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=Bioinformatics for molecular biology - Fall 2011=
+
=Bioinformatics for molecular biology - Fall 2012=
  
'''November 21st to December 2nd'''
+
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.
  
==Description==
+
Past course content is archived at the links below.
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/).
+
==Archived courses==
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==
 
 
 
<pre>
 
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.
 
</pre>
 
 
 
 
 
{| {{table}}
 
| align="center" style="background:#f0f0f0;"|'''Week 1: Monday, November 21st - Friday, November 25th'''
 
| align="center" style="background:#f0f0f0;"|''''''
 
| align="center" style="background:#f0f0f0;"|''''''
 
| align="center" style="background:#f0f0f0;"|''''''
 
|-
 
| 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" 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||  ||  ||
 
|-
 
|}
 
 
 
== 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 ==
 
 
 
<pre>
 
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.
+
http://donaldson.uio.no/wiki/Bioinformatics_for_molecular_biology_2011
 
</pre>
 
 
 
==Bioinformatics links relevant to the course==
 
 
 
{|class="wikitable" style="text-align:left" border="1" cellpadding="5"
 
|+ '''Bioinformatics Links 2011'''
 
!width="20%"|Name
 
!width="40%"|URL
 
!width="40%"|Description
 
|-
 
|style="background:SteelBlue; color:white" colspan="4" align="center"|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.
 
|-
 
|style="background:SteelBlue; color:white" colspan="4" align="center"|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
 
|-
 
|style="background:SteelBlue; color:white" colspan="4" align="center"|Sequence
 
|-
 
|RSAT || [http://rsat.ulb.ac.be/rsat/ RSAT] || A collection of several motif-related tools
 
|-
 
|ConTra|| [http://bioit.dmbr.ugent.be/ConTra/index.php ConTra] || A more user-friendly tool for matching a collection of Position Weighted Matrices against promoter sequences across species
 
|-
 
|style="background:SteelBlue; color:white" colspan="4" align="center"| Structure
 
|-
 
|style="background:SteelBlue; color:white" colspan="4" align="center"| Networks
 
|-
 
|Required files || [Sample network[http://bioinformatics.uio.no/wikifiles//images/8/8c/SAMPLE_1_network.xls.zip]] [Node atributes[http://bioinformatics.uio.no/wikifiles//images/c/c2/SAMPLE_1_nodeatribute.xls.zip]]|| 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 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 http://mailman.uib.no/listinfo/bioinfo.users].
 
 
 
Both lists are run by members of the [http://www.bioinfo.no/about Norwegian Bioinformatics Platform].
 
 
 
 
 
==Archived courses==
 
  
 
http://donaldson.uio.no/wiki/Bioinformatics_for_molecular_biology_2010
 
http://donaldson.uio.no/wiki/Bioinformatics_for_molecular_biology_2010
  
 
http://donaldson.uio.no/wiki/Bioinformatics_for_molecular_biology_2009
 
http://donaldson.uio.no/wiki/Bioinformatics_for_molecular_biology_2009
 
==Wiki help==
 
 
http://excel2wiki.net/index.php
 
 
http://en.wikipedia.org/wiki/Help:Table
 

Latest revision as of 11:31, 22 August 2012

Bioinfo course logo.jpg
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Bioinformatics for molecular biology - Fall 2012

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.

Archived courses

http://donaldson.uio.no/wiki/Bioinformatics_for_molecular_biology_2011

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

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