Bioinformatics course

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 (http://www.biotek.uio.no/ny-web/events/).

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 http://www.uio.no/studier/emner/matnat/molbio/MBV-INF4410/ 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.

            Information: 
                 ragni.indahl@biotek.uio.no (about course administration) 
                 ian.donaldson@biotek.uio.no (about course content)
            Registration: 
                 torill.rortveit@imbv.uio.no

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.

Place

Forskningsparken

Directions to Forsknings parken can be found at http://www.biotek.uio.no/map.html

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.

Programme

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	http://donaldson.uio.no	Introduction
9.15-11.00	Anja Bråthen Kristoffersen	http://heim.ifi.uio.no/~anjab/	Exploratory data analysis Extra material
11:15-13.00	Ole Christian Lingjærde	http://heim.ifi.uio.no/~ole/	An introduction to statistical inference
14.15-16.00	Einar A. Rødland	http://folk.uio.no/einarro/	Multiple hypothesis testing
Day 2 - Tuesday September 8
9.15-11.00	Arnoldo Frigessi	http://www.nr.no/~frigessi/	Multiple comparison
11:15-13.00	Antonio Mora	http://donaldson.uio.no	Introduction to R - Presentation
14.15-16.00	Antonio Mora	http://donaldson.uio.no	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	http://www.heartfailure.no/people/member/nyg_rd.html	Microarray data analysis
14.15-16.00			Microarrays
Day 4 - Thursday September 10
9.15-11.00	Torbjørn Rognes	http://www.rr-research.no/rognes/	Sequence alignments and BLASTing
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
11:15-13.00	Multiple		Sequence lab
14.15-16.00	Multiple		Sequence lab
Day 6 - Monday September 14
9.15-11.00	Bjørn Dalhus		Structural biology review and PyMOL 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
Day 7 - Tuesday September 15
9.15-11.00	Ian Donaldson	http://donaldson.uio.no	Working with gene lists and over-representation analysis
11:15-13.00	Ian Donaldson		Interaction, Complex and Pathway data resources
14.15-16.00	Antonio Mora, Sabry Razick, Paul Boddie		Interaction lab
Day 8 - Wednesday September 16
9.15-10.00	Erik Plahte	http://www.cigene.no/people.html	Modelling paradigms for gene regulatory networks
10.15-11.00	Arne Gjuvsland	http://www.cigene.no/people.html	Causally cohesive genotype-phenotype modelling - systems biology meets genetics
11.15-12.00	Jon Olav Vik	http://www.cigene.no/people.html	cGP map of the cardiomyocyte
12:15-13.00	Harald Martens	http://www.cigene.no/people.html	QTL analysis with biospectroscopy - on cows and milk
13:00-14.15	Lunch
14.15-15.00	Achim Kohler	http://www.cigene.no/people.html	A new phenotyping paradigm for yeast
15.15-16.00	Solve Sæbø	http://www.umb.no/ikbm/ansatte/solve.sabo	Multivariate analysis of yeast genetic data (Regner med at Lars er borte da.)
Day 9 - Thursday September 17
9.15-11.00	Joakim Sundnes	http://simula.no/	TBA: Modelling physiological systems
11:15-13.00	George Magklaras	http://www.no.embnet.org/	EMBNet
14.15-16.00	Kamran Shalchian-Tabrizi	http://www.bioportal.uio.no	BioPortal
Day 10 - Friday September 18
9.15-12.00	Open lab and study session
1.15-16.00	Other ideas: Student presentations, Programming (Python, Taverna, R), Machine learning, Genome browser, text mining and PubGene
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	http://statsoft.com/textbook/stathome.html	Good overview of methods and concepts
SAS manuals	http://support.sas.com/onlinedoc/913/	Thorough overview of analysis procedures found in SAS
GraphPad	http://graphpad.com/help/prism5/prism5help.html?usingstatistical_analyses_step_by_s.htm	See the GraphPad statistical guide for easy introductions to many concepts in statistics
Day 2 - Statistics
R	http://cran.r-project.org/	The Comprehensive R Archive Network
Learning R	http://www.ploscompbiol.org/article/info:doi%2F10.1371%2Fjournal.pcbi.1000482	A Quick Guide to Teaching R Programming to Computational Biology Students
EMBNet Microarray course	http://vit-embnet.unil.ch/CoursEMBnet/Arrays06/Material.html	An online course with R/Bioconductor example tutorials
EMBNet tutorials	http://www.ch.embnet.org/pages/courses2.html	Other helpful tutorials with R examples related to biostatistics
Day 3 - Microarrays