Bioinformatics for molecular biology 2009

This is an archive page for a past course.  For the latest version of this course please see
http://bioinformatics.uio.no/wiki/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://core.rr-research.no/index.php?section=22	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/	Searching sequence databases
11:15-13.00	Robert Lyle		High throughput sequencing
14.15-16.00	Geir K. Sandve	http://www.uio.no/sok?la=en&person=geirksa	Motif scanning and discovery in DNA
Day 5 - Friday September 11
9.15-11.00	Dave W. Ussery	http://www.cbs.dtu.dk/staff/dave/	Comparative genomics Methods to compare genomes Pan-genomics and metagenomics
11:15-13.00	Karin Lagesen	http://folk.uio.no/karinlag/	Sequence lab
14.15-16.00	Geir K. Sandve	http://www.uio.no/sok?la=en&person=geirksa	Sequence lab RSAT ConTra
Day 6 - Monday September 14
9.15-11.00	Bjørn Dalhus		Structural biology review 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 PyMol demonstration PyMol excercise
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	http://donaldson.uio.no	Interaction data resources iRefIndex talk at BioPathways talk
14.15-16.00	Antonio Mora, Sabry Razick, Paul Boddie	http://donaldson.uio.no	Interaction lab Install http://cytoscape.org and http://irefindex.uio.no/wiki/README_Cytoscape_plugin_0.5x
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	Bio-chemometrics_and_multivariate_data_modelling_in_systems_biology
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	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	http://simula.no/	Multiscale 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_and_Eukarytic_megaevolution.pdf
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	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
NMC	http://www.mikromatrise.no/	Norwegian Microarray Consrtium
MACF	http://core.rr-research.no/	UiO MicroArray Facility
Bioinformatics core facility	http://core.rr-research.no/index.php?section=3	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	http://www.cytoscape.org/	Cytoscape home page
Cytoscape	http://cytoscape.org/cgi-bin/moin.cgi/Presentations	Tutorial on Cytoscape
iRefIndex Cytoscape plugin	http://irefindex.uio.no/wiki/README_Cytoscape_plugin_0.5x	iRefIndex installation
iRefIndex	http://irefindex.uio.no	iRefIndex wiki
iRefIndex publication	http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=18823568	Full details of iRefIndex
DAVID	http://www.nature.com/nprot/journal/v4/n1/pdf/nprot.2008.211.pdf	Nature Protocols paper
GSEA	http://www.broadinstitute.org/gsea/doc/subramanian_tamayo_gsea_pnas.pdf	PNAS paper
GSEA	http://www.broadinstitute.org/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 biotek.uio.no 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 biotek.uio.no 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.

https://sympa.uio.no/usit.uio.no/info/cbo-all

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

http://mailman.uib.no/listinfo/bioinfo.users.

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