Difference between revisions of "MBV-INFX410 2016"

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=== Detailed program ===
 
=== Detailed program ===
The program is still under development and may be updated. The times listed here are only tentative and may likely change. We will mix in small breaks and try to have a lunch break between 13:00 - 14:00.
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<span style="background:yellow">The program is still under development and may be updated.</span> The times listed here are only tentative and may likely change. We will mix in small breaks and try to have a lunch break between 13:00 - 14:00.
 
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|+Detailed schedule for MBV-INFX410 2016
 
|+Detailed schedule for MBV-INFX410 2016

Revision as of 13:04, 4 October 2016

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.

Course information

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.

General schedule for MBV-INFX410
Mon Tue Wed Thu Fri
Week 46 Lectures/

exercises

Lectures/

exercises

Lectures/

exercises

Lectures/

exercises

Lectures/

exercises

Week 47 Lectures/

exercises

Lectures/

exercises

Lectures/

exercises

Lectures/

exercises

Lectures/

exercises

Week 48 Obligatory

home assignment

Obligatory

home assignment

Obligatory

home assignment

Obligatory

home assignment

Hand in

home assignment

Week 49 Lectures/

exercises

Lectures/

exercises

Lectures/

exercises

Lectures/

exercises

Exam start

(home assignment)

Week 50 Exam

(home assignment)

Exam

(home assignment)

Exam

(home assignment)

Exam

(home assignment)

Exam end

(home assignment)

Time and place

Most of the teaching will take place in room 1250 on the 1st floor of Biology Buiding (Kristine Bonnevies Hus). The teaching starts at 09:15 and we will end at latest 16:00.

Detailed program

The program is still under development and may be updated. The times listed here are only tentative and may likely change. We will mix in small breaks and try to have a lunch break between 13:00 - 14:00.

Detailed schedule for MBV-INFX410 2016
Week Monday Tuesday Wednesday Thursday Friday
46 Nov 14 Nov 15 Nov 16 Nov 17 Nov 18
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 Nov 28 Nov 29 Nov 30 Dec 1 Dec 2
Obligatory home assignment Obligatory home assignment Obligatory home assignment Obligatory home assignment Hand in home assignment
49 Dec 5 Dec 6 Dec 7 Dec 8 Dec 9
Introduction to statistical inference and R

Basic R and exploring your data

Analysis of gene expression using R NGS Last course day

What does it mean to do bioinformatics?

Gene lists and over-representation analysis

Summary

Hand out exam
50 Dec 12 Dec 13 Dec 14 Dec 15 Dec 16
Home exam Home exam Home exam Home exam Hand in exam

Required reading material / Curriculum

The curriculum comprises all lectures, lecture handouts and exercises, in addition to the articles listed below:

Other good articles (not curriculum)

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