|
|
| (97 intermediate revisions by 4 users not shown) |
| Line 6: |
Line 6: |
| | </div> | | </div> |
| | | | |
| − | =Bioinformatics for molecular biology - Fall 2010= | + | =Bioinformatics for molecular biology - Fall 2012= |
| | | | |
| − | ==Description==
| + | This course is being arranged for the fall semester of 2012 by Dr. Jon Lærdahl. |
| − | 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.
| + | See https://wiki.uio.no/projects/MBV-INFX410/index.php/Main_Page |
| | + | for more information. |
| | | | |
| − | 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/).
| + | Past course content is archived at the links below. |
| − | The UiO page for this course is http://www.uio.no/studier/emner/matnat/molbio/MBV-INF4410/.
| |
| | | | |
| − | '''Registration will be open in May of 2010. Check back here for details'''
| + | ==Archived courses== |
| | | | |
| − | MBV-INF 4410 (M.Sc. level course code)10.0 study points
| + | http://donaldson.uio.no/wiki/Bioinformatics_for_molecular_biology_2011 |
| | | | |
| − | MBV-INF 9410 (Ph.D. level course code) 10.0 study points
| + | http://donaldson.uio.no/wiki/Bioinformatics_for_molecular_biology_2010 |
| | | | |
| − | MBV-INF 9410A (Ph.D. level course code) 8.0 study points
| + | http://donaldson.uio.no/wiki/Bioinformatics_for_molecular_biology_2009 |
| − | | |
| − | The course consists of two weeks of lectures, a final take-home exam (one week) and an essay (M.Sc. level 10 pages and Ph.D. level 20 pages to be completed by end of October).
| |
| − | | |
| − | 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 2010 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 September 6th to 17th.
| |
| − | | |
| − | 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. 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_2009).
| |
| − | Ongoing changes will be made to this page as we organize speakers over the next few months.
| |
| − | Requests and suggestions are welcome.
| |
| − | </pre>
| |
| − | | |
| − | {|class="wikitable" style="text-align:left" border="1" cellpadding="5"
| |
| − | |+ '''Bioinformatics 2010'''
| |
| − | !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 September 6
| |
| − | |-
| |
| − | |9.00-9.15||Ian Donaldson||http://donaldson.uio.no ||Introduction
| |
| − | |-
| |
| − | |9.15-11.00 || Ian Donaldson || 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/3/39/Intro_R_lab_2010.pdf Introduction to R - Presentation]
| |
| − | |-
| |
| − | |14.15-16.00||
| |
| − | Bjørn-Helge Mevik
| |
| − | | |
| − | Katerina Michalickova
| |
| − | || http://www.usit.uio.no/suf/vd/ ||
| |
| − | [http://biotin.uio.no/wikifiles//images/1/1a/Intro_R_lab.pdf Introduction to R - Lab]
| |
| − | |-
| |
| − | |style="background:SteelBlue; color:white" colspan="4" align="center"| Day 2 - Tuesday September 7
| |
| − | |-
| |
| − | |9.15-11.00|| Clara-Cecilie Günther || http://www.nr.no/ ||
| |
| − | [http://bioinformatics.uio.no/wikifiles//images/2/24/Introduction_to_statistical_inference.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/0/08/Installation_and_tutorial_for_MySQL.pdf Installation and tutorial for MySQL]
| |
| − | |-
| |
| − | |style="background:SteelBlue; color:white" colspan="4" align="center"| Day 3 -Wednesday September 8
| |
| − | |-
| |
| − | |9.15-11.00 || Leonardo Meza-Zepeda || Dept. of Tumor Biology, Rikshospitalet-Radiumhospitalet Medical Center ||
| |
| − | [http://bioinformatics.uio.no/wiki/Image:Microarray_technology_1.pdf Microarray technology 1]
| |
| − | | |
| − | [http://bioinformatics.uio.no/wiki/Image:Microarray_technology_2.pdf Microarray technology 2]
| |
| − | |-
| |
| − | |11:15-13.00|| Ståle Nygård || http://core.rr-research.no/index.php?section=22 ||
| |
| − | [http://bioinformatics.uio.no/wiki/Image:Microarray_data_analysis.pdf Microarray data analysis]
| |
| − | |-
| |
| − | |14.15-16.00|| Ståle Nygård || || R Microarray data analysis lab
| |
| − | |-
| |
| − | |style="background:SteelBlue; color:white" colspan="4" align="center"| Day 4 - Thursday September 9
| |
| − | |-
| |
| − | |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]
| |
| − | |-
| |
| − | |style="background:SteelBlue; color:white" colspan="4" align="center"| Day 5 - Friday September 10
| |
| − | |-
| |
| − | |9.15-11.00 ||
| |
| − | Sveinung Gundersen
| |
| − | | |
| − | Geir K. Sandve
| |
| − | ||
| |
| − | || Hyperbrowser tutorial
| |
| − | http://hyperbrowser.uio.no/
| |
| − | |-
| |
| − | |11.15-12:00 || Dave W. Ussery || http://www.cbs.dtu.dk/staff/dave/ || Comparative genomics
| |
| − | [http://bioinformatics.uio.no/wikifiles//images/3/38/Methods_to_compare_genomes.pdf Methods to compare genomes]
| |
| − | |-
| |
| − | |12.00-13:30 || Lunch -vacate room || ||
| |
| − | |-
| |
| − | |13:30-14:15|| Dave W. Ussery || http://www.cbs.dtu.dk/staff/dave/ || Comparative genomics
| |
| − | [http://bioinformatics.uio.no/wikifiles//images/4/4e/Pan-genomics_and_metagenomics.pdf Pan-genomics and metagenomics]
| |
| − | |-
| |
| − | |14.15-16.00|| || || [http://folk.uio.no/karinlag/Sequence_Lab_Dave_Ussery.html Sequence lab]
| |
| − | |-
| |
| − | |style="background:SteelBlue; color:white" colspan="4" align="center"| Day 6 - Monday September 13
| |
| − | |-
| |
| − | |9:00-11:00|| Robert Lyle || ||
| |
| − | [http://bioinformatics.uio.no/wikifiles//images/6/62/High_throughput_sequencing.pdf High throughput sequencing]
| |
| − | |-
| |
| − | |11:15-13.00|| George Magklaras (TBC) || http://www.no.embnet.org/ ||
| |
| − | [http://bioinformatics.uio.no/wikifiles//images/2/25/EMBNet.pdf EMBNet]
| |
| − | |-
| |
| − | |13:00-14:00 || Lunch || ||
| |
| − | |-
| |
| − | |14.15-16.00 || Kamran Shalchian-Tabrizi (TBC) || http://www.bioportal.uio.no ||
| |
| − | [http://bioinformatics.uio.no/wikifiles//images/a/a3/Bioportal_and_Eukarytic_megaevolution.pdf Bioportal_and_Eukarytic_megaevolution.pdf]
| |
| − | |-
| |
| − | |style="background:SteelBlue; color:white" colspan="4" align="center"| Day 7 - Tuesday September 14
| |
| − | |-
| |
| − | |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
| |
| − | | |
| − | [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 || ||
| |
| − | Structural bioinformatics tools, predictors, and 3D modeling
| |
| − | |-
| |
| − | |14.15-16.00|| Jon K. Laerdahl || || Structural tutorials and exercises
| |
| − | | |
| − | PyMol demonstration
| |
| − | | |
| − | PyMol excercise
| |
| − | |-
| |
| − | |style="background:SteelBlue; color:white" colspan="4" align="center"| Day 8 - Wednesday September 15
| |
| − | |-
| |
| − | |9.15-11.00 || Jon K. Laerdahl || || Structural modeling tutorial
| |
| − | |-
| |
| − | |11:15-13.00|| Jon K. Laerdahl || || Structural modeling tutorial
| |
| − | |-
| |
| − | |14.15-16.00|| Jon K. Laerdahl || || Structural modeling tutorial
| |
| − | |-
| |
| − | |style="background:SteelBlue; color:white" colspan="4" align="center"| Day 9 - Thursday September 16
| |
| − | |-
| |
| − | |9.15-11.00 || Ian Donaldson || http://donaldson.uio.no ||
| |
| − | [http://bioinformatics.uio.no/wikifiles//images/c/c4/Working_with_Gene_Lists_and_Over-representation_analysis.pdf Working with gene lists and over-representation analysis]
| |
| − | |-
| |
| − | |11:15-13.00|| Ian Donaldson || http://donaldson.uio.no ||
| |
| − | [http://bioinformatics.uio.no/wikifiles//images/4/47/Interaction_data_resources.pdf Interaction data resources]
| |
| − | | |
| − | [http://bioinformatics.uio.no/wikifiles//images/5/5e/Biopathways_SIG_irefindex.pdf iRefIndex talk at BioPathways talk]
| |
| − | |-
| |
| − | |14.15-16.00|| Sabry Razick, Paul Boddie || http://donaldson.uio.no || Interaction lab
| |
| − | Install CytoScape and the iRefScape plugin. See http://cytoscape.org and http://irefindex.uio.no/wiki/README_Cytoscape_plugin_0.9x
| |
| − | |-
| |
| − | |style="background:SteelBlue; color:white" colspan="4" align="center"| Day 10 - Friday September 17
| |
| − | |-
| |
| − | |9.15-10.00 || ||
| |
| − | |-
| |
| − | |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-INF 4410 must complete a written assignment as part of the course requirements.
| |
| − | | |
| − | The assignment is due by Friday, October 29th. 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.
| |
| − | | |
| − | == Exam ==
| |
| − | | |
| − | <pre>
| |
| − | Please note:
| |
| − | | |
| − | The exam for this course will be a one week take home exam.
| |
| − | | |
| − | That will begin directly after the lectures end.
| |
| − | | |
| − | The exam must be handed in Monday, September 20th by 5 PM.
| |
| − | </pre>
| |
| − | | |
| − | ==Bioinformatics links relevant to the course==
| |
| − | | |
| − | {|class="wikitable" style="text-align:left" border="1" cellpadding="5"
| |
| − | |+ '''Bioinformatics Links 2010'''
| |
| − | !width="20%"|Name
| |
| − | !width="40%"|URL
| |
| − | !width="40%"|Description
| |
| − | |-
| |
| − | |style="background:SteelBlue; color:white" colspan="4" align="center"| Day 1-2: 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
| |
| − | |-
| |
| − | |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
| |
| − | |-
| |
| − | |style="background:SteelBlue; color:white" colspan="4" align="center"| 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
| |
| − | |-
| |
| − | |style="background:SteelBlue; color:white" colspan="4" align="center"| Day 4 - 5 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"| Day 6 -
| |
| − | |-
| |
| − | |style="background:SteelBlue; color:white" colspan="4" align="center"| Day 7 -
| |
| − | |-
| |
| − | |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
| |
| − | |-
| |
| − | |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
| |
| − | |-
| |
| − | |}
| |
| − | | |
| − | ==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].
| |
