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Bioinformatics for Molecular Biology

THIS IS INFORMATION FOR THE COURSE IN 2012. Information on the course in 2015 is here.

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).

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

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 easiest access to Python is through the entrance in the tunnel going through the building.

Lectures/exercises in week 48 will be given in the following lecture rooms:

Assembler: Monday 09:00 - 10:45

Python: Monday 11:00 - 16:00 and Tuesday, whole day

Java: Wednesday 09:00 - 12:15

C: Wednesday 12:15 - 16, and Thursday and Friday, whole days

Java is in 2. etasje, all other rooms in 3. etasje.

Course description

This two week, 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) at least three weeks before the start of the course.

Links to the web pages for the years 2009-2011 is found here. The course 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

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 at https://kiosk.uio.no If your UiO user name is justinbieber you should type uio\justinbieber in the "Brukernavn" field. 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 three weeks 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

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

Basic Unix tutorial with practicals

A tiny taste of simple 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 browsers and

Galaxy

- lectures/exercises

Introduction to statistical inference and multiple hypothesis testing - lecture

Galaxy, workflows, reproducibility, HyperBrowser

- lectures/exercises

Jon K Lærdahl Clara-Cecilie Günter Geir Kjetil Sandve
Thursday 22nd

Basic R programming and exploring your data

- lecture/exercise

Basic statistical testing in R

- lecture/exercise

Regression in R 

- lecture/exercise 

Anja Bråthen Kristoffersen Anja Bråthen Kristoffersen Anja Bråthen Kristoffersen
Friday 23rd

Next generation sequencing (NGS)

- lecture

Introduction to structural biology

- lecture

Ian Donaldson's ID mapping lecture & exercise

Thanks a lot to Ian!

Robert Lyle  Jon K Laerdahl  Jon K Laerdahl
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 Ståle Nygård
Tuesday 27th

The bioinformatics of sequencing and assembling genomes - with a focus on the Atlantic cod and salmon genome projects

- lecture

Sequence searching, alignments, and multiple alignments

- lecture

Working with sequences

- exercises

Lex Nederbragt  Torbjørn Rognes Torbjørn Rognes
Wednesday 28th

Structural bioinformatics tools, predictors & 3D modelling

- lecture

Applied sequence bioinformatics

- exercise

Structural biology in PyMOL

- exercise

Jon K Lærdahl Jon K Lærdahl Jon K Lærdahl
Thursday 29th

Structural bioinformatics Modelling Guide -

lecture

Structural bioinformatics -

exercise 

Structural bioinformatics -

exercise & summary

Jon K Lærdahl Jon K Lærdahl Jon K Lærdahl
Friday 30th

Docking and drug discovery

- lecture

NGS & variant calling lab NGS & variant calling lab
Bjørn Dalhus 

Tim Hughes & Robert Lyle

Tim Huges & Robert Lyle

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

Exam

########

13 December at 10:20: Jalview has been fixed! Good luck with the exam.

12 December at 20:00: The Jalview webservice is down. I have contacted the developers and they will hopefully fix everything very soon.

Update: The exam for the course was sent, by e-mail, to all students on December 6. If you did not receive the exam, please contact Jon immediately!

Some corrections/clarifications:

  • There is an error in Exercise 2 (on page 4). The miRNA named "hsa-miR-206", which you are asked to plot, is not in row number 18 (as written in the exam), but in row number 181. This means that the values we want you to plot is in d$counts[181,]. We will take this error into account when correcting the exams.
  • There are 4 exercises, giving 12, 16, 10, and 36 points. Full score on all tasks will five 74 points.
  • In Exercise 4, sub-task (b), we are asking for 4 protein sequences to be aligned in Jalview. These are the 692 residues sequences from UniProtKB, RefSeq, Ensembl, and translated GenBank.
  • Jalview was down for 14 hours between December 12 and 13. For this reason the deadline for returning the exam was changed to 11 am, Friday December 14.

########

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

The exam will be sent to all participants at 3 pm, Thursday December 6, by e-mail.

Your completed exam must be returned, at the latest, at 11 am, Friday December 14. It should be sent by e-mail to the course administrator Torill Rørtveit (e-mail address: torill.rortveit@imbv.uio.no). Please put the course code and your candidate number in the subject field (e.g. "Exam MBV-INF4410 Candidate:12345").

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-INF4410-12345.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 Monday, January 21, 2013, at 3 pm. It should be at least 1500 words for Ph.D. level students and at least 1000 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.

Choose one of the following topics (one, only):

  1. Choose 3 biological databases from the latest NAR database issue. Write a description of the 3 databases that for each of them includes the following:
    1. What is the main focus of the database?
    2. A description of some searches and their results (screen-shots might improve your description)
    3. A pointer to instructions on how to use the database (a web-link is fine if one exists)
    4. Advice for first time-users. How did you overcome problems, if you had any?
    5. 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?
    6. 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
    7. If you have time, 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
    8. References to articles and other information on the database (e.g. PubMed and/or web-links)
  2. Choose 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 3 applications/programs/tools that for each of them includes the following:
    1. What are the problems/tasks this application is used for?
    2. What are the input and output of the tool? Screen-shots might improve your description
    3. A pointer to instructions on how to use the resource (a web-link is fine if one exists)
    4. Advice for first time-users. How did you overcome problems, if you had any?
    5. A brief description of the method that the tool uses. A good place to look for this information is in the corresponding paper
    6. A brief description of how this method is related or different from other methods that solve the same or similar problems
    7. 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
    8. If you have time, 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
    9. References to articles and other information on the application (e.g. PubMed and/or web-links)
  3. 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.
  4. You may define your own alternative topic. Please send an email to jonkl@medisin.uio.no, before December 14, 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 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