MBV-INFX410 2014
Bioinformatics for Molecular Biology - 2014
THIS PAGE IS BEING UPDATED NOW - PLEASE BE PATIENT
Please bookmark this page. All future changes or announcements for the 2014 course will be posted on this page.
There is a waiting list for the course! If you have signed up for the course, but have decided not to attend, please contact Jon or Torill and make your place available to someone else (See contact details below).
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...) 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 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.
Time and place
The course will be offered in weeks 46 to 50, autumn 2014, i.e. starting on Monday November 10 (Detailed schedule will be available later) The take-home exam must be handed in in week 51 (exact date will be announced later). 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.
The lecture room for lectures/exercises for the rest of the course is not yet decided.
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 XP 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 detailed schedule will be available later in the autumn. Requests and suggestions are welcome.
Required reading material/curriculum
The curriculum comprises all lectures, lecture handouts, exercises and the reviews/articles/written material listed on this page.
Exam
The exam for this course will be a one week, take-home exam.
Your completed exam must be returned after one week. 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.
Written assignment
The students enrolled in MBV-INF4410 or MBV-INF9410, but not MBV-INF9410A, must complete a written assignment as part of the course requirements.
The assignment is due by 3 pm, Friday December 6. It should be of the order of 4000 words for Ph.D. level students and 2500 words for M.Sc. students. The assignment should be sent to Jon K. Lærdahl (e-mail: jonkl@medisin.uio.no) as an e-mail attachment, as a single file. Start the assignment with a brief introduction and state the total number of pages and words (e.g. calculated with Microsoft Word "Word Count").
Choose one of the following topics (one, only):
- Choose at least 3 biological databases from the latest NAR database issue. Write a description of the databases that for each of them includes at least the following:
- What is the main focus of the database?
- A description of some searches and their results (screen-shots might improve your description)
- Instructions on how to use the database
- Advice for first time-users. How did you overcome problems, if you had any?
- A brief description of how this database is related to other databases. What does it link out to and what does it provide that other databases do not provide?
- Information on how often the database appears to be updated. Is it actively developed and maintained? Look for last release date, mailing lists, and user documentation
- A test of the database (or parts of it) to make certain that it is reliable. You could, for example, try doing similar searches in another database and compare the results
- A discussion on how useful you think the database is
- References to articles and other information on the database (e.g. PubMed and/or web-links)
- Choose at least 3 bioinformatics tools or applications, for example from the latest NAR web server issue. Learn how to use the tools. Download and install, if necessary. Write a description of the applications/programs/tools that for each of them includes at least the following:
- What are the problems/tasks this application is used for?
- What are the input and output of the tool? Screen-shots might improve your description
- Instructions on how to use the resource
- Advice for first time-users. How did you overcome problems, if you had any?
- A brief description of the method that the tool uses. A good place to look for this information is in the corresponding paper
- A brief description of how this method is related or different from other methods that solve the same or similar problems
- Information on how often the application appears to be updated. Is it actively developed and maintained? Look for last release date, mailing lists, and user documentation
- A test of the application to make certain that it is reliable. You could, for example, try using another tool that performs a similar analysis and compare the results. Alternatively, you can pose a trivial problem to the tool that you know the answer to
- A discussion on how useful you think the application is
- References to articles and other information on the application (e.g. PubMed and/or web-links)
- Describe how you would use 2 or more of the methods covered in the course in your own research. Your proposal is likely to be better if you include figures and/or tables. Give a short introduction to your problem area, clearly state your hypothesis and how you think it might be addressed by each of the methods. Provide justifications for your proposal as well as expected outcome. Describe potential risks (say, the method provides no meaningful results) and what you would do to mitigate this risk. List any resources you use.
- You may define your own alternative topic. Please send an email to jonkl@medisin.uio.no or talk to Jon, before November 30, to have this approved first.
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 370 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
UiO Lifeportal and more information on the Lifeportal
Norwegian EMBnet node public Galaxy server instance
The Genomic HyperBrowser
Links Directory from bioinformatics.ca