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− | === Bioinformatics mailing list for the Oslo region === | + | === Bioinformatics mailing list for the Oslo region === |
− | The mailing list for computational biology and bioinformatics in the Oslo region is | + | The mailing list for computational biology and bioinformatics in the Oslo region is cbo-all@usit.uio.no. The list has approximately 330 members. The list is used to distribute news about seminars, positions, courses, meetings and other topics that might be of interest to students and researchers with an interest i computational life science i south-eastern Norway. If you want to recieve e-mails that are sent to the list, sign up here |
− | [https://sympa.uio.no/usit.uio.no/info/cbo-all https://sympa.uio.no/usit.uio.no/info/cbo-all] | + | [https://sympa.uio.no/usit.uio.no/info/cbo-all https://sympa.uio.no/usit.uio.no/info/cbo-all] |
by following the link termed "Subscribe". | by following the link termed "Subscribe". |
Revision as of 13:27, 10 October 2012
Contents
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 consists of two weeks of lectures, a final take-home exam (one week), and an essay (10 to 20 pages).
Ph.D. level students may opt to take the course without the essay for only 8 study points (MBV-INF9410A). Both MBV-INF4410 (M.Sc. level) and MBV-INF9410 (Ph.D. level) are 10 study points courses.
Please bookmark this page. All future changes or announcements for the 2012 course will be posted on this page.
Time and place
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. Lunch will usually be between 12:45 and 13:30. You will have to bring your own lunch or buy lunch in the local kantine.
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 building is located next to the Forskningsparken metro and tram stations. 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. The lecture room for week 48 will be announced later.
Course description
This two week, intensive course will introduce students to bioinformatics resources and tools for molecular biology research. All the lectureres are among the top researchers working within the fields of bioinformatics and computational biology in the Oslo region. 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. All students should have a basic understanding of molecular biology, at least roughly corresponding to a single semester course in molecular biology or biochemistry.
Links to the webpages for the years 2009-2011 is found here. The cource will in 2012 have a similar format as previous years, 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.
Contacts
Jon K. Lærdahl (Course coordinator) - e-mail: jonkl@medisin.uio.no, phone: +47 99 507 335
Torill Rørtveit (Course administrator, registration) - e-mail: torill.rortveit@imbv.uio.no
Programme
The schedule below is tentative, and may be changed prior to, and possibly even during, the course. Requests and suggestions are welcome.
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 |
Exam
The exam for this course will be a one week, take-home exam in early December.
More details will be given later.
Written assignment
Students enrolled in MBV-INF4410 or MBV-INF9410, but not MBV-INF9410A, must complete a written assignment as part of the course requirements.
More details soon.
Bioinformatics mailing list for the Oslo region
The mailing list for computational biology and bioinformatics in the Oslo region is cbo-all@usit.uio.no. The list has approximately 330 members. The list is used to distribute news about seminars, positions, courses, meetings and other topics that might be of interest to students and researchers with an interest i computational life science i south-eastern Norway. If you want to recieve e-mails that are sent to the list, sign up here
https://sympa.uio.no/usit.uio.no/info/cbo-all
by following the link termed "Subscribe".