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| | + | =Bioinformatics for molecular biology - Fall 2012= |
| | | | |
| − | ==Bioinformatics for molecular biology (10.0/8.0 credit points)==
| + | This course is being arranged for the fall semester of 2012 by Dr. Jon Lærdahl. |
| | + | See https://wiki.uio.no/projects/MBV-INFX410/index.php/Main_Page |
| | + | for more information. |
| | | | |
| | + | Past course content is archived at the links below. |
| | | | |
| − | '''Description'''
| + | ==Archived courses== |
| − | 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.
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| − | 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/).
| + | http://donaldson.uio.no/wiki/Bioinformatics_for_molecular_biology_2011 |
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| − | '''Registration is now open as of July 3rd, 2009.'''
| + | http://donaldson.uio.no/wiki/Bioinformatics_for_molecular_biology_2010 |
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| − | MBV-INF 4410 (M.Sc. level course code)10.0 study points
| + | http://donaldson.uio.no/wiki/Bioinformatics_for_molecular_biology_2009 |
| − | | |
| − | MBV-INF 9410A (Ph.D. level course code) 10.0 study points
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| − | | |
| − | MBV-INF 9410B (Ph.D. level course code) 8.0 study points
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| − | | |
| − | 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.
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| − | | |
| − | 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.
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| − | | |
| − | Please bookmark this page. All future changes or announcements for the 2009 course will be posted to this page.
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| − | | |
| − | | |
| − | | |
| − | '''Information:'''
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| − | ragni.indahl@biotek.uio.no (about course administration)
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| − | ian.donaldson@biotek.uio.no (about course content)
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| − | '''Registration:'''
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| − | torill.rortveit@imbv.uio.no
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| − | | |
| − | ==Dates and times==
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| − | The course will occur in weeks 37 and 38 (September 7th and 14th).
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| − | | |
| − | Each day will consist of three time slots for lectures and/or practical labs between 9 AM and 4 PM.
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| − | | |
| − | ==Place==
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| − | Forskningsparken
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| − | | |
| − | Directions to Forsknings parken can be found at http://www.biotek.uio.no/map.html
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| − |
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| − | Mondays to Thursdays: Room 10 (one level down from the main entrance)
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| − | Fridays: Room 7 (one level down from the main entrance)
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| − | | |
| − | Exceptions: none so far
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| − | | |
| − | 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.
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| − | | |
| − | ==Programme==
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| − | Please note:
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| − | The displayed programme is a preliminary schedule under development.
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| − | Changes are possible.
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| − | | |
| − | | |
| − | {|class="wikitable" style="text-align:left" border="1" cellpadding="5"
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| − | |+ '''Bioinformatics 2009'''
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| − | !width="50"|Time
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| − | !width="150"|Speaker
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| − | !width="250"|Contact
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| − | !width="350"|Details and suggested readings
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| − | |-
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| − | |style="background:SteelBlue; color:white" colspan="4" align="center"| Day 1 - Monday September 7
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| − | |-
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| − | |9.00-9.15||Ian Donaldson||http://donaldson.uio.no ||Introduction
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| − | |-
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| − | |9.15-11.00 || Anja Bråthen Kristoffersen || http://heim.ifi.uio.no/~anjab/ ||
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| − | [http://bioinformatics.uio.no/wiki/Image:Exploratory_Data_Analysis.pdf Exploratory data analysis]
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| − | [http://bioinformatics.uio.no/wiki/Image:Exploratory_data_analysis_extra_materials.zip Extra material]
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| − | |-
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| − | |11:15-13.00|| Ole Christian Lingjærde || http://heim.ifi.uio.no/~ole/ ||
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| − | [http://bioinformatics.uio.no/wiki/Image:Introduction_to_statistical_inference.pdf An introduction to statistical inference]
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| − | |-
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| − | |14.15-16.00|| Einar A. Rødland || http://folk.uio.no/einarro/ ||
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| − | [http://bioinformatics.uio.no/wiki/Image:Multiple_hypothesis_testing.pdf Multiple hypothesis testing]
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| − | |-
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| − | |style="background:SteelBlue; color:white" colspan="4" align="center"| Day 2 - Tuesday September 8
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| − | |-
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| − | |9.15-11.00 || Arnoldo Frigessi || http://www.nr.no/~frigessi/ ||
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| − | [http://bioinformatics.uio.no/wiki/Image:Multiple_comparison.pdf Multiple comparison]
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| − | |-
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| − | |11:15-13.00|| Antonio Mora || http://donaldson.uio.no ||
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| − | [http://biotin.uio.no/wikifiles//images/d/de/Intro_R_presentation.pdf Introduction to R - Presentation]
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| − | |-
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| − | |14.15-16.00|| Antonio Mora || http://donaldson.uio.no ||
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| − | [http://biotin.uio.no/wikifiles//images/1/1a/Intro_R_lab.pdf Introduction to R - Lab]
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| − | |-
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| − | |style="background:SteelBlue; color:white" colspan="4" align="center"| Day 3 -Wednesday September 9
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| − | |-
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| − | |9.15-11.00 || Leonardo Meza-Zepeda || Dept. of Tumor Biology, Rikshospitalet-Radiumhospitalet Medical Center ||
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| − | [http://bioinformatics.uio.no/wiki/Image:Microarray_technology_1.pdf Microarray technology 1]
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| − | [http://bioinformatics.uio.no/wiki/Image:Microarray_technology_2.pdf Microarray technology 2]
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| − | |-
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| − | |11:15-13.00|| Ståle Nygård || http://core.rr-research.no/index.php?section=22 ||
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| − | [http://bioinformatics.uio.no/wiki/Image:Microarray_data_analysis.pdf Microarray data analysis]
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| − | |-
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| − | |14.15-16.00|| || || Microarrays
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| − | |-
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| − | |style="background:SteelBlue; color:white" colspan="4" align="center"| Day 4 - Thursday September 10
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| − | |9.15-11.00 || Torbjørn Rognes || http://www.rr-research.no/rognes/ ||
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| − | [http://bioinformatics.uio.no/wikifiles//images/8/81/Searching_sequence_databases.pdf Searching sequence databases]
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| − | |11:15-13.00|| Robert Lyle || ||
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| − | [http://bioinformatics.uio.no/wikifiles//images/6/62/High_throughput_sequencing.pdf High throughput sequencing]
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| − | |-
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| − | |14.15-16.00|| Geir K. Sandve || http://www.uio.no/sok?la=en&person=geirksa ||
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| − | [http://bioinformatics.uio.no/wikifiles//images/d/d5/Motif_discovery.pdf Motif scanning and discovery in DNA]
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| − | |-
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| − | |style="background:SteelBlue; color:white" colspan="4" align="center"| Day 5 - Friday September 11
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| − | |-
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| − | |9.15-11.00 || Dave W. Ussery || http://www.cbs.dtu.dk/staff/dave/ ||
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| − | Comparative genomics
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| − | [http://bioinformatics.uio.no/wikifiles//images/3/38/Methods_to_compare_genomes.pdf Methods to compare genomes]
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| − | [http://bioinformatics.uio.no/wikifiles//images/4/4e/Pan-genomics_and_metagenomics.pdf Pan-genomics and metagenomics]
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| − | |-
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| − | |11:15-13.00|| Karin Lagesen|| http://folk.uio.no/karinlag/ || Sequence lab
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| − | |-
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| − | |14.15-16.00|| Geir K. Sandve || http://www.uio.no/sok?la=en&person=geirksa || Sequence lab
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| − | |-
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| − | |style="background:SteelBlue; color:white" colspan="4" align="center"| Day 6 - Monday September 14
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| − | |-
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| − | |9.15-11.00 || Bjørn Dalhus || ||
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| − | [http://bioinformatics.uio.no/wiki/Image:An_overview_of_structural_biology.pdf Structural biology review]
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| − | [http://www.pymol.org/ PyMOL]
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| − | [http://bioinformatics.uio.no/wikifiles//images/0/09/InstallingPyMOL.pdf Installing PyMol]
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| − | |11:15-13.00|| Jon K. Laerdahl || ||
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| − | [http://bioinformatics.uio.no/wikifiles//images/2/23/Structural_biology_tools.pdf Structural bioinformatics tools, predictors, and 3D modeling]
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| − | |-
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| − | |14.15-16.00|| Dalhus and Laerdahl || || Structural tutorials and exercises
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| − | [http://bioinformatics.uio.no/wikifiles//images/e/ef/PyMol_demo.pdf PyMol demonstration]
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| − | [http://bioinformatics.uio.no/wikifiles//images/b/b2/PyMol_excercise.pdf PyMol excercise]
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| − | | |
| − | |-
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| − | |style="background:SteelBlue; color:white" colspan="4" align="center"| Day 7 - Tuesday September 15
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| − | |-
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| − | |9.15-11.00 || Ian Donaldson || http://donaldson.uio.no || Working with gene lists and over-representation analysis
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| − | |-
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| − | |11:15-13.00|| Ian Donaldson || http://donaldson.uio.no || Interaction, Complex and Pathway data resources
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| − | |-
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| − | |14.15-16.00|| Antonio Mora, Sabry Razick, Paul Boddie || http://donaldson.uio.no || Interaction lab
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| − | Install http://cytoscape.org and http://irefindex.uio.no/wiki/README_Cytoscape_plugin_0.5x
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| − | |-
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| − | |style="background:SteelBlue; color:white" colspan="4" align="center"| Day 8 - Wednesday September 16
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| − | |-
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| − | |9.15-10.00 || Erik Plahte || http://www.cigene.no/people.html || Modelling paradigms for gene regulatory networks
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| − | |-
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| − | |10.15-11.00 || Arne Gjuvsland || http://www.cigene.no/people.html || Causally cohesive genotype-phenotype modelling - systems biology meets genetics
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| − | |-
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| − | |11.15-12.00 || Jon Olav Vik || http://www.cigene.no/people.html || cGP map of the cardiomyocyte
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| − | |-
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| − | |12:15-13.00|| Harald Martens || http://www.cigene.no/people.html || QTL analysis with biospectroscopy - on cows and milk
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| − | |-
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| − | |13:00-14.15|| Lunch || ||
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| − | |-
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| − | |14.15-15.00|| Achim Kohler || http://www.cigene.no/people.html || A new phenotyping paradigm for yeast
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| − | |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?
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| − | |-
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| − | |style="background:SteelBlue; color:white" colspan="4" align="center"| Day 9 - Thursday September 17
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| − | |-
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| − | |9.15-11.00 || Joakim Sundnes || http://simula.no/ || TBA: Modelling physiological systems
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| − | |-
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| − | |11:15-13.00|| George Magklaras || http://www.no.embnet.org/ ||EMBNet
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| − | |-
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| − | |14.15-16.00|| Kamran Shalchian-Tabrizi || http://www.bioportal.uio.no || BioPortal
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| − | |-
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| − | |style="background:SteelBlue; color:white" colspan="4" align="center"| Day 10 - Friday September 18
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| − | |-
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| − | |9.15-12.00
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| − | |colspan="3"|Open lab and study session
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| − | |-
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| − | |1.15-16.00
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| − | |colspan="3"|Other ideas: Student presentations, Programming (Python, Taverna, R), Machine learning, Genome browser, text mining and PubGene
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| − | |-
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| − | |style="background:SteelBlue; color:white" colspan="4" align="center"| Day 11 - Monday September 21
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| − | |-
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| − | |9.15-13.15
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| − | |colspan="3"|Exam (4 hour written open book)
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| − | |}
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| − | | |
| − | ==Bioinformatics links relevant to the course==
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| − | | |
| − | {|class="wikitable" style="text-align:left" border="1" cellpadding="5"
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| − | |+ '''Bioinformatics Links 2009'''
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| − | !width="150"|Name
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| − | !width="350"|URL
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| − | !width="350"|Description
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| − | |-
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| − | |style="background:SteelBlue; color:white" colspan="4" align="center"| Day 1 - Statistics
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| − | |-
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| − | |StatSoft textbook || http://statsoft.com/textbook/stathome.html || Good overview of methods and concepts
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| − | |-
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| − | |SAS manuals || http://support.sas.com/onlinedoc/913/ || Thorough overview of analysis procedures found in SAS
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| − | |-
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| − | |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
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| − | |-
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| − | |style="background:SteelBlue; color:white" colspan="4" align="center"| Day 2 - Statistics
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| − | |-
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| − | | R || http://cran.r-project.org/ || The Comprehensive R Archive Network
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| − | |-
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| − | |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
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| − | |-
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| − | |EMBNet Microarray course || http://vit-embnet.unil.ch/CoursEMBnet/Arrays06/Material.html || An online course with R/Bioconductor example tutorials
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| − | |-
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| − | |EMBNet tutorials || http://www.ch.embnet.org/pages/courses2.html || Other helpful tutorials with R examples related to biostatistics
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| − | |-
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| − | |style="background:SteelBlue; color:white" colspan="4" align="center"| Day 3 - Microarrays
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| − | |-
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| − | |NMC || http://www.mikromatrise.no/ || Norwegian Microarray Consrtium
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| − | |-
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| − | | MACF || http://core.rr-research.no/ || UiO MicroArray Facility
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| − | |-
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| − | |style="background:SteelBlue; color:white" colspan="4" align="center"| Day 4 - Microarrays
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| − | |-
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| − | |style="background:SteelBlue; color:white" colspan="4" align="center"| Day 5 - Microarrays
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| − | |-
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| − | |style="background:SteelBlue; color:white" colspan="4" align="center"| Day 6 - Microarrays
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| − | |-
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| − | |style="background:SteelBlue; color:white" colspan="4" align="center"| Day 7 - Microarrays
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| − | |-
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| − | |Cytoscape || http://www.cytoscape.org/ || Cytoscape home page
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| − | |-
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| − | |Cytoscape||http://cytoscape.org/cgi-bin/moin.cgi/Presentations|| Tutorial on Cytoscape
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| − | |-
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| − | |iRefIndex Cytoscape plugin || http://irefindex.uio.no/wiki/README_Cytoscape_plugin_0.5x || iRefIndex installation
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| − | |-
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| − | |iRefIndex || http://irefindex.uio.no || iRefIndex wiki
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| − | |-
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| − | |iRefIndex publication || http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=18823568 || Full details of iRefIndex
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| − | |-
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| − | |}
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