Course code BIN310

BIN310 Selected topics in genome analysis

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Showing course contents for the educational year 2014 - 2015 .

Course responsible: Torgeir Rhodén Hvidsten
Teachers: Niklas Mähler, Lars Gustav Snipen
ECTS credits: 10
Faculty: Department of Chemistry, Biotechnology and Food Science
Teaching language: EN, NO
(NO=norsk, EN=Engelsk)
Limits of class size:
Minimum 5, maximum 100
Teaching exam periods:
This course starts in Autumn parallel. This course has teaching/evaluation in Autumn parallel, .
Course frequency: Odd years
First time: Study year 2006-2007
Course contents:
There are weekly lectures and supervised exercises in the computer lab. It is important that students try to solve the exercises prior to attending the supervised computer lab. The computer lab can then be used to clarify difficult topics.
Learning outcome:

KNOWLEDGE: Students will be able to explain: The optimal algorithms for pairwise alignments, and the scoring models. The principles behind the heuristic algorithms for mutliple alignments and the commonly used evolutionary models in phylogenetic analyses. How sequences can be described by probabilistic models like profiles, ordinary Markov models and hidden Markov models, train such models from data and use them for sequence classification. Simpler linear models and multivariate methods for analyzing gene ekspression data.

SKILLS: Students will be able to: Apply elements from the topics above to solve a project assignment in the course. Implementing the algorithms in R and use this scripting language for effective processing of large data sets. Present material in a written report and orally.

Learning activities:
Two lectures weekly. Two to four hours supervised solving of problems in the computer lab weekly. These hours can also to some degree be used for ad-hoc lectures on topics of special interest, if requested by the students. Oral presentation of written report.
Teaching support:
Active use of the course website.
Will be specified at the beginning of the course.
Introduction to bioinformatics equivalent to BIN210. Programming knowledge equivalent to INF120. Statistics equivalent to STAT200/STAT210.
Recommended prerequisites:
Statistics equivalent to STAT300 or STAT310.
Mandatory activity:
A report will be written on a topic announced at the start of the course. There will also be an oral presentation of the report.
Written exam, 3.5 hrs.
Nominal workload:
Lectures: 26 hours. Exercises with instructor present: 44 hours. Individual study: 230 hours.
Entrance requirements:
Special requirements in Science
Type of course:
Lectures: 2 hours per week. Computer lab exercises: 4 hours per week.
Students must bring their own laptop to computer-labs
The exam will be approved by an external examiner. 25 radomly selected exam papers will be evaluated by the external examiner.
Allowed examination aids: No calculator, no other aids
Examination details: Written exam: A - E / Ikke bestått