tonje Engevik Eriksen


Supervisor
Phone: +4777623314 tonje.engevik.eriksen@uit.no