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This is the wiki for the courses [http://www.uio.no/studier/emner/matnat/molbio/MBV-INF4410 MBV-INF4410], [http://www.uio.no/studier/emner/matnat/molbio/MBV-INF9410 MBV-INF9410], and [http://www.uio.no/studier/emner/matnat/molbio/MBV-INF9410A MBV-INF9410A] offered by the Department of Molecular Biosciences and Department of Informatics at the University of Oslo (UiO). | This is the wiki for the courses [http://www.uio.no/studier/emner/matnat/molbio/MBV-INF4410 MBV-INF4410], [http://www.uio.no/studier/emner/matnat/molbio/MBV-INF9410 MBV-INF9410], and [http://www.uio.no/studier/emner/matnat/molbio/MBV-INF9410A MBV-INF9410A] offered by the Department of Molecular Biosciences and Department of Informatics at the University of Oslo (UiO). | ||
| − | '''The course will be offered in weeks 47 and 48, autumn 2012, ''i.e. ''November 19 - November 30.'''Each day, Monday to Friday, will consist of three time slots for lectures and/or exercises/practical labs between 09:00 and 16:00. | + | '''The course will be offered in weeks 47 and 48, autumn 2012, ''i.e. ''November 19 - November 30. '''Each day, Monday to Friday, will consist of three time slots for lectures and/or exercises/practical labs between 09:00 and 16:00. |
'''Lecture room:''' All lectures/exercises in week 47 will be given in lecture room '''Python''' in Ole-Johan Dahls hus (IFI2). A map showing the location of the building is found [http://www.uio.no/om/finn-fram/omrader/gaustad/ga06 here]. The room Python is on the 1st floor (2. etasje) in the northern end of the building, the end closest to the tram line. The easist access to '''Python''' is through the entrance in the tunnel going through the building. | '''Lecture room:''' All lectures/exercises in week 47 will be given in lecture room '''Python''' in Ole-Johan Dahls hus (IFI2). A map showing the location of the building is found [http://www.uio.no/om/finn-fram/omrader/gaustad/ga06 here]. The room Python is on the 1st floor (2. etasje) in the northern end of the building, the end closest to the tram line. The easist access to '''Python''' is through the entrance in the tunnel going through the building. | ||
Revision as of 13:36, 9 October 2012
Bioinformatics for Molecular Biology
This is the wiki for the courses MBV-INF4410, MBV-INF9410, and MBV-INF9410A offered by the Department of Molecular Biosciences and Department of Informatics at the University of Oslo (UiO).
The course will be offered in weeks 47 and 48, autumn 2012, i.e. November 19 - November 30. Each day, Monday to Friday, will consist of three time slots for lectures and/or exercises/practical labs between 09:00 and 16:00.
Lecture room: All lectures/exercises in week 47 will be given in lecture room Python in Ole-Johan Dahls hus (IFI2). A map showing the location of the building is found here. The room Python is on the 1st floor (2. etasje) in the northern end of the building, the end closest to the tram line. The easist access to Python is through the entrance in the tunnel going through the building.
This two week, intensive course will introduce students to bioinformatics resources and tools for molecular biology research. Some of the best researchers in Norway will talk about their fields in general as well as their own work. Students must bring their own lap-top for in-course demonstrations as well as for practical lab exercises. The course is mainly intended for biology students, but also for computer science students or students from other fields of science with an interest for and some experience with molecular biology. No prior background in bioinformatics or computer science is required.
The webpages for 2011 is found here.
The cource will in 2012 have a similar format, but with some few changes.
- New course responsible is Dr. Jon K. Lærdahl (jonkl@medisin.uio.no) from Centre for Molecular Biology and Neuroscience (CMBN) and Department of Medical Microbiology, Oslo University Hospital (OUH) - Rikshospitalet. Lærdahl is also employed by the Bioinformatics Core Facility at OUH and UiO.
- There will be some lectures focusing on the UNIX shell, scripting and the Python programming language.
- Examination (home exam) and written assignment will be in a similar format as previous years.
Programme (preliminary!)
| Week 1: Monday, November 19 - Friday, November 23 | ||||
| Session 1 | Session 2 | Session 3 | ||
| 09:00 - 10:45 | 11:00 - 12:45 | 13:30 - 16:00 | ||
| Monday 19th |
Introduction Biological databases on the web Accessing data |
Basic UNIX tutorial with practicals Simple examples of scripting | ||
| Jon K. Lærdahl | Jon K. Lærdahl | Jon K. Lærdahl | ||
| Tuesday 20th |
Basic Python programming |
Python workshop | Python workshop | |
| Karin Lagesen | Karin Lagesen | Karin Lagesen | ||
| Wednesday 21st |
Genome browser and Galaxy - lectures/exercises |
Introduction to statistical inference and multiple hypothesis testing - lecture |
Galaxy, workflows, reproducability, HyperBrowser - lectures/exercises | |
| Jon K. Lærdahl | Clara-Cecilie Günter | Geir Kjetil Sandve | ||
| Thursday 22nd |
Exploratory data analysis - lecture |
Introduction to R and R-lab | R-lab | |
| Anja Bråthern Kristoffersen | Anja Bråthern Kristoffersen | Anja Bråthern Kristoffersen | ||
| Friday 23rd |
High throughput sequencing - lecture |
High throughput sequencing lab | High throughput sequencing lab | |
| Robert Lyle | Robert Lyle | Robert Lyle | ||
| Week 2: Monday, November 26 - Friday, November 30 | ||||
| Session 1 | Session 2 | Session 3 | ||
| 09:00 - 10:45 | 11:00 - 12:45 | 13:30 - 16:00 | ||
| Monday 26th | Microarrays - lecture | Microarrays - practicals |
Gene lists & over-representation analysis (ORA) - lectures/practicals | |
| Ståle Nygård | Ståle Nygård | Karin Lagesen | ||
| Tuesday 27th |
Sequence searching, alignments, and multiple alignments - lecture |
Working with sequences - exercises |
Working with sequences - exercises | |
| Torbjørn Rognes | Torbjørn Rognes | Torbjørn Rognes | ||
| Wednesday 28th | JalView |
Structural biology review - lecture |
Structural biology tools, predictors & 3D modelling - lecture | |
| Jon K Lærdahl | Jon K Lærdahl | Jon K Lærdahl | ||
| Thursday 29th | Working with PyMOL | 3D modlling guide | Modelling exercise | |
| Jon K Lærdahl | Jon K Lærdahl | Jon K Lærdahl | ||
| Friday 30th | Modelling exercise | Docking and drug discovery | Docking and drug discovery | |
| Jon K Lærdahl | Jon K Lærdahl | Jon K Lærdahl | ||
