Difference between revisions of "Bioinformatics course"

From irefindex
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==Programme==
 
==Programme==
  
−
<pre>
+
 
−
Please note:
+
'''Note:
−
The schedule displayed below is based on last years course
+
The schedule displayed below is tentative.
−
(see http://donaldson.uio.no/wiki/Bioinformatics_for_molecular_biology_2010).
 
 
Ongoing changes will be made to this page as we organize  
 
Ongoing changes will be made to this page as we organize  
 
speakers before and during the course.   
 
speakers before and during the course.   
 
Requests and suggestions are welcome.
 
Requests and suggestions are welcome.
−
</pre>
+
For examples of material presented last year, see [http://donaldson.uio.no/wiki/Bioinformatics_for_molecular_biology_2010 Bioinformatics for molecular biology 2010]).'''
−
 
 
−
{| {{table}}
 
−
| Week 1: Monday, November 21st - Friday, November 25th||||||
 
−
|-
 
−
| Day of the week||1. Session  ||2. Session ||3. Session
 
−
|-
 
−
| ||09:00 – 10:45 ||11:00 – 12:45 ||14:00 – 15:45
 
−
|-
 
−
| Mon. 21st||Databases||Databases lab||MySQL lab
 
−
|-
 
−
| ||Donaldson||Donaldson||Donaldson
 
−
|-
 
−
| Tue. 22nd||Perl||More Perl||Perl lab
 
−
|-
 
−
| ||Donaldson||Donaldson||Donaldson
 
−
|-
 
−
| Wed. 23rd||Introduction to R||R lab||R lab
 
−
|-
 
−
| ||Bjørn-Helge Mevik||Bjørn-Helge Mevik, Katerina Michalickova, Antonio Mora ||Bjørn-Helge Mevik,  Katerina Michalickova, Antonio Mora
 
−
|-
 
−
| Thur. 24th||Exploratory data analysis||An introduction to statistical inference||Multiple hypothesis testing
 
−
|-
 
−
| ||Anja Bråthern Kristoffersen||Ole Christian Lingjærde||Einar A. Rødland
 
−
|-
 
−
| Fri. 25th||1. Session  ||2. Session ||3. Session
 
−
|-
 
−
| ||09:00 – 10:45 ||11:00 – 12:00||13:30 – 15:45
 
−
|-
 
−
| ||Microarray data analysis||Microarray data lab||Gene Ontology Over-representation analysis in DAVID. Lab.
 
−
|-
 
−
| ||Ståle Nygård||Ståle Nygård||Donaldson
 
−
|-
 
−
| ||||||
 
−
|-
 
−
| ||||||
 
−
|-
 
−
| Week 2: Monday, November 28th - Friday, December 2nd.||||||
 
−
|-
 
−
| ||1. Session  ||2. Session ||3. Session
 
−
|-
 
−
| ||09:00 – 10:45 ||11:00 – 12:45 ||14:00 – 15:45
 
−
|-
 
−
| Mon 28th||Interaction and pathway data||Cytoscape lab||Cytoscape plugin lab
 
−
|-
 
−
| ||Donaldson||Donaldson||Donaldson
 
−
|-
 
−
| Tue. 29th ||ht sequencing||ht sequence lab||
 
−
|-
 
−
| ||Robert Lyle||Robert Lyle||
 
−
|-
 
−
| Wed 30th||Searching sequence databases and multiple sequence alignments||Motif scanning and discovery in DNA||Sequence lab
 
−
|-
 
−
| ||Torbjørn Rognes||Geir Sandve||Geir Sandve
 
−
|-
 
−
| Thur 1st||Structural biology review, PyMOL and installing PyMOL||Structural biology tools, predictors and 3D modelling||PyMOL and structural biology tutorial
 
−
|-
 
−
| ||Jon K. Laerdahl||Jon K. Laerdahl||Jon K. Laerdahl
 
−
|-
 
−
| Fri 2nd||1. Session  ||2. Session ||3. Session
 
−
|-
 
−
| ||09:00 – 10:45 ||11:00 – 12:00||13:30 – 15:45
 
−
|-
 
−
| ||Modeling guide||Modeling excercises||Homology modeling excercise
 
−
|-
 
−
| ||Jon K. Laerdahl||Jon K. Laerdahl||Jon K. Laerdahl
 
−
|-
 
−
|
 
−
|}
 
  
−
 
+
{| class="wikitable" style="text-align:left" cellpadding="5"
−
{| {{table}}
+
!width="20%"|
−
| align="center" style="background:#f0f0f0;"|'''Week 1: Monday, November 21st - Friday, November 25th'''
+
!width="27%"|
−
| align="center" style="background:#f0f0f0;"|''''''
+
!width="27%"|
−
| align="center" style="background:#f0f0f0;"|''''''
+
!width="27%"|
−
| align="center" style="background:#f0f0f0;"|''''''
 
 
|-
 
|-
−
| Day of the week||1. Session  ||2. Session ||3. Session
+
| align="center" style="background:grey;" colspan="4"|'''Week 1: Monday, November 21st - Friday, November 25th'''
 +
|-style="background: steelblue; color: black"
 +
| ||Session 1||Session 2||Session 3  
 
|-
 
|-
 
| ||09:00 – 10:45 ||11:00 – 12:45 ||14:00 – 15:45  
 
| ||09:00 – 10:45 ||11:00 – 12:45 ||14:00 – 15:45  
−
|-
+
|-style="background: lightgrey; color: black"
 
| Mon. 21st||Databases||Databases lab||MySQL lab
 
| Mon. 21st||Databases||Databases lab||MySQL lab
−
|-
+
|-style="background: lightgrey; color: black"
 
| ||Donaldson||Donaldson||Donaldson
 
| ||Donaldson||Donaldson||Donaldson
 
|-
 
|-
Line 150: Line 82:
 
|-
 
|-
 
| ||Donaldson||Donaldson||Donaldson
 
| ||Donaldson||Donaldson||Donaldson
−
|-
+
|-style="background: lightgrey; color: black"
 
| Wed. 23rd||Introduction to R||R lab||R lab
 
| Wed. 23rd||Introduction to R||R lab||R lab
−
|-
+
|-style="background: lightgrey; color: black"
 
| ||Bjørn-Helge Mevik||Bjørn-Helge Mevik,  Katerina Michalickova, Antonio Mora ||Bjørn-Helge Mevik,  Katerina Michalickova, Antonio Mora  
 
| ||Bjørn-Helge Mevik||Bjørn-Helge Mevik,  Katerina Michalickova, Antonio Mora ||Bjørn-Helge Mevik,  Katerina Michalickova, Antonio Mora  
 
|-
 
|-
Line 158: Line 90:
 
|-
 
|-
 
| ||Anja Bråthern Kristoffersen||Ole Christian Lingjærde||Einar A. Rødland
 
| ||Anja Bråthern Kristoffersen||Ole Christian Lingjærde||Einar A. Rødland
−
|-
+
|-style="background: steelblue; color: black"
−
| Fri. 25th||1. Session  ||2. Session ||3. Session
+
| Fri. 25th||Session 1 ||Session 2 ||Session 3
−
|-
+
|-style="background: lightgrey; color: black"
 
| ||09:00 – 10:45 ||11:00 – 12:00||13:30 – 15:45  
 
| ||09:00 – 10:45 ||11:00 – 12:00||13:30 – 15:45  
−
|-
+
|-style="background: lightgrey; color: black"
 
| ||Microarray data analysis||Microarray data lab||Gene Ontology Over-representation analysis in DAVID.  Lab.
 
| ||Microarray data analysis||Microarray data lab||Gene Ontology Over-representation analysis in DAVID.  Lab.
−
|-
+
|-style="background: lightgrey; color: black"
 
| ||Ståle Nygård||Ståle Nygård||Donaldson
 
| ||Ståle Nygård||Ståle Nygård||Donaldson
 
|-
 
|-
Line 171: Line 103:
 
| ||||||
 
| ||||||
 
|-
 
|-
−
| Week 2: Monday, November 28th - Friday, December 2nd.||||||
+
| align="center" style="background:grey;" colspan="4"|'''Week 2: Monday, November 28th - Friday, December 2nd.
−
|-
+
|-style="background: steelblue; color: black"
−
| ||1. Session  ||2. Session ||3. Session
+
| ||Session 1 ||Session 2||Session 3
 
|-
 
|-
 
| ||09:00 – 10:45 ||11:00 – 12:45 ||14:00 – 15:45  
 
| ||09:00 – 10:45 ||11:00 – 12:45 ||14:00 – 15:45  
−
|-
+
|-style="background: lightgrey; color: black"
 
| Mon 28th||Interaction and pathway data||Cytoscape lab||Cytoscape plugin lab
 
| Mon 28th||Interaction and pathway data||Cytoscape lab||Cytoscape plugin lab
−
|-
+
|-style="background: lightgrey; color: black"
 
| ||Donaldson||Donaldson||Donaldson
 
| ||Donaldson||Donaldson||Donaldson
 
|-
 
|-
Line 184: Line 116:
 
|-
 
|-
 
| ||Robert Lyle||Robert Lyle||
 
| ||Robert Lyle||Robert Lyle||
−
|-
+
|-style="background: lightgrey; color: black"
 
| Wed 30th||Searching sequence databases and multiple sequence alignments||Motif scanning and discovery in DNA||Sequence lab
 
| Wed 30th||Searching sequence databases and multiple sequence alignments||Motif scanning and discovery in DNA||Sequence lab
−
|-
+
|-style="background: lightgrey; color: black"
 
| ||Torbjørn Rognes||Geir Sandve||Geir Sandve
 
| ||Torbjørn Rognes||Geir Sandve||Geir Sandve
 
|-
 
|-
Line 192: Line 124:
 
|-
 
|-
 
| ||Jon K. Laerdahl||Jon K. Laerdahl||Jon K. Laerdahl
 
| ||Jon K. Laerdahl||Jon K. Laerdahl||Jon K. Laerdahl
−
|-
+
|-style="background: steelblue; color: black"
−
| Fri 2nd||1. Session  ||2. Session ||3. Session
+
| Fri 2nd||Session 1 ||Session 2 ||Session 3  
−
|-
+
|-style="background: lightgrey; color: black"
 
| ||09:00 – 10:45 ||11:00 – 12:00||13:30 – 15:45  
 
| ||09:00 – 10:45 ||11:00 – 12:00||13:30 – 15:45  
−
|-
+
|-style="background: lightgrey; color: black"
 
| ||Modeling guide||Modeling excercises||Homology modeling excercise
 
| ||Modeling guide||Modeling excercises||Homology modeling excercise
−
|-
+
|-style="background: lightgrey; color: black"
 
| ||Jon K. Laerdahl||Jon K. Laerdahl||Jon K. Laerdahl
 
| ||Jon K. Laerdahl||Jon K. Laerdahl||Jon K. Laerdahl
 
|-
 
|-
 
|  
 
|  
−
|}
 
−
 
−
 
−
 
−
{|class="wikitable" style="text-align:left" border="1" cellpadding="5"
 
−
|+ '''Bioinformatics 2011'''
 
−
!width="5%"|Time
 
−
!width="15%"|Speaker
 
−
!width="30%"|Contact
 
−
!width="50%"|Details and suggested readings
 
−
|-
 
−
|style="background:SteelBlue; color:white" colspan="4" align="center"| Day 1 - Monday November 21st
 
−
|-
 
−
|9.00-9.15||Ian Donaldson||http://donaldson.uio.no ||Introduction
 
−
|-
 
−
|9.15-11.00 || Anja Bråthern Kristoffersen || http://donaldson.uio.no || 
 
−
[http://donaldson.uio.no/wikifiles//images/2/29/Exploratory_data_analysis.pdf Exploratory data analysis]
 
−
[http://bioinformatics.uio.no/wiki/Image:Exploratory_data_analysis_extra_materials.zip Extra material]
 
−
|-
 
−
|11:15-13.00|| Bjørn-Helge Mevik || http://www.usit.uio.no/suf/vd/ ||
 
−
[http://donaldson.uio.no/wikifiles//images/7/70/Intro_R_2010.pdf Introduction to R - Presentation]
 
−
|-
 
−
|14.15-16.00||
 
−
Bjørn-Helge Mevik
 
−
 
−
Katerina Michalickova
 
−
|| http://www.usit.uio.no/suf/vd/ ||
 
−
[http://donaldson.uio.no/wikifiles//images/3/39/Intro_R_lab_2010.pdf Introduction to R - Lab]
 
−
|-
 
−
|style="background:SteelBlue; color:white" colspan="4" align="center"| Day 2 - Tuesday November 22nd
 
−
|-
 
−
|9.15-11.00|| Clara-Cecilie Günther  || http://www.nr.no/ ||
 
−
[http://donaldson.uio.no/wikifiles//images/4/4a/StatInference_2010.pdf An introduction to statistical inference]
 
−
|-
 
−
|11:15-13.00|| Einar A. Rødland  || http://folk.uio.no/einarro/ ||
 
−
[http://donaldson.uio.no/wikifiles//images/6/62/Multiple_hypothesis_testing_2010.pdf Multiple hypothesis testing]
 
−
|-
 
−
|14.15-16.00 ||Ian Donaldson||http://donaldson.uio.no ||
 
−
[http://donaldson.uio.no/wikifiles//images/d/dc/MySQL_installation_and_tutorial.pdf MySQL installation and tutorial]
 
−
 
−
|-
 
−
|style="background:SteelBlue; color:white" colspan="4" align="center"| Day 3 -Wednesday November 23rd
 
−
|-
 
−
|9.15-11.00 || Leonardo Meza-Zepeda || Dept. of Tumor Biology, Rikshospitalet-Radiumhospitalet Medical Center ||
 
−
[http://donaldson.uio.no/wikifiles//images/0/03/MicroarrayTechnology_2010.pdf  Microarray technology]
 
−
 
−
[http://donaldson.uio.no/wikifiles//images/9/9f/Integration_LAMZ_2010.pdf Integrated genomic analysis]
 
−
|-
 
−
|11:15-13.00|| Ståle Nygård || http://core.rr-research.no/index.php?section=22 ||
 
−
[http://donaldson.uio.no/wikifiles//images/7/75/Microarray-sn-2010.pdf Microarray data analysis]
 
−
|-
 
−
|14.15-16.00|| Ståle Nygård ||  || [http://donaldson.uio.no/wikifiles//images/5/58/R-lab-sn-2010.pdf R Microarray data analysis lab]
 
−
|-
 
−
|style="background:SteelBlue; color:white" colspan="4" align="center"| Day 4 - Thursday November 24th
 
−
|-
 
−
|9.15-11.00 || Torbjørn Rognes || http://www.rr-research.no/rognes/ || 
 
−
[http://bioinformatics.uio.no/wikifiles//images/3/37/Searching_sequence_databases_and_multiple_sequence_alignments_2010.pdf Searching sequence databases and multiple sequence alighments.]
 
−
|-
 
−
|11:15-13.00|| Geir K. Sandve || http://www.uio.no/sok?la=en&person=geirksa || [http://bioinformatics.uio.no/wikifiles//images/d/d5/Motif_discovery.pdf Motif scanning and discovery in DNA]
 
−
|-
 
−
|14.15-16.00||
 
−
Geir K. Sandve
 
−
 
−
Halfden
 
−
 
−
Vegard Nygaard
 
−
|| 
 
−
||
 
−
Sequence lab
 
−
 
−
[http://rsat.ulb.ac.be/rsat/ RSAT]
 
−
 
−
[http://bioit.dmbr.ugent.be/ConTra/index.php ConTra]
 
−
 
−
[http://bioinformatics.uio.no/wikifiles//images/a/a2/Pres9sep10_general_tf_analysis_in_HB.pdf General TF analysis - a simple approach]
 
−
|-
 
−
|style="background:SteelBlue; color:white" colspan="4" align="center"| Day 5 - Friday November 25th
 
−
|-
 
−
|9.15-11.00 ||
 
−
Sveinung Gundersen
 
−
 
−
Geir K. Sandve
 
−
|| 
 
−
|| 
 
−
[http://donaldson.uio.no/wikifiles//images/1/15/Hyperbrowser_2010.pdf The Genomic Hyperbrowser]
 
−
 
−
[http://donaldson.uio.no/wikifiles//images/f/fb/HyperBrowser_Hands-on.pdf The Hyperbrowser tutorial]
 
−
 
−
Hyperbrowser tutorial  http://hyperbrowser.uio.no/
 
−
|-
 
−
|11.15-12:00 || Dave W. Ussery || http://www.cbs.dtu.dk/staff/dave/ ||  Comparative genomics
 
−
[http://donaldson.uio.no/wikifiles//images/3/3c/Cautionary_Tales_NGS-2010.pdf Cautionary Tales for Next Generation Sequencing]
 
−
|-
 
−
|12.00-13:30 || Lunch -vacate room ||  || 
 
−
|-
 
−
|13:30-14:15|| Dave W. Ussery || http://www.cbs.dtu.dk/staff/dave/ ||  Comparative genomics
 
−
[http://donaldson.uio.no/wikifiles//images/a/a6/Comparative_genomics-2010.pdf Comparative genomics - bacterial genomes.]
 
−
|-
 
−
|14.15-15.30||  ||  ||  [http://folk.uio.no/karinlag/Sequence_Lab_Dave_Ussery.html Sequence lab]
 
−
 
−
[http://donaldson.uio.no/wikifiles//images/0/04/1999_ThreeViews.pdf Three views]
 
−
 
−
[http://donaldson.uio.no/wikifiles//images/b/bc/2000_EcoliAtlas.pdf EColi. Atlas]
 
−
 
−
[http://donaldson.uio.no/wikifiles//images/4/4d/2008_BLASTatlas_MolBiosystems.pdf BLAST Atlas]
 
−
 
−
[http://donaldson.uio.no/wikifiles//images/5/50/2009_GeneWizBrowser_SIGS.pdf GeneWiz Browser]
 
−
 
−
[http://donaldson.uio.no/wikifiles//images/f/f1/2009_PhysicalMapsChromosomes_ELS.pdf Physical Maps of Chromosomes]
 
−
 
−
[http://donaldson.uio.no/wikifiles//images/7/71/2010_1000thGenome_Microbiology.pdf The 1000th Genome]
 
−
 
−
|-
 
−
|16.00-  || TGIF ||  ||  Forskningsparken pub
 
−
|-
 
−
|style="background:SteelBlue; color:white" colspan="4" align="center"| Day 6 - Monday November 28th
 
−
|-
 
−
|9:00-11:00|| Robert Lyle ||  ||
 
−
[http://donaldson.uio.no/wikifiles//images/6/66/High-throughput_sequencing_2010.pdf High throughput sequencing]
 
−
|-
 
−
|11:15-13.00|| George Magklaras ||  http://www.no.embnet.org/ ||
 
−
[http://donaldson.uio.no/wikifiles//images/7/76/Biological-sequence-mining-MRS-2010.pdf Biological sequence mining with MRS]
 
−
 
−
[http://donaldson.uio.no/wikifiles//images/f/f5/MRS-EMBOSS-lab.pdf MRS and EMBOSS lab]
 
−
|-
 
−
|13:00-14:00 || Lunch ||  || 
 
−
|-
 
−
|14.15-16.00 || Kamran Shalchian-Tabrizi (TBC) || http://www.bioportal.uio.no || 
 
−
[http://donaldson.uio.no/wikifiles//images/c/c0/Bioportal_2010.pdf Bioportal]
 
−
|-
 
−
|style="background:SteelBlue; color:white" colspan="4" align="center"| Day 7 - Tuesday November 29th
 
−
|-
 
−
|9.15-11.00 || Jon K. Laerdahl  ||
 
−
http://folk.uio.no/jonkl/ 
 
−
 
−
http://www.rr-research.no/rognes/
 
−
 
−
http://www.bioinformatikk.no/
 
−
|| 
 
−
[http://folk.uio.no/jonkl/private/StructBiolReviewJKL0910.pdf Structural biology review]
 
−
 
−
[http://www.pymol.org/ PyMOL]
 
−
 
−
[http://donaldson.uio.no/wikifiles//images/9/9e/InstallingPyMOL_2010.pdf Installing PyMol]
 
−
|-
 
−
|11:15-13.00|| Jon K. Laerdahl ||  ||
 
−
[http://folk.uio.no/jonkl/private/StructBioInfJKL0910.pdf Structural bioinformatics tools, predictors, and 3D modeling]
 
−
|-
 
−
|14.15-16.00|| Jon K. Laerdahl ||  || [http://folk.uio.no/jonkl/pubstuff/PyMOL_Tutorial-JKL.pdf PyMOL and structural biology tutorial]
 
−
|-
 
−
|style="background:SteelBlue; color:white" colspan="4" align="center"| Day 8 - Wednesday November 30th
 
−
|-
 
−
|9.15-11.00 || Jon K. Laerdahl ||  ||  Structural modeling tutorial: Practical exercises
 
−
 
−
[http://folk.uio.no/jonkl/private/JKL-ModelingGuide.pdf Modeling Guide]
 
−
|-
 
−
|11:15-13.00|| Jon K. Laerdahl || ||  [http://folk.uio.no/jonkl/pubstuff/ModCrs-Exercises-JKL.pdf Modeling excercises]
 
−
|-
 
−
|14.15-16.00|| Jon K. Laerdahl ||  || [http://folk.uio.no/jonkl/pubstuff/HomologyModel-Exercise-JKL.pdf Homology modeling exercise]
 
−
|-
 
−
|style="background:SteelBlue; color:white" colspan="4" align="center"| Day 9 - Thursday December 1st
 
−
|-
 
−
|9.15-11.00 || Ian Donaldson || http://donaldson.uio.no || 
 
−
[http://donaldson.uio.no/wikifiles//images/1/1e/Interaction_data_resources_2010.pdf Interaction data resources]
 
−
 
−
[http://donaldson.uio.no/wikifiles//images/8/81/Identifier_conversion_excercise_2010.pdf Identifier conversion excercise]
 
−
|-
 
−
|11:15-13.00|| Sabry Razick, Paul Boddie || http://donaldson.uio.no || 
 
−
[http://cytoscape.wodaklab.org/wiki/Presentations/Basic Cytoscape tutorial and lab]
 
−
|-
 
−
|14.15-16.00|| Sabry Razick, Paul Boddie || http://donaldson.uio.no || iRefScape plugin tutorial and lab.  See http://cytoscape.org and http://irefindex.uio.no/wiki/README_Cytoscape_plugin_0.9x. Tutorial :http://irefindex.uio.no/wikifiles//images/5/59/Interaction_lab_2010.pdf
 
−
|-
 
−
|style="background:SteelBlue; color:white" colspan="4" align="center"| Day 10 - Friday December 2nd
 
−
|-
 
−
|9.15-10.00 || Ian Donaldson || || [http://donaldson.uio.no/wikifiles//images/a/a7/GO%2C_DAVID_and_iRefScape_revisited_2010.pdf GO DAVID and IRefScape revisited]
 
−
 
−
[http://donaldson.uio.no/wikifiles//images/9/96/Working_with_Gene_Lists_and_Over-representation_analysis_2010.pdf Working with gene lists and over-representation analysis]
 
−
|-
 
−
|10.15-11.00 || Arne Gjuvsland || http://www.cigene.no/people.html || 
 
−
[http://bioinformatics.uio.no/wikifiles//images/3/38/Causally_Cohesive_Genotype_Phenotype_models.pdf Causally cohesive genotype-phenotype modelling - systems biology meets genetics]
 
−
|-
 
−
|11.15-12.00 || Jon Olav Vik || http://www.cigene.no/people.html || 
 
−
[http://bioinformatics.uio.no/wikifiles//images/5/50/First_steps_toward_a_GP_map_of_the_heart_muscle_cell.pdf cGP map of the cardiomyocyte]
 
−
|-
 
−
|12.00-13:30 || Lunch -vacate room ||  || 
 
−
|-
 
−
|13:30-14:15|| Katerina Michalickova ||
 
−
http://hpc.uio.no/index.php/Main_Page
 
−
 
−
http://www.usit.uio.no/suf/vd/
 
−
|| [http://hpc.uio.no/images/5/52/Titan_newcomers.pdf TITAN cluster for beginners]   
 
−
|-
 
−
|14.30-15.15|| || ||
 
−
|-
 
−
|15.15-16.00||  ||  ||
 
−
|-
 
 
|}
 
|}
  

Revision as of 15:12, 18 August 2011

Bioinfo course logo.jpg
About this image

Bioinformatics for molecular biology - Fall 2011

November 21st to December 2nd

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/). The UiO page for this course is http://www.uio.no/studier/emner/matnat/molbio/MBV-INF4410/.

Registration is open now (June of 2011).

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 (10 to 20 pages) to be completed by the middle of December.

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 2011 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 November 21st to December 2nd.

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

Place

Forskningsparken

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

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 (Monday to Thursday) and 12 to 13:30 on Fridays. Please completely vacate the room during these lunch times.

Programme

Note: The schedule displayed below is tentative. Ongoing changes will be made to this page as we organize speakers before and during the course. Requests and suggestions are welcome. For examples of material presented last year, see Bioinformatics for molecular biology 2010).

Week 1: Monday, November 21st - Friday, November 25th
Session 1 Session 2 Session 3
09:00 – 10:45 11:00 – 12:45 14:00 – 15:45
Mon. 21st Databases Databases lab MySQL lab
Donaldson Donaldson Donaldson
Tue. 22nd Perl More Perl Perl lab
Donaldson Donaldson Donaldson
Wed. 23rd Introduction to R R lab R lab
Bjørn-Helge Mevik Bjørn-Helge Mevik, Katerina Michalickova, Antonio Mora Bjørn-Helge Mevik, Katerina Michalickova, Antonio Mora
Thur. 24th Exploratory data analysis An introduction to statistical inference Multiple hypothesis testing
Anja Bråthern Kristoffersen Ole Christian Lingjærde Einar A. Rødland
Fri. 25th Session 1 Session 2 Session 3
09:00 – 10:45 11:00 – 12:00 13:30 – 15:45
Microarray data analysis Microarray data lab Gene Ontology Over-representation analysis in DAVID. Lab.
Ståle Nygård Ståle Nygård Donaldson
Week 2: Monday, November 28th - Friday, December 2nd.
Session 1 Session 2 Session 3
09:00 – 10:45 11:00 – 12:45 14:00 – 15:45
Mon 28th Interaction and pathway data Cytoscape lab Cytoscape plugin lab
Donaldson Donaldson Donaldson
Tue. 29th ht sequencing ht sequence lab
Robert Lyle Robert Lyle
Wed 30th Searching sequence databases and multiple sequence alignments Motif scanning and discovery in DNA Sequence lab
Torbjørn Rognes Geir Sandve Geir Sandve
Thur 1st Structural biology review, PyMOL and installing PyMOL Structural biology tools, predictors and 3D modelling PyMOL and structural biology tutorial
Jon K. Laerdahl Jon K. Laerdahl Jon K. Laerdahl
Fri 2nd Session 1 Session 2 Session 3
09:00 – 10:45 11:00 – 12:00 13:30 – 15:45
Modeling guide Modeling excercises Homology modeling excercise
Jon K. Laerdahl Jon K. Laerdahl Jon K. Laerdahl

Written assignment

Students enrolled in MBV-INF4410 or 9410 must complete a written assignment as part of the course requirements.

The assignment is due by Friday, December 16th. 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 10 pages and 20 pages (2000 to 4000 words). This is a rough guide (I wont be counting pages and words - quality and conciseness count more than quantity).

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.

Exam

Please note:

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

The exam will be emailed to candidates on Monday, December 5th before 5PM.  

The exam must be emailed back by Monday, December 12th at 5 PM to 

Torill Rortveit (torill.rortveit@imbv.uio.no) as a single PDF document

(Microsoft Word or an Open Office Document is also acceptable).  The document 

should be named with the course code and your candidate number only 

(e.g. MBV-INF 4410-1.pdf).  Do not place your name in the document.

Bioinformatics links relevant to the course

Bioinformatics Links 2011
Name URL Description
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
R http://cran.r-project.org/ The Comprehensive R Archive Network

Introduction to R

Exploratory data analysis

Hypothesis testing

http://bioinformatics.ca/workshops/2009/course-content See the CBW course on "Exploratory Data Analysis Essential Statistics using R" at the bottom of this page. Slides and lecture recordings from Modules 1-3 cover much of the same material covered in the first two days of this course.
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
R reference card http://cran.r-project.org/doc/contrib/Short-refcard.pdf A reference card for R syntax
UCLA tutorials http://www.ats.ucla.edu/stat/r/ Useful example code while learning R
R vs. other languages http://www.johndcook.com/R_language_for_programmers.html A brief description of how R differs from other programming languages. Useful if you already know a programming language.
Which test do I use http://www.practicalstats.com/which/index.html An interactive guide to choosing which statistical test to use.
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
SIB tutorials http://edu.isb-sib.ch/ Portal to the SIB bioinformatics tutorials - includes R, Unix, Perl, statisitics and lots more.
CBW tutorials http://bioinformatics.ca Portal to the Canadian Bioinformatics Workshop material. Includes R, statistics and lots more.
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
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
Structure
Networks
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
Cytoscape http://cytoscape.wodaklab.org/wiki/How_to_increase_memory_for_Cytoscape Solution to common problem with working with large networks in Cytoscape.
iRefIndex Cytoscape plugin http://irefindex.uio.no/wiki/README_Cytoscape_plugin_0.9x 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

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.


Archived courses

http://donaldson.uio.no/wiki/Bioinformatics_for_molecular_biology_2010

http://donaldson.uio.no/wiki/Bioinformatics_for_molecular_biology_2009

Wiki help

http://excel2wiki.net/index.php

http://en.wikipedia.org/wiki/Help:Table

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