MBV-INFX410 2016

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Bioinformatics for Molecular Biology - 2016

Messages

  • All students must be present at the start of the course, on November 14 at 09:15 in room 1250 in Kristine Bonnevies (KB) Hus (biology building). 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).

Course information

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.

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)

Computers/laptops, internet access, and UiO user account

All students are strongly encouraged to bring their own laptops.

  • It should be possible to connect the computer to the UiO wireless network
  • You must have a root/administrator password that gives you access to installing new software on the computer
  • Please bring an external mouse, and do not rely on touchpad/trackpad only
  • You must have a valid UiO user account and must be able to log onto a computer on the UiO network
  • Instructions on how to find your username and get a new password can be found here. To get a UiO username/password at the UiO helpdesk you need valid ID.

If you are struggling with anything of the above, in particular if you have forgotten your UiO user name/password or you do not have one, you must contact Jon (see contact details) as soon as possible, and at least one week before the start of the course.

On the first day of the course we will set up your laptop so that it can be used for the exercises/tutorials, the home exam and hopefully in your future work. How to get a reasonable setup is described here.

If you already are an expert programmer and Unix guru, go here.

Time and place (Rooms)

The teaching starts at 09:15 and we will end at latest 16:00. Most of the teaching will take place in room 1250 on the 1st floor of Biology Buiding (Kristine Bonnevies Hus, KB). This is a computer room with Desktop machines you can use. Some days we have to change rooms and use a seminar room without desktops. Therefore you have to bring your own laptops (or share with someone else) those days (see the detailed program). NB: November 17 and 18 we will be at Ole Johan Dahls hus (OJD) on the other side of the subway line in the Python seminar room on the second floor.

Detailed program

The times listed here are only tentative and may likely change. We will mix in small breaks here and there and try to have a lunch break between 12:00 - 13:00.

Detailed schedule for MBV-INFX410 2016
Week Monday Tuesday Wednesday Thursday Friday
46 Nov 14 Nov 15 Nov 16 Nov 17 Nov 18
Room 1250 KB

09:15 - 12:00

Course introduction. (lecture)

Introduction to bioinformatics and sequence databases (lecture)


12:00 - 13:00

Lunch

13:15 - 14:00

Setting up laptops

Basic Unix (lecture (slides by Jon K. Lærdahl))

14:15 - 16:00

Basic Unix (exercises)

Room 1250 KB

09:15 - 11:00

Genome browsers (lecture/ exercise)

and Jalview (lecture /demo)

11:15 - 12:00

Working with sequences

and databases (lectures)

12:00 - 13:00

Lunch

13:15 - 16:00

Applied sequence bioinformatics (exercise)

Room 4613 KB

09:15 - 12:00

Galaxy/Life Portal (lectures/exercises)

12:00 - 13:00

Lunch (we might have to skip this and finish early)

13:15 - 14:00

More Unix (lecture)

Room Python OJD

09:15 - 16:00

Python workshop

(lectures / exercises)

Room Python OJD

09:15 - 16:00

Python workshop

(lectures / exercises)

47 Nov 21 Nov 22 Nov 23 Nov 24 Nov 25
Room 1250 KB

09:15 - 16:00

Sequence searching and alignments (lectures part1 part2, exercises (New exercise 32))

Room Python OJD

09:15 - 16:00

Structural Bioinformatics

(lectures and exercises)

Room Python OJD

09:15 - 16:00

Structural Bioinformatics

(lectures and exercises)

Room 4613 KB 9:15-12

Room 1250 KB 13:15-16

09:15 - 12:00

Docking and drug discovery

13:15 - 16:00

Practical Unix/Python exercise

Room 2203a KB 9:15 - 12

Room 1250 KB 13:15-16

Statistical epigenomics (& reproducibility).

Lectures / exercises

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
Room 1250 KB

09:15 - 16:00

Introduction to statistical inference and R.

Basic R.

Room 1250 KB

09:15 - 16:00

Analysing transcriptome data using R

Room 1250 KB

09:15 - 16:00

Next Generation Sequencing & variant calling

Room 4613 KB

Last course day

09:15 - 11:00

What does it mean to do bioinformatics?

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

Useful links

Trond Hasle Amundsen's Local guide to Linux and Unix

EMBnet Quick guide Unix

Useful command line one-liners by Stephen Turner

Jalview and Jalview refcard

UCSC Genome browser

Free UCSC Genome browser tutorial   from OpenHelix

Portal to Galaxy

Galaxy 101 and other Galaxy screencasts/tutorials

UiO Lifeportal and more information on the Lifeportal

The Genomic HyperBrowser

Links Directory from bioinformatics.ca

The 2015 Nucleic Acids Research Database Issue

The 2015 Nucleic Acids Research Web Server Issue

UiO and OUS Bioinformatics Core Facility