Difference between revisions of "INF-BIOX121 H14"

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Monday - Thursday from 9:00 to 16:00 (teachers will stay until 17:00), some lectures, mostly hands-on exercises. All lecture material and most of the practical will be added [[INF-BIOX121 H14 course material|here]].
 
Monday - Thursday from 9:00 to 16:00 (teachers will stay until 17:00), some lectures, mostly hands-on exercises. All lecture material and most of the practical will be added [[INF-BIOX121 H14 course material|here]].
  
 
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NOTE The schedule below is tentative, and may be changed prior to the course.
  
 
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Revision as of 09:45, 11 September 2014

High Throughput Sequencing technologies and bioinformatics analysis

This is the wiki for the fall 2014 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 StudentWeb. NOTE registration is now closed and you should have been notified if you have been offered a place for credit..

Participants not taking the course for credits should have registered before August 28. NOTE registration is now closed. Feedback on participation will be given on or soon after September 5th. (Soon to be) active users of the organising platforms will be given priority.

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 2014 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 2014, i.e. 'October 6 - 24. Each day, four days a week (with most likely Fridays off), 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. 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 excempt for this course day.

Fall 2014 schedule

Monday - Thursday from 9:00 to 16:00 (teachers will stay until 17:00), 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.


Morning

9:00 - 12:00

Afternoon

13:00 - 17:00

Monday September 22 Unix pre-course for people new to the unix command-line Unix pre-course for people new to the unix command-line
 
Monday October 6
Introduction to High-throughput sequencing technologies and applications


File formats

Quality control of sequencing data
Tuesday October 7 miRNA miRNA
Wednesday October 8 miRNA miRNA
Thursday October 9 de novo Assembly de novo Assembly
Friday October 10 Day off Day off
 
Monday October 13
de novo Assembly 

de novo Assembly 

Tuesday October 14 How to become a efficient bioinformatician (lectures, discussions) How to become a efficient bioinformatician (lectures, discussions)
Wednesday October 15 RNA-seq RNA-seq
Thursday October 16

RNA-seq

RNA-seq
Friday October 17

Day off

Day off
 
Monday October 20 ChIP-seq ChIP-seq
Tuesday October 21 Variant calling Variant calling
Wednesday October 22 Variant calling Variant calling
Thursday October 23 Statistical genomics Statistical genomics, course wrap-up
Friday October 24 Day off Day off
 
Thursday November 6 Written exam (time and place to be determined)
Friday November 7 Oral exam (time and place to be determined) Oral exam (time and place 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 at medisin.uio.no ASAP after having been accepted for the course.

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.

NOTE: reading these papers are optional for non-credit students, however, having read them 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.

Exam

For students taking the course for 10 study points, the exam for this course will be

  • a written exam on the curriculum on November 6th, time and place to be announced
  • an individualhome exam combined with an oral examination of the home exam on November 7th. 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.

NOTE  80% attendance is required to take the final exam.

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.