Difference between revisions of "MBV-INFX410 2013"

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Bioinformatics for Molecular Biology - 2013

Please bookmark this page. All future changes or announcements for the 2013 course will be posted on this page.

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

The course consists of five weeks of lectures, exercises, a take-home exam (one week), and a take-home exam/assignment (roughly 20 pages). 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. 

Ph.D. level students may opt to take the course without the take-home partial exam/assignment for only 8 study points (MBV-INF9410A). Both MBV-INF4410 (M.Sc. level) and MBV-INF9410 (Ph.D. level) are 10 study point courses.

Course description

This intensive course will introduce students to bioinformatics resources and tools for molecular biology research. All the lecturers 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 5-10 university study points in molecular biology, biochemistry, or similar. If you are uncertain if your biology background is strong enough, please contact Jon (See contact details below) before you sign up for the course.

Course responsible is Dr. Jon K. Lærdahl (jonkl@medisin.uio.no) from the Department of Microbiology, Oslo University Hospital (OUH) - Rikshospitalet. Lærdahl is also employed by the CLS initiative at UiO and the Bioinformatics Core Facility (CF) at OUH and UiO.

Links to the web pages for the years 2009-2011 is found here and for 2012 here. 

Notes on the course format: The course has previously been given as an intensive course over two weeks with a take-home exam in the 3rd to 4th week. A take-home assignment was also a compulsory part of the 10 study points versions of the course. The compact format was ideal for students coming from outside Oslo, but it was also exhausting for students and lecturers. It gave little time to digest and dive more deeply into the various topics presented in the course. In 2013, the course will be given in weeks 46-51. However, it will only be necessary to be physically present in Oslo for parts of the course, i.e. the lectures/exercises and, if practically possible, the students presentation day. The schedule is presented below, but there might be small adjustments to this schedule. The course content will be similar to the course in 2012.

Time and place

The course will be offered in weeks 46 to 50, autumn 2013, i.e. starting on Monday November 11 (See schedule above). The take-home exam must be handed in in week 51, on Wednesday December 18. Each day of lectures/exercises 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 weeks 46 and 47 (Monday to Thursday) 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 easiest access to Python is through the entrance in the tunnel going through the building.

Lectures/exercises in week 48 (Tuesday to Friday) will be given in the lecture room Store Auditorium in Kristen Nygaards hus (IFI1), found here. Student presentations on Monday December 9 will take place in lecture room Prolog in OJDs hus.

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@ibv.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.  

PhD students Gro Nilsen and Ksenia Khelik from the Department of Informatics will help during all exercises.

The finale lecture/exercise programme will be made available early in the autumn, but the topics covered will be mainly the same as in 2012. Requests and suggestions are welcome.

On Wednesday November 20, between 11:15 and 12:00, there will be a combined course lecture and CLS seminar by Jonas Paulsen from Oslo University Hospital. This will be on the study of chromatin 3D structure.

Bioinformatics mailing list for the Oslo region

The mailing list for computational biology and bioinformatics in the Oslo region is cbo-all@usit.uio.no. The list has approximately 330 members. The list is used to distribute news about seminars, positions, courses, meetings and other topics that might be of interest to students and researchers with an interest in computational life science in south-eastern Norway. If you want to receive e-mails that are sent to the list, sign up here

https://sympa.uio.no/usit.uio.no/info/cbo-all

by following the link termed "Subscribe".

Useful links

Trond Hasle Amundsen's Local guide to Linux and Unix

EMBnet Quick guide Unix

UCSC Genome browser

Free UCSC Genome browser tutorial   from OpenHelix

Portal to Galaxy

Galaxy 101 and other Galaxy screencasts/tutorials

The Genomic HyperBrowser