autumn 2018

KJE-2004 Bioinformatics - An introduction - 10 stp

Sist endret: 08.02.2019

The course is administrated by

Faculty of Science and Technology

Studiested

Tromsø |

Application deadline

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

Theoretical and practical subject. The course is available as a singular or elective course independent of study program, also to exchange students. The course is offered on condition that a minimum number of students register for the course.

Admission requirements

Applicants from Nordic countries: Generell studiekompetanse eller realkompetanse + Matematikk R1 og R2 og enten Fysikk (1+2) eller Kjemi (1+2) eller Biologi (1+2) eller Informasjonsteknologi( 1+2) eller Geologi (1+2) eller Teknologi og forskningslære (1+2).

International applicants: Higher Education Entrance Qualification and certified language requirements in English. It is a requirement that students have  some prior knowledge of biology and ecology, chemistry and mathematics (Participants must have taken introductory level university courses, and achieved pass grades, in these subjects).

A list of the requirements for the Higher Education Entrance Qualification in Norway can be found on the Norwegian Agency for Quality Assurance in Education website - nokut.no

Application code: 9336 (Nordic applicants).

Course contents

With the recent revolution in our biological understanding and available data, and the rapid development of new technologies it is today expected that modern biologists are competent in using bioinformatics tools. This course introduces students to Bioinformatics and Bioinformatics tools, and provides participants with hands-on training. Students will be introduced to biological sequence data (DNA and protein sequences, whole genomes, metagenomes etc.), learn to access major sequence databases and use a variety of web-based services. During the course the students will learn to retrieve, analyze, compare and visualize genetic sequences. The following main topics will be addressed: biological databases, sequence alignments, molecular phylogenetics, DNA sequencing technologies (including Next-generation seq. technologies; NGS), genome annotation, and NGS applications.

Objective of the course

Knowledge:

 

The candidate

 

Background basics:

  • has basic knowledge about DNA and RNA structure, the central dogma, gene structure and control, and the tree of life and evolution.
  • has basic knowledge about primary and secondary protein structure, and implications for bioinformatics.

 

Biological databases:

  • has insights into public databases, primary and secondary databases, file formats in bioinformatics and data quality.

 

Sequence alignments:

  • knows the principals of sequence alignments.
  • has knowledge about pairwise sequence alignments and database similarity searching (BLAST and FASTA).
  • has knowledge about local and global alignments, and the dot-plot and dynamic programming methods.
  • has knowledge about patterns, profiles and multiple sequence alignments (progressive alignment method, Clustal, T-Coffee, iterative methods).
  • knows about protein motif and domain databases (Pfam, InterPro), and sequence logos.

 

Evolutionary processes:

  • has background knowledge on mechanisms of mutations and evolutionary prodesses
  • has background knowledge about principals for inferring phylogenies.
  • has knowledge into basic principles of structure and interpretation of phylogenetic trees.
  • has knowledge about how to reconstruct phylogenetic trees.

 

Next-generation DNA sequencing (NGS) and informatics:

  • has knowledge about the history of DNA sequencing and its experimental applications.
  • knows about early bioinformatics methods.
  • has knowledge about how to visualize NGS data.

 

Genome characteristics:

  • has knowledge about general genome features.
  • knows how to predict genes, splice sites, promoters.
  • has knowledge about detection of genes, introns/exons.

 

Skills:

 

The candidate

  • can describe the basic properties of DNA,  RNA and protein. Explain the central dogma, and is able to outline structures and types of biological databases.
  • can score alignments, use search tools, elaborate on substitution scoring matrices, dynamic programming, profiles and hidden Markov models.
  • can carry out phylogenetic analyses using different methods, test resulting trees using the bootstrapping method, and interpret the result.
  • is able to recognize typical gene features and assign function to genes (genome annotation).
  • can elaborate on different DNA sequencing methods (Sanger and NGS methods).
  • can outline applications of sequencing and expression profiling techniques .
  • can present academic material

 

General competence:

The candidate

  • understands the relation between DNA, RNA and protein, and can use this information to discuss their function.
  • can participate in discussions concerning bioinformatics with others.
  • has the ability to plan and execute basic bioinformatics tasks; aligning and handling sequences, database searching, phylogenetic analysis, and basic annotation.
  • can interpret and communicate scientific material on bioinformatics.

Language of instruction

The language of instruction is English and all of the syllabus material is in English. Examination questions will be given in English but may be answered either in English or Norwegian/Scandinavian language.

Teaching methods

Lectures: 27 h, Laboratory: 24 h PC-based exercises.

Assessment

Compulsory attendance in laboratory exercises. Approved project reports. Written 4 h examination at the end of the course. Letter grades (A-F). Candidates that receive the grade F can repeat the exam the following semester.

Date for examination

Written examination 28.11.2018

The date for the exam can be changed. The final date will be announced in the StudentWeb early in May and early in November.

Schedule

Course overlap

BIO-2304 Introduction to Bioinformatics 10 stp

Recommended reading/syllabus

New book: Concepts in bioinformatics and genomics, Eds. Momand & McCurdy, 2017, Oxford University Press

Contact the course responsible for more information. Details of the course are given through Canvas, the new learning portal of the university. You must be a registered student for the course in order to gain access to Canvas.

Lectures Autumn 2018
First attendance: 16.08.18 at 14:15, MH U6.SAUD, MH-bygget. First attendance is mandatory. More information will be given in the first lecture.
Lectures prof. Peik Haugen
prof. Nils Peder Willassen
Lab gruppe 1 prof. Peik Haugen
prof. Nils Peder Willassen
Lab gruppe 2 prof. Peik Haugen
prof. Nils Peder Willassen


Kontakt
Profilbilde Renate Lie Larsen

Renate Lie Larsen


Seniorkonsulent, studieadministrasjon, Innkjøper institutt for kjemi,
Telefon: +4777644074 renate.larsen@uit.no

Peik Haugen.jpg

Haugen, Peik


Professor, Molekylære biosystemer, Norstruct
Telefon: +4777645288
Mobil: 95122932 peik.haugen@uit.no