spring 2020

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

Sist endret: 14.03.2020

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.

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