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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

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 microbial 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.Ìý

ÌýThe aim is to provide a theoretical introduction of the topics, tools and current trends in microbial genomics and metagenomics, followed by practical exercises using the methodology on Next generation sequence data.ÌýMajorÌýtopicsÌýwillÌýinclude:Ìý

• µþ¾±´Ç¾±²Ô´Ú´Ç°ù³¾²¹³Ù¾±³¦²õÌý²õ´Ç´Ú³Ù·É²¹°ù±ðÌý±è±ô²¹³Ù´Ú´Ç°ù³¾²õÌý
• Genomics: quality control,ÌýassemblyÌýand annotationÌý
• °ä´Ç³¾±è²¹°ù²¹³Ù¾±±¹±ðÌý²µ±ð²Ô´Ç³¾¾±³¦²õÌý²¹²Ô»åÌý³Ù°ù²¹²Ô²õ³¦°ù¾±±è³Ù´Ç³¾¾±³¦²õÌý
• EvolutionaryÌýrelationships andÌýgeneticÌýdiversityÌý
• ²Ñ±ð³Ù²¹²µ±ð²Ô´Ç³¾¾±³¦²õ,Ìý²¹³¾±è±ô¾±³¦´Ç²ÔÌý²¹²Ô»åÌý³¦´Ç³¾³¾³Ü²Ô¾±³Ù²âÌý±è°ù´Ç´Ú¾±±ô¾±²Ô²µÌý

Objectives of the course

The studentÌýhasÌýacquired a solid and broad theoretical basis to understand bioinformatics.ÌýThis means that the student:Ìý

°­²Ô´Ç·É±ô±ð»å²µ±ðÌý

µþ¾±´Ç¾±²Ô´Ú´Ç°ù³¾²¹³Ù¾±³¦²õÌý²õ´Ç´Ú³Ù·É²¹°ù±ðÌý±è±ô²¹³Ù´Ú´Ç°ù³¾²õÌý

• has knowledge about relevant software environments, including Linux,ÌýAnacondaÌýand virtual machines.Ìý
• can apply command line in Linux environments.ÌýÌýÌýÌý
• can apply knowledge to choose software platform for manipulating raw next-generation sequence dataÌý

Genomics: quality control,ÌýassemblyÌýand annotationÌý

• has knowledge about the principles behind quality assessment of genomics reads and sequencesÌý
• has thorough knowledge about the basis different behind assembly methods and toolsÌý
• can apply the knowledge to select tools for gene prediction and functional assignment of microbial genomesÌý

°ä´Ç³¾±è²¹°ù²¹³Ù¾±±¹±ðÌý²µ±ð²Ô´Ç³¾¾±³¦²õÌý²¹²Ô»åÌý³Ù°ù²¹²Ô²õ³¦°ù¾±±è³Ù´Ç³¾¾±³¦²õÌý

• has advanced knowledgeÌýtaboutÌýunderlying methods how two or more genomes can be aligned and compared.Ìý
• has advanced knowledge for the basis behind transcriptomics (differential expressed genes) and analyze the resultsÌý

EvolutionaryÌýrelationships andÌýgeneticÌýdiversityÌý

• has advanced knowledge about principles behind phylogenetic and phylogenomic analysesÌý
• has thorough knowledge about software used for evolutionary studiesÌý
• has advanced knowledge on the practical aspects ofÌýanalysingÌýgenetic diversityÌý

²Ñ±ð³Ù²¹²µ±ð²Ô´Ç³¾¾±³¦²õ,Ìý²¹³¾±è±ô¾±³¦´Ç²ÔÌý²¹²Ô»åÌý³¦´Ç³¾³¾³Ü²Ô¾±³Ù²âÌý±è°ù´Ç´Ú¾±±ô¾±²Ô²µÌý

• has an advanced knowledge about the different principles and methods used in community profilingÌý
• has advanced knowledge in analysis of microbial communitiesÌý

Ìý

SkillsÌý

• Can evaluate and selectÌýbioinformatics tools and sequence data fromÌýpublicallyÌýavailable repositories, and use them to address biologicalÌýquestionsÌý
• Can use bioinformatic tools for analyzing genomes, transcriptomes, genetic variation, evolutionaryÌýrelationshipsÌýand microbial communities.Ìý

Ìý

GeneralÌýcompetence Ìý Ìý

• can participate in discussions concerning microbial genomics and metagenomics with students, research fellows and the public.Ìý
• has the ability toÌýplan and execute advanced bioinformatics tasks; processing andÌýanalysingÌýmicrobial genomes, comparative genomic analyses, transcriptome analysis, infer phylogenetic relationships and genetic variations, and microbial community analysis.Ìý
• can interpret, communicate and debate thoroughly on independent bioinformatics data and results.Ìý
• can apply the knowledge to new research domainsÌý
• Can use the acquired knowledge and carry out team assignments on new research topics by analyzing a given dataset.Ìý
• Can effectively present aims, analysis methods,ÌýresultsÌýand conclusions of a research project for research fellows and general public.Ìý

Teaching methods

Information to incoming exchange students

This course is open for inbound exchange students.

Do you have questions about this module? Please check the following website to contact the course coordinator for exchange students at the faculty:

Assessment

Access to the examination requires completing the following course work requirements:ÌýÌý

• Approval of eight out of ten submitted reportsÌý

Examination:Ìý

• Oral presentation of a group project counting 100%Ìý
• AssessmentÌýscale:ÌýPass/failÌý

Students who fail the exam may register for a re-sit exam early in the following semesterÌý

Recommended reading/syllabus