spring 2020

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

Sist endret: 14.10.2019

The course is provided by

Faculty of Biosciences, Fisheries and Economics

Location

Tromsø |

Application deadline

Registration deadline for PhD students at UiT The Arctic University of Norway: December 15. 

Application deadline for other applicants: December 1.

Type of course

Single course PhD, master students can participate if sufficient places are available (BIO-3010).

Admission requirements

PhD students or holders of a Norwegian master´s degree of five years or 3+ 2 years (or equivalent) may be admitted.

The course has 10 seats. If the number of applicants exceeds the number of places available, applicants will be ranked in this order:

1. PhD students at UiT

2. Participants in the Associate Professor programme at UiT (must hold a Master´s  degree)

3. Registered PhD students from other universities

4. Applicants documenting that they have a Norwegian Master´s degree (or equivalent)

The course will be cancelled if less than four participants.

PhD students at UiT register for the course through StudentWeb. Registrations for the spring semester starts in the middle of December.

Other applicants apply for admission through SøknadsWeb. Application code 9304.

Non-UiT PhD students must upload a document from their university stating that they are registered PhD students. This group of applicants does not have to prove English proficiency and are exempt from semester fee.

Holders of a Master´s degree must upload a Master´s Diploma with Diploma Supplement / English translation of the diploma. Applicants from listed countries must document proficiency in English. To find out if this applies to you, see the following list:
Proficiency in English must be documented - list of countries.

For more information on accepted English proficiency tests and scores, as well as exemptions from the English proficiency tests, please see the following document:: Proficiency in english - PhD level studies

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

Course content

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.

Objectives 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 in February/March. Exact dates will be determined after course registration has been closed.

Assessment

Written project work. Grade: Pass/Fail.

Schedule



Kontakt
Maren-Marie-Thode-Iversen-Bredde-180px-

Maren Marie Thode Iversen


Rådgiver
Telefon: +4777646610 maren.m.iversen@uit.no

Ingjerd - Branno.png

Nilsen, Ingjerd Gauslaa


Rådgiver, ph.d.-utdanningen
Telefon: +4777646018 ingjerd.nilsen@uit.no

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Ines Heiland


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

HOW TO APPLY

PhD students enrolled at UiT register for the course through StudentWeb

Other applicants apply for admission through SøknadsWeb. Choose the application code 9303 and write the course code (BIO-8011) in the remark field. You'll find a manual for SøknadsWeb here.

Remember to upload documentation of your education or your status as a PhD student. Applicants who can document their status as a PhD student are exempt to pay the semester fee.