Course code BIN420

BIN420 Bioinformatics for functional metagenomics

Norsk emneinformasjon

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Showing course contents for the educational year 2018 - 2019 .

Course responsible: Phillip Byron Pope
Teachers: Torgeir Rhodén Hvidsten, Lars Gustav Snipen
ECTS credits: 5
Faculty: Faculty of Chemistry, Biotechnology and Food Science
Teaching language: EN
(NO=norsk, EN=Engelsk)
Limits of class size:
10
Teaching exam periods:
Autum semester
Course frequency: Will be given in 2017 only
First time: Study year 2017-2018
Course contents:
Microbial communities are renowned for the influences they exert in nature as well as industrial applications. They encompass an extraordinary level of species complexity that is invaluable to the overall function of the community. However, our understanding is severely restricted due to the inherent species complexity and the fact that the majority of microbes that exist in nature cannot be cultivated. This course will introduce, explore and assess the vast array of sequencing technology and bioinformatic methods that are available to address these core issues. The course will include an array of contrasting tools to decrypt microbial communities, including those that assess community structure (metagenomics, predictive genome-reconstruction) and function (metatranscriptomics, metaproteomics
Learning outcome:
  • Ability to design experiments and select appropriate methods and/or software
  • Explain the microbial population structure within a microbial community
  • Ability to perform and assess assembly and taxonomic binning methods as well as interpret output quality
  • Ability to combine the output from different omics methods to interpret the predicted function of uncultured microorganisms within a microbial community
  • Explain the shortcomings about these types of analyses
Learning activities:

Intensive one week course and one project assignment with written report. Each course day will consist of:

two, one hour lecturesa supervised computer lab (five hours).
Teaching support:
Canvas
Syllabus:
Will be specified at the beginning of the course.
Prerequisites:
Master in bioinformatics, or related topics. Must know UNIX at a user-level.
Recommended prerequisites:
Familiarity with a programming language (preferably Python and/or R) is expected. Basic knowledge in microbiology is also required.
Mandatory activity:
A written project report
Assessment:
There will be one project assignment where the students will present their findings in a written report (counts 100%).
Nominal workload:

Lectures: 10 hours

Computer labs: 25 hours

Individual study: 115 hours

Type of course:

2 lectures per day (1 hour each)

1 computer labs per day (5 hours)

Examiner:
The reports will be approved by an external examiner.
Examination details: Written report: Bestått / Ikke bestått