- 1 High Throughput Sequencing technologies and bioinformatics analysis
- 2 Time and place
- 3 Course description
- 4 Fall 2013 schedule
- 5 Contact information
- 6 Teachers
- 7 Computers/laptops, internet access, and UiO user account
- 8 Curriculum and suggested reading
- 9 Exam
- 10 Bioinformatics mailing list for the Oslo region
- 11 Useful links
- 12 Messages
High Throughput Sequencing technologies and bioinformatics analysis
This is the wiki for the fall 2013 edition of the credited courses INF-BIO9120 and INF-BIO5120 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 StudentWeb. Participants not taking the course for credits should register here before August 13 and read this wiki.
Click here for other courses in Computational Life Science/Bioinformatics at UiO.
The High Throughput Sequencing technologies and bioinformatics analysis course consists of two weeks of lectures and practicals, and a final take-home exam (one week), plus reading material
Both INF-BIO5120 (M.Sc. level) and INF-BIO9120 (Ph.D. level) are 5 study point courses.
Please bookmark this page. All future changes or announcements for the 2013 course will be posted on this page.
Time and place
The course will be offered in weeks 38 and 39, autumn 2013, i.e. September 16 - September 27. Each day, Monday to Friday, 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.
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 two 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 of small RNA-seq and mRNA-seq, de novo genome assembly, and variant calling.
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. Participants without this knowledge need to take the introductory unix course on Tuesday September 3rd - details will be provided upon registration.
Fall 2013 schedule
Monday - Friday from 9:00 to 17:00, some lectures, mostly hands-on exercises. All lecture material and most of the practical will be added here.
9:00 - 12:00
13:00 - 17:00
|Tuesday September 3rd||Unix pre-course for people new to the unix command-line (teacher: KM)||Unix pre-course for people new to the unix command-line (KM)|
|Monday September 16th||
File formats (DV)
|Tuesday September 17th||miRNA (MMW, DV)|| miRNA (MMW, DV)|
|Wednesday September 18th||RNA-seq (LMZ, SL, JCB)||RNA-seq (LMZ, SL, JCB)|
|Thursday September 19th||RNA-seq (LMZ, SL, JCB)||RNA-seq (LMZ, SL, JCB)|
|Friday September 20th||Variant calling (TH)||Variant calling (TH)|
|Monday September 23||Variant calling (TH)||Variant calling (TH)|
|Tuesday September 24||de novo Assembly (LN)||de novo Assembly (LN)|
|Wednesday September 25||de novo Assembly (LN)||de novo Assembly (LN)|
|Thursday September 26||Statistical genomics (Galaxy, Hyperbrowser) (GKS, SG)||Statistical genomics (Galaxy, Hyperbrowser)(GKS, SG)|
|Friday September 27||
Wrap-up and conclusions (all)
Handout of exam exercises (all)
Course evaluation (all)
|Installation of programs on your own laptop (MMW, DV, KM)|
|Monday October 21||Examination||Examination|
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: firstname.lastname@example.org
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)
Daniel Vodák (DV, Bioinformatics core facility, Dept. of Tumor Biology, Norwegian Radium Hospital, Oslo University Hospital)
Geir Kjetil Sandve (GKJ, Dept. of Informatics, University of Oslo)
Jan Christian Bryne (JCB, Northern Genomics AS)
Leonardo A. Meza-Zepeda (LMZ, Genomics Core Facility, Dept. of Tumor Biology, Norwegian Radium Hospital, Oslo University Hospital)
Merete Molton Worren (MMW, Bioinformatics core facility, Dept. of Tumor Biology, Norwegian Radium Hospital, Oslo University Hospital)
Susanne Lorenz (SL, Genomics Core Facility, Dept. of Tumor Biology, Norwegian Radium Hospital, Oslo University Hospital)
Sveinung Gundersen (SG, Dept. of Tumor Biology, Norwegian Radium Hospital, Oslo University Hospital)
Timothy Hughes (TH, Norwegian Sequencing Centre, Oslo Univ. Hospital)
Katerina Michalickova (KM, Research Computing Services Group, USIT, University of Oslo)
Computers/laptops, internet access, and UiO user account
All students will be provided with a Linux virtual machine with all software pre-installed. We will set aside time to help students install software on their own laptop, feel free to bring your laptop at the appropriate time (see schedule).
Curriculum and suggested reading
The curriculum consists of papers adding up to 1 study point. The exam will contain questions from these papers. Reading these papers before coming to the course is highly recommended.
NOTE: reading these papers are optional for non-credit students, however, having read them before the course will make what we teach in the course a lot more understandable.
Specific details of the curriculum, and a list of further suggested papers, can be found here: this page.
For students taking the course for 5 study points, the exam for this course will be an individual, take-home exam on October 21st. Students will present their work to two-three teachers, followed by some questioning (20-30 minutes in total).
The exam will be handed out to all participants during the last course day.
Bioinformatics mailing list for the Oslo region
The mailing list for computational biology and bioinformatics in the Oslo region is email@example.com. 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 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"
- seqwiki: overview of HTS analysis software, providers, etc
- the 'Next Generation Sequencing' wikibook
- seqanswers: helpful forums
- biostars: Q&A site for general bioinformatics
Follow this page for updates during and after the course.