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Bioinformatics for Molecular Biology

This is the wiki for the courses MBV-INF4410, MBV-INF9410, and MBV-INF9410A offered by the Department of Molecular Biosciences and Department of Informatics at the University of Oslo (UiO).

The course consists of two weeks of lectures, a final take-home exam (one week) and an essay (10 to 20 pages) to be completed by the middle of December.

Ph.D. level students may opt to take the course without the essay for only 8 study points (MBV-INF9410A).

Please bookmark this page. All future changes or announcements for the 2012 course will be posted on this page.

Time and place

The course will be offered in weeks 47 and 48, autumn 2012, i.e. November 19 - November 30. Each day, Monday to Friday, will consist of three time slots for lectures and/or exercises/practical labs between 09:00 and 16:00. Lunch will usually be between 12:45 and 13:30. You will have to bring your own lunch or buy lunch in the local kantine. 

Lecture room: All lectures/exercises in week 47 will be given in lecture room Python in Ole-Johan Dahls hus (IFI2). A map showing the location of the building is found here. The building is located next to the Forskningsparken metro and tram stations. The room Python is on the 1st floor (2. etasje) in the northern end of the building, the end closest to the tram line. The easist access to Python is through the entrance in the tunnel going through the building. The lecture room for week 48 will be announced later.     

Course description

This two week, intensive course will introduce students to bioinformatics resources and tools for molecular biology research. All the lectureres are among the top researchers working within the fields of bioinformatics and computational biology in the Oslo region. Students must bring their own lap-top for in-course demonstrations as well as for practical lab exercises. The course is mainly intended for biology students, but also for computer science students or students from other fields of science with an interest for and some experience with molecular biology. No prior background in bioinformatics or computer science is required. All students should have a basic understanding of molecular biology, at least roughly corresponding to a single semester course in molecular biology or biochemistry.

Links to the webpages for the years 2009-2011 is found here. The cource will in 2012 have a similar format as previous years, but with some few changes.

• New course responsible is Dr. Jon K. Lærdahl (jonkl@medisin.uio.no) from Centre for Molecular Biology and Neuroscience (CMBN) and Department of Medical Microbiology, Oslo University Hospital (OUH) - Rikshospitalet. Lærdahl is also employed by the Bioinformatics Core Facility at OUH and UiO.
• There will be some lectures focusing on the UNIX shell, scripting and the Python programming language.
• Examination (home exam) and written assignment will be in a similar format as previous years.  

Contacts

Jon K. Lærdahl (Course coordinator) - e-mail: jonkl@medisin.uio.no, phone: +47 99 507 335

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

Programme

The schedule below is tentative, and may be changed prior to, and possibly even during, the course. Requests and suggestions are welcome.  

Week 1: Monday, November 19 - Friday, November 23
	Session 1	Session 2		Session 3
	09:00 - 10:45	11:00 - 12:45		13:30 - 16:00
Monday 19th	Introduction Biological databases on the web Accessing data		Basic UNIX tutorial with practicals Simple examples of scripting
	Jon K. Lærdahl	Jon K. Lærdahl		Jon K. Lærdahl
Tuesday 20th	Basic Python programming	Python workshop		Python workshop
	Karin Lagesen	Karin Lagesen		Karin Lagesen
Wednesday 21st	Genome browser and Galaxy - lectures/exercises	Introduction to statistical inference and multiple hypothesis testing - lecture		Galaxy, workflows, reproducability, HyperBrowser - lectures/exercises
	Jon K. Lærdahl	Clara-Cecilie Günter		Geir Kjetil Sandve
Thursday 22nd	Exploratory data analysis - lecture	Introduction to R and R-lab		R-lab
	Anja Bråthern Kristoffersen	Anja Bråthern Kristoffersen		Anja Bråthern Kristoffersen
Friday 23rd	High throughput sequencing - lecture	High throughput sequencing lab		High throughput sequencing lab
	Robert Lyle	Robert Lyle		Robert Lyle
Week 2: Monday, November 26 - Friday, November 30
	Session 1	Session 2		Session 3
	09:00 - 10:45	11:00 - 12:45		13:30 - 16:00
Monday 26th	Microarrays - lecture	Microarrays - practicals		Gene lists & over-representation analysis (ORA) - lectures/practicals
	Ståle Nygård	Ståle Nygård		Karin Lagesen
Tuesday 27th	Sequence searching, alignments, and multiple alignments - lecture	Working with sequences - exercises		Working with sequences - exercises
	Torbjørn Rognes	Torbjørn Rognes		Torbjørn Rognes
Wednesday 28th	JalView	Structural biology review - lecture		Structural biology tools, predictors & 3D modelling - lecture
	Jon K Lærdahl	Jon K Lærdahl		Jon K Lærdahl
Thursday 29th	Working with PyMOL	3D modlling guide		Modelling exercise
	Jon K Lærdahl	Jon K Lærdahl		Jon K Lærdahl
Friday 30th	Modelling exercise	Docking and drug discovery		Docking and drug discovery
	Jon K Lærdahl	Jon K Lærdahl		Jon K Lærdahl

Exam

The exam for this course will be a one week, take-home exam.

More details will be given later.