Bioinformatics for molecular biology 2009

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Bioinformatics for molecular biology (10.0/8.0 credit points)

Description 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 (

Registration is now open as of July 3rd, 2009.

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

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

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

The course can be taken as a full course (10 credit points) or as a short version without writing the essay (8 credit points) for Ph.D. level students.

NOTE: The description of the course at is old and will be updated to reflect the course content and format described on this page.

Please bookmark this page. All future changes or announcements for the 2009 course will be posted to this page.

        (about course administration) 
        (about course content)

Dates and times

The course will occur in weeks 37 and 38 (September 7th and 14th).

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



Directions to Forsknings parken can be found at

Mondays to Thursdays: Room 10 (one level down from the main entrance)

Fridays: Room 7 (one level down from the main entrance)

Exceptions: none so far

Lunch is on your own between 1:00 PM and 2:15 PM (except 15th and 22nd: 11:00 AM to 12:30). Please completely vacate the room during these lunch times.


Please note: The displayed programme is a preliminary schedule under development. Changes are possible.

Bioinformatics 2009
Time Speaker Contact Details and suggested readings
Day 1 - Monday September 7
9.00-9.15 Ian Donaldson Introduction
9.15-11.00 Anja Bråthen Kristoffersen

Exploratory data analysis Extra material

11:15-13.00 Ole Christian Lingjærde

An introduction to statistical inference

14.15-16.00 Einar A. Rødland

Multiple hypothesis testing

Day 2 - Tuesday September 8
9.15-11.00 Arnoldo Frigessi

Multiple comparison

11:15-13.00 Antonio Mora

Introduction to R - Presentation

14.15-16.00 Antonio Mora

Introduction to R - Lab

Day 3 -Wednesday September 9
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 Microarrays
Day 4 - Thursday September 10
9.15-11.00 Torbjørn Rognes

Searching sequence databases

11:15-13.00 Robert Lyle

High throughput sequencing

14.15-16.00 Geir K. Sandve

Motif scanning and discovery in DNA

Day 5 - Friday September 11
9.15-11.00 Dave W. Ussery

Comparative genomics Methods to compare genomes Pan-genomics and metagenomics

11:15-13.00 Karin Lagesen Sequence lab
14.15-16.00 Geir K. Sandve

Sequence lab



Day 6 - Monday September 14
9.15-11.00 Bjørn Dalhus

Structural biology review


Installing PyMol

11:15-13.00 Jon K. Laerdahl

Structural bioinformatics tools, predictors, and 3D modeling

14.15-16.00 Dalhus and Laerdahl Structural tutorials and exercises

PyMol demonstration

PyMol excercise

Day 7 - Tuesday September 15
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 8 - Wednesday September 16
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

12:15-13.00 Harald Martens


13:00-14.15 Lunch
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?

Day 9 - Thursday September 17
9.15-11.00 Joakim Sundnes

Multiscale modelling physiological systems

11:15-13.00 George Magklaras


14.15-16.00 Kamran Shalchian-Tabrizi


Day 10 - Friday September 18
9.15-12.00 Course Review
1.15-16.00 Pizza and Feedback session
Day 11 - Monday September 21
9.15-13.15 Exam (4 hour written open book)

Bioinformatics links relevant to the course

Bioinformatics Links 2009
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

Written assignment

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.

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.