MBV-INFX410 2016

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Bioinformatics for Molecular Biology - 2016

UNDER CONSTRUCTION!!!!!

All students must be present at the start of the course, at 09:15, on November 14. Missing students will not be allowed to follow the course or to take the exam. If you for some reason are not able to attend, please contact Jon Bråte (See contact details below).

This is the wiki for the courses MBV-INF4410 and MBV-INF9410 offered by the Department of Biosciences and Department of Informatics at the University of Oslo (UiO). Both MBV-INF4410 (M.Sc. level) and MBV-INF9410 (Ph.D. level) are 10 study point courses. The 8 study points variant of the course (MBV-INF9410A) will not be given after 2013.

The course consists of five weeks of lectures, exercises, obligatory assignments, and a take-home exam (one week). Obligatory assignments must be completed and approved before the exam and in the same semester. An additional, limited, oral examination may be arranged in cases where this is necessary for the student evaluation. The course is open also for non-UiO students. It is only necessary to be physically present in Oslo for certain parts of the course.

Here is an overview of the course. The contents of the different lectures and exercises will be available shortly.

Week 46 Week 47 Week 48 Week 49 Week 50
Mon Lectures/

exercises

Lectures/

exercises

Obligatory

home assignment

Lectures/

exercises

Exam start

(home assignment)

Tue Lectures/

exercises

Lectures/

exercises

Home assignment Lectures/

exercises

Exam start

(home assignment)

Wed Lectures/

exercises

Lectures/

exercises

Home assignment Lectures/

exercises

Exam start

(home assignment)

Thu Lectures/

exercises

Lectures/

exercises

Home assignment Lectures/

exercises

Exam start

(home assignment)

Fri Lectures/

exercises

Lectures/

exercises

Hand in

home assignment

Lectures/

exercises

Exam end

(home assignment)

Time and place

Room 1250, 1st floor of Biology Buiding (Kristine Bonnevies Hus).

Detailed program

The program is still under development and may be updated

Week Monday Tuesday Wednesday Thursday Friday
Nov 14 Nov 15 Nov 16 Nov 17 Nov 18
46 09:15 - 11:00:

Course introduction (lecture)

11:15 - 13:00:

Biological databases,

Unix (lectures/exercises)

14:15 - 16:00:

Basic Unix (excercises)

09:15 - 11:00:

Ensembl genome browser

and Jalview (lectures/demo)

11:15 - 13:00:

Working with sequences

and databases (lectures/exercises)

14:15 - 16:00:

Applied sequence bioinformatics

09:15 - 11:00:

More Unix and

UCSC genome browser (lectures/exercises)

11:15 - 13:00:

Galaxy / Life Portal (lectures/exercises)

14:15 - 16:00:

09:15 - 16:00:

Python workshop

(lectures / exercises)

09:15 - 16:00:

Python workshop

(lectures / exercises)

47 Nov 21 Nov 22 Nov 23 Nov 24 Nov 25
09:15 - 16:00:

Sequence searching and alignments

(lectures and exercises)

09:15 - 16:00:

Structural bioinformatics

(lectures and exercises)

09:15 - 16:00:

Structural bioinformatics

(lectures and exercises)

Docking and drug discovery

Practical Unix/Python exercise

Reproducibility /

Statistical epigenomics

48
49
50

Contacts

Jon Bråte (Course coordinator) - e-mail: jon.brate@ibv.uio.no, phone: +47 922 44 582

Torill Rørtveit (Course administrator, registration) - e-mail: torill.rortveit@ibv.uio.no