Bioinformatics course

Bioinformatics for molecular biology - Fall 2011

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 will be open in June of 2011. Check back here for details

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

Please note:
The schedule displayed below is based on last years course 
(see http://donaldson.uio.no/wiki/Bioinformatics_for_molecular_biology_2010).
Ongoing changes will be made to this page as we organize 
speakers before and during the course.  
Requests and suggestions are welcome.

Bioinformatics 2011

Time	Speaker	Contact	Details and suggested readings
Day 1 - Monday November 21st
9.00-9.15	Ian Donaldson	http://donaldson.uio.no	Introduction
9.15-11.00	Ian Donaldson	http://donaldson.uio.no	Exploratory data analysis Extra material
11:15-13.00	Bjørn-Helge Mevik	http://www.usit.uio.no/suf/vd/	Introduction to R - Presentation
14.15-16.00	Bjørn-Helge Mevik Katerina Michalickova	http://www.usit.uio.no/suf/vd/	Introduction to R - Lab
Day 2 - Tuesday November 22nd
9.15-11.00	Clara-Cecilie Günther	http://www.nr.no/	An introduction to statistical inference
11:15-13.00	Einar A. Rødland	http://folk.uio.no/einarro/	Multiple hypothesis testing
14.15-16.00	Ian Donaldson	http://donaldson.uio.no	MySQL installation and tutorial
Day 3 -Wednesday November 23rd
9.15-11.00	Leonardo Meza-Zepeda	Dept. of Tumor Biology, Rikshospitalet-Radiumhospitalet Medical Center	Microarray technology Integrated genomic analysis
11:15-13.00	Ståle Nygård	http://core.rr-research.no/index.php?section=22	Microarray data analysis
14.15-16.00	Ståle Nygård		R Microarray data analysis lab
Day 4 - Thursday November 24th
9.15-11.00	Torbjørn Rognes	http://www.rr-research.no/rognes/	Searching sequence databases and multiple sequence alighments.
11:15-13.00	Geir K. Sandve	http://www.uio.no/sok?la=en&person=geirksa	Motif scanning and discovery in DNA
14.15-16.00	Geir K. Sandve Halfden Vegard Nygaard		Sequence lab RSAT ConTra General TF analysis - a simple approach
Day 5 - Friday November 25th
9.15-11.00	Sveinung Gundersen Geir K. Sandve		The Genomic Hyperbrowser 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 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 Comparative genomics - bacterial genomes.
14.15-15.30			Sequence lab Three views EColi. Atlas BLAST Atlas GeneWiz Browser Physical Maps of Chromosomes The 1000th Genome
16.00-	TGIF		Forskningsparken pub
Day 6 - Monday November 28th
9:00-11:00	Robert Lyle		High throughput sequencing
11:15-13.00	George Magklaras	http://www.no.embnet.org/	Biological sequence mining with MRS MRS and EMBOSS lab
13:00-14:00	Lunch
14.15-16.00	Kamran Shalchian-Tabrizi (TBC)	http://www.bioportal.uio.no	Bioportal
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/	Structural biology review PyMOL Installing PyMol
11:15-13.00	Jon K. Laerdahl		Structural bioinformatics tools, predictors, and 3D modeling
14.15-16.00	Jon K. Laerdahl		PyMOL and structural biology tutorial
Day 8 - Wednesday November 30th
9.15-11.00	Jon K. Laerdahl		Structural modeling tutorial: Practical exercises Modeling Guide
11:15-13.00	Jon K. Laerdahl		Modeling excercises
14.15-16.00	Jon K. Laerdahl		Homology modeling exercise
Day 9 - Thursday December 1st
9.15-11.00	Ian Donaldson	http://donaldson.uio.no	Interaction data resources Identifier conversion excercise
11:15-13.00	Sabry Razick, Paul Boddie	http://donaldson.uio.no	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
Day 10 - Friday December 2nd
9.15-10.00	Ian Donaldson		GO DAVID and IRefScape revisited Working with gene lists and over-representation analysis
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
12.00-13:30	Lunch -vacate room
13:30-14:15	Katerina Michalickova	http://hpc.uio.no/index.php/Main_Page http://www.usit.uio.no/suf/vd/	TITAN cluster for beginners
14.30-15.15
15.15-16.00

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, September 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.