- 1 High Throughput Sequencing technologies and bioinformatics analysis
- 2 Time and place
- 3 Course description
- 4 Course material
- 5 Fall 2015 schedule
- 6 Contact information
- 7 Teachers
- 8 Computers/laptops, internet access, and UiO user account
- 9 Curriculum and suggested reading
- 10 Exam
- 11 Bioinformatics mailing list for the Oslo region
- 12 Useful links
High Throughput Sequencing technologies and bioinformatics analysis
This is the wiki for the fall 2015 edition of the credited courses INF-BIO9121 and INF-BIO5121 offered by the Department of Informatics and the Department of Biosciences at the University of Oslo (UiO). Students taking the course for credit should register through UiO StudentWeb. Non UiO students are welcome and should check this website. NOTE registration is now closed. There is a maximum of 30 students (INF-BIO5121 and INF-BIO9121 altogether). NOTE the course is no longer offered to participants not interested in taking the course for credits.
The High Throughput Sequencing technologies and bioinformatics analysis course consists of three weeks, four days each week, of lectures and practicals, and a final take-home exam (one week), plus reading material.
Both INF-BIO5121 (M.Sc. level) and INF-BIO9121 (Ph.D. level) are 10 study point courses.
Please bookmark this page. All future changes or announcements for the 2015 course will be posted on this page.
Click here for other courses in Computational Life Science/Bioinformatics at UiO.
Time and place
The course will be offered in weeks 41, 42 and 43, autumn 2015, i.e. October 5 - 22. Each day, Monday - Thursday, will consist of lectures and (mainly) exercises/practical labs between 09:00 and 17:00. Lunch will usually be between 12:00 and 13:00. You will have to bring your own lunch or buy lunch in the local cantina. NOTE Fridays off!
Lecture room: All lectures/exercises will be given in lecture room Cobol (room 3452) 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.
This three week, intensive course will provide knowledge of high throughput sequencing technologies and hands-on experience with the analysis of data from various sequencing platforms and applications. Subjects are control of quantity and quality of data, analysis RNA-seq data, de novo genome assembly, variant calling and statistical genomics.
All participants should have a basic understanding of molecular biology, at least roughly corresponding to 5-10 university study points in molecular biology, biochemistry, or similar. If you are uncertain if your biology background is strong enough, please contact the course coordinators (see contact details below) at least three weeks before the start of the course.
No prior background in bioinformatics or computer science is required, however, we expect students to have a basic understanding of the unix shell. For this, we organise an introductory unix course about a week before the course starts, see the schedule below - details will be provided upon acceptance. Participants who are familiar with the shell can ask to be exempt for this course day.
All lecture slides and tutorials will be made available through http://inf-biox121.readthedocs.org/en/2015/.
Fall 2015 schedule
Monday - Thursday from 9:00 to 16:00 (teachers will stay until 17:00 if requested), some lectures, mostly hands-on exercises. All lecture material and most of the practical will be added here.
NOTE The schedule below is tentative, and may be changed prior to the course.
9:00 - 12:00
13:00 - 17:00
|Monday September 21||Unix pre-course for people new to the unix command-line (Lex)||Unix pre-course for people new to the unix command-line (Lex)|
|Monday October 5||Intro to High Throughput Sequencing and applications; Principles and problems of HTS data analysis||Experimental design, Quality control of sequencing reads|
|Tuesday October 6||Mapping and variant calling (Tim)||Mapping and variant calling (Tim)|
|Wednesday October 7||Mapping and variant calling (Tim)||Galaxy (Sveinung), Mapping and variant calling (Tim)|
|Thursday October 8||Mapping and variant calling (Tim)||Mapping and variant calling (Tim)|
|Friday October 9||Day off||Day off|
|Monday October 12||De novo genome assembly (Lex)||De novo genome assembly (Lex)|
|Tuesday October 13||De novo genome assembly (Lex)||De novo genome assembly (Lex)|
|Wednesday October 14||De novo genome assembly (Lex)||De novo genome assembly (Lex)|
|Thursday October 15||How to become an efficient bioinformatician||How to become an efficient bioinformatician|
|Friday October 16||Day off||Day off|
|Monday October 19||RNA seq: differential expression analysis (Monica)||RNA seq: differential expression analysis (Monica)|
|Tuesday October 20||RNA seq: differential expression analysis (Monica)||RNA seq: differential expression analysis (Monica)|
|Wednesday October 21||RNA seq: differential expression analysis (Monica)||RNA seq: differential expression analysis (Monica)|
|Thursday October 22||Statistical genomics (Hyperbrowser) (Boris/Sveinung)||Statistical genomics (Hyperbrowser) (Boris/Sveinung) and course wrap-up|
|Friday October 23||Day off||Day off|
|Wednesday/Thursday November 4/5||Oral exam (time and place to be determined)||Oral exam (time and place to be determined)|
|Friday November 7||Written exam (time and place to be determined)|
Lex Nederbragt (Course coordinator) - e-mail: lex.nederbragt - at - ibv.uio.no
Karin Lagesen (Course co-coordinator) - e-mail: karin.lagesen - at - medisin.uio.no
Course administration/registration - e-mail: email@example.com
Lex Nederbragt (LN, Norwegian Sequencing Centre, Dept. of Biosciences/Dept. of Informatics, University of Oslo)
Karin Lagesen (KL, Norwegian Sequencing Centre, Oslo Univ. Hospital/Dept. of Informatics)
Monica Solbakken (MS, Centre for Ecological and Evolutionary Synthesis, Dept. of Biosciences, University of Oslo)
Sveinung Gundersen (SG, ELIXIR.NO / The Genomic HyperBrowser team, Dept. of Informatics, University of Oslo)
Boris Simovski (BS, Research Group for Biomedical Informatics, Dept. of Informatics, University of Oslo)
Timothy Hughes (TH, Researcher, NORMENT , Oslo Univ. Hospital)
Computers/laptops, internet access, and UiO user account
All students will be provided with a Linux environment with all software pre-installed. An active UiO account is needed to complete the course.
Using the machine in the course room
- If you cannot log in to a machine, ask the teachers for a guest user account. Use this account only to log into the PC/MAC in the course room. NOTE that this account most likely only is valid for two week. NOTE also that locally saved data will be lost after the account stops being valid
- always use your UiO account to log into the course server (server whose name end with hpc.uio.no)
- on Windows, in the applications menu, look for the IFI-Linux.xw32 program and launch that; this should log you in to a linux machine
- on MAC, if you cannot log in to the course server, first type
ssh username@login, enter your password, try again
Downloading results obtained during the course
- all users: use WinSCP, Fetch, Filezilla, Cyberduck or another such program. Fill in the server details (cod3.hpc.uio.no) and your username and password. A window will open with files/folder on the local PC on the left, files/folder on the server on the right. Simply drag-and-drop files between the two.
- Linux and Mac users: you can also use the command line. Open a terminal window, navigate to the folder you want to data to be copied to and use this command:
rsync -av YOUR_USERNAME@servername.hpc.uio.no:/path/to/data/on/server/files .
NOTE the '.' at the end of the command, which stands for 'the current folder'
Curriculum and suggested reading
The curriculum consists of a set of scientific articles. The exam will contain questions on the material presented in these papers. Specific details of the curriculum, and a list of further suggested papers, can be found here.
The exam for this course will be:
- a written exam on the curriculum on November 6th, time and place to be announced
- an individual, home exam combined with an oral examination of the home exam on November 4th and 5th. Students will present their work to two-three teachers, followed by some questioning (20-30 minutes in total). This home exam will be handed out to all participants during the last course day.
NOTE Both exams have to be passed to earn 10 study credits.
Bioinformatics mailing list for the Oslo region
The mailing list for computational biology and bioinformatics in the Oslo region is firstname.lastname@example.org. The list has approximately 400 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 in computational life science in south-eastern Norway. If you want to receive e-mails that are sent to the list, sign up here by following the link termed "Subscribe".
Trond Hasle Amundsen's "Local guide to Linux and Unix"