Difference between revisions of "MBV-INFX410 2014"

Latest revision as of 15:17, 28 October 2015

Bioinformatics for Molecular Biology - 2014

THIS IS THE WIKI FOR 2014. INFORMATION FOR 2015 IS FOUND HERE!

Please bookmark this page. All future changes or announcements for the 2014 course will be posted on this page.

Dec 19: All exams have been received from the students (except those with valid reasons to be delayed). The exams will be corrected as soon as possible. 

Dec 10: The exam for the course was sent, by e-mail, to all qualified students on December 10. If you did not receive the exam, please contact Jon immediately!

Nov 27: On Friday December 5, between 13:00 and 15:00, there will be a helpdesk session in lecture room Java (2. etasje). This is not a compulsory part of the course and there will not be any lectures. There will not be any new messages and no messages or hints about the exam (that is not also put on the wiki). This is an opportunity to get help with parts of the curriculum you are struggling with. Jon will be present, but will most likely not be able to answer all questions about the parts of the curriculum that has been taught by other teachers.

All students must be present at the start of the course, at 09:00, on November 10. 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 (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.

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 laptop 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 (Aug 2014: this server might be permanently down...), for 2012 here, and for 2013 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 no time to digest and dive more deeply into the various topics presented in the course. Since 2013, the course will be given over 5 weeks. However, it will only be necessary to be physically present in Oslo for parts of the course, i.e. the lectures/exercises. The schedule is presented below, but there might be small adjustments to this later.

Time and place

The course will be offered in weeks 46 to 50, autumn 2014, i.e. starting on Monday November 10 (See schedule below). The take-home exam must be handed in in week 51, on Wednesday December 17. 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 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.

Lecture room for Monday December 1 and Thursday December 4 will be Caml (3. etasje). On Tuesday December 2 and Wednesday December 3, we will be in the room Prolog (2. etasje). Both rooms are in Ole-Johan Dahls 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

Computers/laptops, internet access, and UiO user account

All students must bring a laptop with either a Windows (Windows 7 or more recent), Unix/Linux, or OS X (i.e. an Apple computer) operating system.

• The computer should not be more than 2-3 years old
• 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
• 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
• If you are unsure if you have a UiO user account and a valid password, you should try to log in using kiosk.uio.no or win.uio.no as described here. If you are unable to log in, try the hints you find here.
• Instructions (in Norwegian) about how to find your user name and get a new password can be found here.

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 above) as soon as possible, and at least one week before the start of the course.

To get a UiO username/password at the UiO helpdesk you need valid ID.

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.

Programme

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

Merete Molton Worren from the Bioinformatics Core Facility will help dusing the laptop setup session on Monday, November 10.

On Wednesday November 19, between 11:15 and 12:00, there will be a combined course lecture and CLS seminar given by staff from the Research Support Services Group, USIT, University of Oslo. This will be about the LifePortal at UiO. This lecture will take place in Informatikksalen in Ole-Johan Dahls hus. This is in 5. etasje (three floors up from lecture room Python). More information is found here

The brief lecture on PCSK9 can be found here, if you are interested. This is not a part of the curriculum.

Required reading material/curriculum

The curriculum comprises all lectures, lecture handouts, exercises and the reviews/articles/written material listed on this page.

An obligatory and compulsory assignment must be returned, by e-mail, to the course coordinator Jon K. Lærdahl (e-mail address: jonkl@medisin.uio.no) before Monday December, at 09:00. Note that students that do not get this assignment approved, will not be allowed to take the exam.

Exam

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Some messages:

• If Image Export does not work in Jalview 2.8.2, try this fix from the Jalview FAQ. If that does not help, wait a few hours and try again, try a different computer, ask Jon, or if everything else fails, use a screen dump instead. In this case, write in your answers why you had to do this.
• The exam for the course was sent, by e-mail, to all qualified students on December 10. If you did not receive the exam, please contact Jon immediately!

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The exam for this course will be a one week, take-home exam. Only students that have returned the obligatory assignment, and got this assignment approved, will be allowed to take the exam.

The exam will be sent to all qualified participants at 3 pm, Wednesday December 10, by e-mail. 

Your completed exam must be returned, at the latest, at 3 pm, Wednesday December 17. It should be sent by e-mail to the course administrator Torill Rørtveit (e-mail address: torill.rortveit@ibv.uio.no). Please put the course code and your candidate number (for this course) in the subject field (e.g. "Exam MBV-INF4410 Candidate:15").

The exam must be handed in as a single PDF document (Microsoft Word or an Open Office Document is also acceptable). The document should be named with the course code and your candidate number only (e.g. MBV-INF4410-15.pdf). Do not place your name in the document.

An additional, limited, oral examination may be arranged in cases where this is necessary for the student evaluation.

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 400 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

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 2014 Nucleic Acids Research Database Issue

The 2014 Nucleic Acids Research Web Server Issue

UiO and OUS Bioinformatics Core Facility