Course code BIN310

BIN310 Selected Topics in Microbial Genomics

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Showing course contents for the educational year starting in 2021 .

Course responsible: Lars Gustav Snipen
ECTS credits: 10
Faculty: Faculty of Chemistry, Biotechnology and Food Science
Teaching language: EN, NO
(NO=norsk, EN=Engelsk)
Limits of class size:
40
Teaching exam periods:
This course starts in autumn parallel. This course has teaching/evaluation in autumn parallel.
Course frequency: Odd years
First time: 2006V
Preferential right:

Students who have the course compulsory as part of a study program at KBM will be given priority

Course contents:

Modern sequencing technology, shotgun and amplicon sequencing. Assembly and annotations of genomes and metagenomes. Simulation of sequencing data, both Illumina and Nanopore. Analyses of data from microbial communities (readcount-tables).

Competence in Bioinformatics contributes to all UN goals for sustainable development that involves biology (health, hood, nature).

Learning outcome:

KNOWLEDGE: The ideas behind commonly used algorithms for processing and analysis of sequence data. Get to know a UNIX computing cluster and simple shell scripting. Know some common statistical methods for metagenome-studies and apply these on real data using R and R-packages.

SKILLS: Be able to apply elements from the topics above to solve project assignments in the course. Making simple shell-scripts and R-scripts and run heavier analyses on a UNIX computing cluster. Present material both orally and in a written report.

GENERAL COMPETENCE: Be able to make use of, and understand, the future computational pipelines of (meta)genome studies. Practical programming competence, directed toward analysis og bio-data.

Learning activities:
The basis for the course is a series of written material as markdown documents as well as a number of screencasts. All physical teaching will be at weekly hours used for discussions and solutions to exercises as well as simple lectures over certain topics of special interest. There will also be oral presentations over some project reports.
Teaching support:
Active use of Canvas.
Syllabus:
Will be specified at the beginning of the course.
Prerequisites:

Introduction to bioinformatics (BIN210) - Some knowledge of modern sequencing - Basics on sequence alignments, pairwise, multiple, database search (BLAST) - Basics on phylogeni

Introduction to statistics (STAT100) - Familiar with stochastic variables and parameters - Basic calculus of probability, conditional probabilities

Introduction to programming (STIN100) - Be familiar with datatypes numeric, character, logical, factor - Be familiar with data structures vector (array), matrix, table (tibble/data.frame), list - Be familiar with concepts like loops and functions/methods

No advanced coding will be required, but we have no time for general teaching in coding. All coding will be in R and shell (bash).

Recommended prerequisites:
Programming and statistics beyond the introductory level. 
Assessment:
Portfolio asessment. Several project assignments will be given, and all must be passed in order to pass the course.
Nominal workload:
70 hours with instructor present: 180 hours self study
Entrance requirements:
Special requirements in Science
Type of course:
6 hours teaching activities per week. This is a mixture of lectures, hand-on exercises and solving problems in Groups.
Note:
Students must bring their own laptop to computer-labs.
Examiner:
External examiner will approve the projects and evaluate a selection of them
Examination details: Portfolio: A - E / F