INF-BIOX120 H14

High Throughput Sequencing technologies and bioinformatics analysis

This is the wiki for the fall 2014 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  before August 28 (link will be added soon)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 three weeks, four days each week, 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 10 study point courses. NOTE at the time of writing this page still mentions 5 study points, this is incorrect.

Please bookmark this page. All future changes or announcements for the 2014 course will be posted on this page.

Time and place

The course will be offered in weeks 41, 42 and 43, autumn 2014, i.e. 'October 6 - 24. Each day, four days a week (Monday or Friday off, to be determined), 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.

Course description

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 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 2014 schedule

To be determined

Contact information

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: studieinfo@ifi.uio.no

Teachers

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)
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 environment with all software pre-installed. UiO accounts are needed to complete the course. If you don't have a UiO account, please contact karin.lagesen@medisin.uio.no ASAP after having been accepted for the course.

Curriculum and suggested reading

To be determined

Exam

For students taking the course for 10 study points, the exam for this course will be an individual, take-home exam a date TBD. 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 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 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".

Useful links

Trond Hasle Amundsen's "Local guide to Linux and Unix"

Community resources:

• seqwiki: overview of HTS analysis software, providers, etc
• the 'Next Generation Sequencing' wikibook
• seqanswers: helpful forums
• biostars: Q&A site for general bioinformatics
  

Messages

Follow this page for updates during and after the course.