Bioinformatics for molecular biology 2009
Contents
Bioinformatics for molecular biology (10.0/8.0 credit points)
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/).
Registration is now open as of July 3rd, 2009.
MBV-INF 4410 (M.Sc. level course code)10.0 study points
MBV-INF 9410A (Ph.D. level course code) 10.0 study points
MBV-INF 9410B (Ph.D. level course code) 8.0 study points
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.
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.
Please bookmark this page. All future changes or announcements for the 2009 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 in weeks 37 and 38 (September 7th and 14th).
Each day will consist of three time slots for lectures and/or practical labs between 9 AM and 4 PM.
Place
Forskningsparken
Directions to Forsknings parken can be found at http://www.biotek.uio.no/map.html
Mondays to Thursdays: Room 10 (one level down from the main entrance)
Fridays: Room 7 (one level down from the main entrance)
Exceptions: none so far
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.
Programme
Please note: The displayed programme is a preliminary schedule under development. Changes are possible.
| Time | Speaker | Contact | Details and suggested readings |
|---|---|---|---|
| Day 1 - Monday September 7 | |||
| 9.00-9.15 | Ian Donaldson | http://donaldson.uio.no | Introduction |
| 9.15-11.00 | Anja Bråthen Kristoffersen | http://heim.ifi.uio.no/~anjab/ | |
| 11:15-13.00 | Ole Christian Lingjærde | http://heim.ifi.uio.no/~ole/ | |
| 14.15-16.00 | Einar A. Rødland | http://folk.uio.no/einarro/ | |
| Day 2 - Tuesday September 8 | |||
| 9.15-11.00 | Arnoldo Frigessi | http://www.nr.no/~frigessi/ | |
| 11:15-13.00 | Antonio Mora | http://donaldson.uio.no | |
| 14.15-16.00 | Antonio Mora | http://donaldson.uio.no | |
| Day 3 -Wednesday September 9 | |||
| 9.15-11.00 | Leonardo Meza-Zepeda | Dept. of Tumor Biology, Rikshospitalet-Radiumhospitalet Medical Center | |
| 11:15-13.00 | Ståle Nygård | http://core.rr-research.no/index.php?section=22 | |
| 14.15-16.00 | Microarrays | ||
| Day 4 - Thursday September 10 | |||
| 9.15-11.00 | Torbjørn Rognes | http://www.rr-research.no/rognes/ | |
| 11:15-13.00 | Robert Lyle | ||
| 14.15-16.00 | Geir K. Sandve | http://www.uio.no/sok?la=en&person=geirksa | |
| Day 5 - Friday September 11 | |||
| 9.15-11.00 | Dave W. Ussery | http://www.cbs.dtu.dk/staff/dave/ |
Comparative genomics Methods to compare genomes Pan-genomics and metagenomics |
| 11:15-13.00 | Karin Lagesen | http://folk.uio.no/karinlag/ | Sequence lab |
| 14.15-16.00 | Geir K. Sandve | http://www.uio.no/sok?la=en&person=geirksa |
Sequence lab |
| Day 6 - Monday September 14 | |||
| 9.15-11.00 | Bjørn Dalhus | ||
| 11:15-13.00 | Jon K. Laerdahl |
Structural bioinformatics tools, predictors, and 3D modeling | |
| 14.15-16.00 | Dalhus and Laerdahl | Structural tutorials and exercises | |
| Day 7 - Tuesday September 15 | |||
| 9.15-11.00 | Ian Donaldson | http://donaldson.uio.no | |
| 11:15-13.00 | Ian Donaldson | http://donaldson.uio.no | |
| 14.15-16.00 | Antonio Mora, Sabry Razick, Paul Boddie | http://donaldson.uio.no | Interaction lab
Install http://cytoscape.org and http://irefindex.uio.no/wiki/README_Cytoscape_plugin_0.5x |
| Day 8 - Wednesday September 16 | |||
| 9.15-10.00 | Erik Plahte | http://www.cigene.no/people.html | |
| 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 | |
| 12:15-13.00 | Harald Martens | http://www.cigene.no/people.html |
Bio-chemometrics_and_multivariate_data_modelling_in_systems_biology |
| 13:00-14.15 | Lunch | ||
| 14.15-15.00 | Achim Kohler | http://www.cigene.no/people.html | |
| 15.15-16.00 | Solve Sæbø | http://www.umb.no/ikbm/ansatte/solve.sabo | |
| Day 9 - Thursday September 17 | |||
| 9.15-11.00 | Joakim Sundnes | http://simula.no/ | |
| 11:15-13.00 | George Magklaras | http://www.no.embnet.org/ | |
| 14.15-16.00 | Kamran Shalchian-Tabrizi | http://www.bioportal.uio.no | |
| Day 10 - Friday September 18 | |||
| 9.15-12.00 | Course Review | ||
| 1.15-16.00 | Pizza and Feedback session | ||
| Day 11 - Monday September 21 | |||
| 9.15-13.15 | Exam (4 hour written open book) | ||
Bioinformatics links relevant to the course
| Name | URL | Description | |
|---|---|---|---|
| Day 1 - 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 | |
| Day 2 - Statistics | |||
| R | http://cran.r-project.org/ | The Comprehensive R Archive Network | |
| 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 | |
| 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 | |
| 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 | |
| Day 4 - 5 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 | |
| Day 6 - | |||
| Day 7 - | |||
| 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 | |
| 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 | |
Written assignment
Students enrolled in MBV-INF 4410 must complete a written assignment as part of the course requirements.
The assignment is due by October 27th. 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.
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.
