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spring 2020

KJE-3604 Bioinformatics: Microbial genomics and metagenomics - 10 ECTS

Sist endret: 18.04.2020

The course is provided by

Faculty of Science and Technology

Location

Tromsø |

Application deadline

Applicants from Nordic countries: 1st of December for the spring semester.

Applicants from outside the Nordic countries: 1st of October for the spring semester

Type of course

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

Admission requirements

Required: A bachelor’s degree in chemistry or biotechnology or equivalent, with a grade C or better in the Norwegian grading system.

Recommended: KJE-2004 or equivalent.

Course content

Bioinformatics is a combination of biological science and information technology used in analyzing and deriving conclusions from large data sets. This course introduces the students to bacterial genomics and metagenomics. Genome-scale sequencing projects have led to an explosion of genetic information (gene sequences) available for analysis. The student will learn how these sequences can lead to a much fuller understanding of many biological processes.

 

The aim is to provide a theoretical introduction of the topics, tools and current trends in bacterial genomics and metagenomics, followed by practical exercises using the methodology on Next generation sequence data. Major topics will include:

 

  • Genome sequencing: Quality control of sequence data, sequence assembly, assembly evaluation and functional annotation
  • Comparative genomics: Contrasting multiple genome sequences and visualization of results
  • Transcriptomics (RNA-sequencing): Identification of differential expressed genes
  • Whole genome phylogenetic analysis: Reconstruction of phylogeny based on complete genome sequences
  • Metagenome sequencing: Preprocessing of raw sequence data and preparation for downstream sequence analysis
  • Taxonomic classification of metagenomes: Taxonomic profiling of bacterial communities and comparison of profiles from different communities

Objectives of the course

The student will have acquired a solid and broad theoretical basis to understand bioinformatics. This means that the student

 

Knowledge

  • has advanced knowledge in genomics and the analysis of this type of data including:
  • quality control and assembly of sequence data
  • evaluation of sequence assemblies
  • functional annotation of DNA sequences
  • RNA sequence analysis
  • whole genome phylogeny
  • taxonomic and functional profiling and binning of metagenomes
  • has thorough knowledge of the scholarly or artistic theories and methods in the field
  • can apply knowledge to new areas within the academic field
  • can analyze academic problems on the basis of the history, traditions, distinctive character and place in society of the academic field

 

Skills

  • can analyze and deal critically with various sources of information and use them to structure and formulate scholarly arguments
  • can analyze existing theories, methods and interpretations in the of microbial genomics and metagenomics, and work independently on practical and theoretical problems
  • can use relevant bioinformatical analysis methods for research and scholarly development work in an independent manner
  • can carry out an independent, limited research or development project under supervision and in accordance with applicable norms for research ethics

 

Competence

  • can analyze relevant academic, professional and research ethical problems
  • can apply his/her knowledge and skills in new areas in order to carry out advanced assignments and projects
  • can communicate extensive independent work and masters language and terminology used in the field of microbial genomics and metagenomics
  • can communicate about academic issues, analyses and conclusions in the field of microbial genomics and metagenomics, both with specialists and the general public
  • can contribute to new thinking and innovation processes

Teaching methods

The course will be taught as a combination of lectures, demonstrations and practical lab work. Lectures and hands-on laboratory exercises: 80 h

Assessment

Evaluation of orally presented report. Pass/fail.

Work requirement: Minimum eight out of ten reports submitted in Canvas.

Students who fail the exam may register for re-sit the following semester.

Date for examination

Oral examination 03.06.2020

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-3323 Bioinformatics: Genomes and genomics 6 stp
KJE-8602 Bioinformatics - genome and genome analysis 5 stp


Kontakt
Profilbilde Renate Lie Larsen

Renate Lie Larsen


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

Erik Hjerde.jpg

Hjerde, Erik


Forsker, Molekylære biosystemer og bioinformatikk, Norstruct
Telefon: +4777623372 erik.hjerde@uit.no