Difference between revisions of "Bioinformatics course"
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!width="350"|Details and suggested readings | !width="350"|Details and suggested readings | ||
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| − | |style="background:SteelBlue; color:white" colspan="4" align="center"| Day 1 - Monday | + | |style="background:SteelBlue; color:white" colspan="4" align="center"| Day 1 - Monday September 7 |
|- | |- | ||
|9.00-9.15||Ian Donaldson||ian.donaldson at biotek.uio.no||Introduction | |9.00-9.15||Ian Donaldson||ian.donaldson at biotek.uio.no||Introduction | ||
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|14.15-16.00|| || || | |14.15-16.00|| || || | ||
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| − | |style="background:SteelBlue; color:white" colspan="4" align="center"| Day 2 - Tuesday | + | |style="background:SteelBlue; color:white" colspan="4" align="center"| Day 2 - Tuesday September 8 |
|- | |- | ||
|9.15-11.00 || || || Statistics II | |9.15-11.00 || || || Statistics II | ||
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|14.15-16.00|| || || | |14.15-16.00|| || || | ||
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| − | |style="background:SteelBlue; color:white" colspan="4" align="center"| Day 3 -Wednesday | + | |style="background:SteelBlue; color:white" colspan="4" align="center"| Day 3 -Wednesday September 9 |
|- | |- | ||
|9.15-11.00 || || || Microarrays | |9.15-11.00 || || || Microarrays | ||
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|14.15-16.00|| || || Microarrays | |14.15-16.00|| || || Microarrays | ||
|- | |- | ||
| − | |style="background:SteelBlue; color:white" colspan="4" align="center"| Day 4 - Thursday | + | |style="background:SteelBlue; color:white" colspan="4" align="center"| Day 4 - Thursday September 10 |
|- | |- | ||
|9.15-11.00 || Torbjørn Rognes || torognes at ifi.uio.no || Sequence alignments and BLASTing | |9.15-11.00 || Torbjørn Rognes || torognes at ifi.uio.no || Sequence alignments and BLASTing | ||
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|14.15-16.00|| Geir K. Sandve || || Motif scanning and discovery in DNA | |14.15-16.00|| Geir K. Sandve || || Motif scanning and discovery in DNA | ||
|- | |- | ||
| − | |style="background:SteelBlue; color:white" colspan="4" align="center"| Day 5 - Friday | + | |style="background:SteelBlue; color:white" colspan="4" align="center"| Day 5 - Friday September 11 |
|- | |- | ||
|9.15-11.00 || Dave W. Ussery || || Comparative genomics | |9.15-11.00 || Dave W. Ussery || || Comparative genomics | ||
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|14.15-16.00|| Multiple || || Sequence lab | |14.15-16.00|| Multiple || || Sequence lab | ||
|- | |- | ||
| − | |style="background:SteelBlue; color:white" colspan="4" align="center"| Day 6 - Monday | + | |style="background:SteelBlue; color:white" colspan="4" align="center"| Day 6 - Monday September 14 |
|- | |- | ||
|9.15-11.00 || Bjørn Dalhus || || Structural biology review and PyMOL (TBC) | |9.15-11.00 || Bjørn Dalhus || || Structural biology review and PyMOL (TBC) | ||
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|14.15-16.00|| Dalhus and Laerdahl || || Structural tutorials and exercises (TBC) | |14.15-16.00|| Dalhus and Laerdahl || || Structural tutorials and exercises (TBC) | ||
|- | |- | ||
| − | |style="background:SteelBlue; color:white" colspan="4" align="center"| Day 7 - Tuesday | + | |style="background:SteelBlue; color:white" colspan="4" align="center"| Day 7 - Tuesday September 15 |
|- | |- | ||
|9.15-11.00 || Ian Donaldson || ian.donaldson@biotek.uio.no || Working with gene lists and over-representation analysis | |9.15-11.00 || Ian Donaldson || ian.donaldson@biotek.uio.no || Working with gene lists and over-representation analysis | ||
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|14.15-16.00|| Antonio Mora, Sabry Razick, Paul Boddie || || Interaction lab | |14.15-16.00|| Antonio Mora, Sabry Razick, Paul Boddie || || Interaction lab | ||
|- | |- | ||
| − | |style="background:SteelBlue; color:white" colspan="4" align="center"| Day 8 - Wednesday | + | |style="background:SteelBlue; color:white" colspan="4" align="center"| Day 8 - Wednesday September 16 |
|- | |- | ||
|9.15-11.00 || Stig Omholt || || Causally cohesive genotype-phenotype modelling for understanding complex traits (TBC) | |9.15-11.00 || Stig Omholt || || Causally cohesive genotype-phenotype modelling for understanding complex traits (TBC) | ||
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|14.15-16.00|| || || Methods for genome-wide association studies on high-dimensional phenotypic data (TBC) | |14.15-16.00|| || || Methods for genome-wide association studies on high-dimensional phenotypic data (TBC) | ||
|- | |- | ||
| − | |style="background:SteelBlue; color:white" colspan="4" align="center"| Day 9 - Thursday | + | |style="background:SteelBlue; color:white" colspan="4" align="center"| Day 9 - Thursday September 17 |
|- | |- | ||
|9.15-12.00 | |9.15-12.00 | ||
|colspan="3"|Other ideas: Student presentations, Programming (Python, Taverna, R), Machine learning, BioPortal, EMBNet, Genome browser, text mining and PubGene, SIMULA and modelling | |colspan="3"|Other ideas: Student presentations, Programming (Python, Taverna, R), Machine learning, BioPortal, EMBNet, Genome browser, text mining and PubGene, SIMULA and modelling | ||
|- | |- | ||
| − | |style="background:SteelBlue; color:white" colspan="4" align="center"| Day 10 - Friday | + | |style="background:SteelBlue; color:white" colspan="4" align="center"| Day 10 - Friday September 18 |
|- | |- | ||
|9.15-12.00 | |9.15-12.00 | ||
|colspan="3"|Open lab and study session | |colspan="3"|Open lab and study session | ||
|- | |- | ||
| − | |style="background:SteelBlue; color:white" colspan="4" align="center"| Day | + | |style="background:SteelBlue; color:white" colspan="4" align="center"| Day 11 - Monday September |
|- | |- | ||
|9.15-13.15 | |9.15-13.15 | ||
|colspan="3"|Exam (4 hour written open book) | |colspan="3"|Exam (4 hour written open book) | ||
|} | |} | ||
Revision as of 12:27, 19 June 2009
Contents
Bioinformatics at the University of Oslo
Bioinformatics xxx: A course in bioinformatics for molecular biology (8.0 credit points)
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 data. Students are encouraged to bring a lap-top; we will be set up for in-course demonstrations as well as practical lab excercises. The course is intended for biology students. No prior background in bioinformatics or computer science is required.
Please bookmark this page. All future changes or announcements for the 2009 course will be posted to this page.
Registration is not yet open.
Information: ian.donaldson@biotek.uio.no
Registration: ragni.indahl@biotek.uio.no
Dates and times
The course is provisionally set to 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
Mondays to Thursdays: Room 10
Fridays: Room 7
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 | ian.donaldson at biotek.uio.no | Introduction |
| 9.15-11.00 | Statistics I | ||
| 11:15-13.00 | |||
| 14.15-16.00 | |||
| Day 2 - Tuesday September 8 | |||
| 9.15-11.00 | Statistics II | ||
| 11:15-13.00 | |||
| 14.15-16.00 | |||
| Day 3 -Wednesday September 9 | |||
| 9.15-11.00 | Microarrays | ||
| 11:15-13.00 | Microarrays | ||
| 14.15-16.00 | Microarrays | ||
| Day 4 - Thursday September 10 | |||
| 9.15-11.00 | Torbjørn Rognes | torognes at ifi.uio.no | Sequence alignments and BLASTing |
| 11:15-13.00 | Robert Lyle | High throughput sequencing | |
| 14.15-16.00 | Geir K. Sandve | Motif scanning and discovery in DNA | |
| Day 5 - Friday September 11 | |||
| 9.15-11.00 | Dave W. Ussery | Comparative genomics | |
| 11:15-13.00 | Multiple | Sequence lab | |
| 14.15-16.00 | Multiple | Sequence lab | |
| Day 6 - Monday September 14 | |||
| 9.15-11.00 | Bjørn Dalhus | Structural biology review and PyMOL (TBC) | |
| 11:15-13.00 | Jon K. Laerdahl | Structural bioinformatics tools, predictors, and 3D modeling (TBC) | |
| 14.15-16.00 | Dalhus and Laerdahl | Structural tutorials and exercises (TBC) | |
| Day 7 - Tuesday September 15 | |||
| 9.15-11.00 | Ian Donaldson | ian.donaldson@biotek.uio.no | Working with gene lists and over-representation analysis |
| 11:15-13.00 | Ian Donaldson | Interaction, Complex and Pathway data resources | |
| 14.15-16.00 | Antonio Mora, Sabry Razick, Paul Boddie | Interaction lab | |
| Day 8 - Wednesday September 16 | |||
| 9.15-11.00 | Stig Omholt | Causally cohesive genotype-phenotype modelling for understanding complex traits (TBC) | |
| 11:15-13.00 | Multivariate analysis of genetic data illustrated on yeast and human data (TBC) | ||
| 14.15-16.00 | Methods for genome-wide association studies on high-dimensional phenotypic data (TBC) | ||
| Day 9 - Thursday September 17 | |||
| 9.15-12.00 | Other ideas: Student presentations, Programming (Python, Taverna, R), Machine learning, BioPortal, EMBNet, Genome browser, text mining and PubGene, SIMULA and modelling | ||
| Day 10 - Friday September 18 | |||
| 9.15-12.00 | Open lab and study session | ||
| Day 11 - Monday September | |||
| 9.15-13.15 | Exam (4 hour written open book) | ||
