Bioinformatics course

From irefindex
Bioinfo course logo.jpg
About this image

Bioinformatics for molecular biology - Fall 2010


The aim of the course is to introduce students to bioinformatics resources and tools for molecular biology research by having some of the best researchers in Norway to talk about their field in general and then present their own work. Students are encouraged to bring a lap-top; we will be set up for in-course demonstrations as well as practical lab exercises. The course is intended for biology students or computer science/math students. No prior background in bioinformatics or computer science is required.

The course is jointly delivered by the Biotechnology Centre of Oslo, the Department of Molecular Biosciences (IMBV), the Department of Informatics (IFI) and the Norwegian University of Life Sciences. This course is one of the Ph.D. School courses offered by the Biotechnology Centre of Oslo ( The UiO page for this course is

Registration will be open in May of 2010. Check back here for details

MBV-INF 4410 (M.Sc. level course code)10.0 study points

MBV-INF 9410 (Ph.D. level course code) 10.0 study points

MBV-INF 9410A (Ph.D. level course code) 8.0 study points

The course consists of two weeks of lectures, a final take-home exam (one week) and an essay (M.Sc. level 10 pages and Ph.D. level 20 pages to be completed by end of October).

Ph.D. level students may opt to take the course without the essay for only 8 study points.

Please bookmark this page. All future changes or announcements for the 2010 course will be posted to this page.

        (about course administration) 
        (about course content)

Dates and times

The course will occur September 6th to 17th.

Each day will consist of three time slots for lectures and/or practical labs between 9 AM and 4 PM.



Directions to Forskningsparken can be found at

Mondays to Friday morning: Room 10 (one level down from the main entrance) The room is booked each day from 09:00 to 16:00 EXCEPT Fridays when the room must be vacated from 12 to 13:30.

Exceptions: none so far

Lunch is on your own between 1:00 PM and 2:15 PM. Please completely vacate the room during these lunch times.


Please note:
The schedule displayed below is based on last years course 
Ongoing changes will be made to this page as we organize speakers over the next few months.  
Requests and suggestions are welcome.
Bioinformatics 2010
Time Speaker Contact Details and suggested readings
Day 1 - Monday September 6
9.00-9.15 Ian Donaldson Introduction
9.15-11.00 Anja Bråthen Kristoffersen (TBC)

Exploratory data analysis Extra material

11:15-13.00 TBA

Introduction to R - Presentation

14.15-16.00 TBA

Introduction to R - Lab

Day 2 - Tuesday September 7
9.15-11.00 Ole Christian Lingjærde

An introduction to statistical inference

11:15-13.00 Einar A. Rødland

Multiple hypothesis testing

Day 3 -Wednesday September 8
9.15-11.00 Leonardo Meza-Zepeda Dept. of Tumor Biology, Rikshospitalet-Radiumhospitalet Medical Center

Microarray technology 1

Microarray technology 2

11:15-13.00 Ståle Nygård

Microarray data analysis

14.15-16.00 Ståle Nygård R Microarray data analysis lab
Day 4 - Thursday September 9
9.15-11.00 Torbjørn Rognes

Searching sequence databases

11:15-13.00 Geir K. Sandve Motif scanning and discovery in DNA

Geir K. Sandve


Vegard Nygaard

Sequence lab



Day 5 - Friday September 10

Sveinung Gundersen

Geir K. Sandve

Hyperbrowser tutorial

11.15-12:00 Dave W. Ussery Comparative genomics

Methods to compare genomes

12.00-13:30 Lunch -vacate room
13:30-14:15 Dave W. Ussery Comparative genomics

Pan-genomics and metagenomics

14.15-16.00 Sequence lab
Day 6 - Monday September 13
9:00-11:00 Robert Lyle

High throughput sequencing

11:15-13.00 George Magklaras


13:00-14:00 Lunch
14.15-16.00 Kamran Shalchian-Tabrizi


Day 7 - Tuesday September 14
9.15-11.00 Jon K. Laerdahl

Structural biology review


Installing PyMol

11:15-13.00 Jon K. Laerdahl

Structural bioinformatics tools, predictors, and 3D modeling

14.15-16.00 Jon K. Laerdahl Structural tutorials and exercises

PyMol demonstration

PyMol excercise

Day 8 - Wednesday September 15
9.15-11.00 Jon K. Laerdahl Structural modeling tutorial
11:15-13.00 Jon K. Laerdahl Structural modeling tutorial
14.15-16.00 Jon K. Laerdahl Structural modeling tutorial
Day 9 - Thursday September 16
9.15-11.00 Ian Donaldson

Working with gene lists and over-representation analysis

11:15-13.00 Ian Donaldson

Interaction data resources

iRefIndex talk at BioPathways talk

14.15-16.00 Antonio Mora, Sabry Razick, Paul Boddie Interaction lab

Install and

Day 10 - Friday September 17
9.15-10.00 Erik Plahte

Modelling paradigms for gene regulatory networks

10.15-11.00 Arne Gjuvsland

Causally cohesive genotype-phenotype modelling - systems biology meets genetics

11.15-12.00 Jon Olav Vik

cGP map of the cardiomyocyte

12.00-13:30 Lunch -vacate room
13:30-14:15 Harald Martens


14.15-15.00 Achim Kohler

A new phenotyping paradigm for yeast

15.15-16.00 Solve Sæbø

Disease diagnostics from microarrays: Improved accuracy by using background knowledge on gene-gene dependencies?

Written assignment

Please note:
The displayed essay topics are from last year as an example. 
The 2010 course assignments will be different.

Students enrolled in MBV-INF 4410 must complete a written assignment as part of the course requirements.

The assignment is due by October 27th. It should be emailed to ian.donaldson at preferably as a PDF document (Microsoft Word or OpenOffice is also acceptable). The assignment is to be between 1000 to 2000 words and no more than 10 pages. Topics include:

1) write an explanation of three or more methods that were covered in the course. These should be simple explanations aimed at someone approaching the topic for the first time. Your explanation may include derivations of equations (if they are clearly explained), figures or tables. Use examples. Describe how the concept can be applied to a problem in biological research and what limitations the method has. List any resources you use as well as references to additional material that a student might use if they want to follow up on the topic further. Please indicate whether your material may be used on the course's wiki page.

2) describe how you would use two or more of the methods covered in the course in your own research. Your proposal may include figures 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.

3) you may define your own alternative topic. Please send an email to ian.donaldson at to have your topic approved first.


Please note:
The exam for this course will be a one week take home exam.

Bioinformatics links relevant to the course

Bioinformatics Links 2010
Name URL Description
Day 1 - Statistics
StatSoft textbook Good overview of methods and concepts
SAS manuals Thorough overview of analysis procedures found in SAS
GraphPad See the GraphPad statistical guide for easy introductions to many concepts in statistics
Day 2 - Statistics
R The Comprehensive R Archive Network
Learning R A Quick Guide to Teaching R Programming to Computational Biology Students
EMBNet Microarray course An online course with R/Bioconductor example tutorials
EMBNet tutorials Other helpful tutorials with R examples related to biostatistics
Day 3 - Microarrays
NMC Norwegian Microarray Consrtium
MACF UiO MicroArray Facility
Bioinformatics core facility The Bioinformatics Core Facility established at Rikshospitalet-Radiumhospitalet (RR) will provide its users at RR and the University of Oslo with a range of services within bioinformatics, including analysis of DNA and protein sequences, analysis of microarray data, protein structure analysis and access to useful databases and web services
Day 4 - 5 Sequence
RSAT RSAT A collection of several motif-related tools
ConTra ConTra A more user-friendly tool for matching a collection of Position Weighted Matrices against promoter sequences across species
Day 6 -
Day 7 -
Required files [Sample network[1]] [Node atributes[2]] Please download these and uncompress before using
Cytoscape Cytoscape home page
Cytoscape Tutorial on Cytoscape
iRefIndex Cytoscape plugin iRefIndex installation
iRefIndex iRefIndex wiki
iRefIndex publication Full details of iRefIndex
DAVID Nature Protocols paper
GSEA Gene Set Enrichment Analysis application

Bioinformatics Mailing Lists

If you are interested in being informed of future courses, talks and new related to bioinformatics in the Oslo region, then consider signing up for the cbo mailing list.

You might also consider the Norwegian-wide bioinformatics email list. You can sign up at

Both lists are run by members of the Norwegian Bioinformatics Platform.