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

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. 

 The 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. Major topics will include: 

• Bioinformatics software platforms 
• Genomics: quality control, assembly and annotation 
• Comparative genomics and transcriptomics 
• Evolutionary relationships and genetic diversity 
• Metagenomics, amplicon and community profiling 

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

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

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.

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

Knowledge 

Bioinformatics software platforms 

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

Genomics: quality control, assembly and annotation 

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

Comparative genomics and transcriptomics 

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

Evolutionary relationships and genetic diversity 

• has advanced knowledge about principles behind phylogenetic and phylogenomic analyses 
• has thorough knowledge about software used for evolutionary studies 
• has advanced knowledge on the practical aspects of analysing genetic diversity 

Metagenomics, amplicon and community profiling 

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

Skills 

• Can evaluate and select bioinformatics tools and sequence data from publically available repositories, and use them to address biological questions 
• Can use bioinformatic tools for analyzing genomes, transcriptomes, genetic variation, evolutionary relationships and microbial communities. 

General competence    

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

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

• Approval of eight out of ten submitted reports 

Examination: 

• Oral presentation of a group project counting 100% 
• Assessment scale: Pass/fail 

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

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