Difference between revisions of "INF-BIOX120 H13"

From projects/clsi
Jump to: navigation, search
(Teachers: Added / in Karins affiliations)
(Fall 2013 schedule)
Line 27: Line 27:
 
== Fall 2013 schedule  ==
 
== Fall 2013 schedule  ==
  
To be announced. Monday - Friday from 9:00 to 17:00, some lectures, mostly hands-on exercises<span style="font-size: 20px; line-height: 1.5em;" />
+
To be announced. Monday - Friday from 9:00 to 17:00, some lectures, mostly hands-on exercises
 +
 
 +
 
 +
 
 +
{| width="200" border="1" cellpadding="1" cellspacing="1"
 +
|-
 +
! scope="col" | <br>
 +
! scope="col" |
 +
Morning
 +
 
 +
9:00 - 12:00
 +
 
 +
! scope="col" |
 +
Afternoon
 +
 
 +
12:30 - 17:00
 +
 
 +
|-
 +
| Monday September 16th
 +
| Introduction to Hight-throughput sequencing technologies and applications
 +
|
 +
File formats
 +
 
 +
Quality control of sequencing data
 +
 
 +
|-
 +
| Tuesday September 17th
 +
|
 +
|
 +
|-
 +
| Wednesday September 18th
 +
|
 +
|
 +
|-
 +
| Thursday September 19th
 +
|
 +
|
 +
|-
 +
| Friday September 20th
 +
|
 +
|
 +
|-
 +
|
 +
|
 +
|
 +
|-
 +
|
 +
|
 +
|
 +
|-
 +
|
 +
|
 +
|
 +
|-
 +
|
 +
|
 +
|
 +
|}
  
 
== Contact information ==
 
== Contact information ==

Revision as of 08:42, 11 June 2013

High Throughput Sequencing technologies and bioinformatics analysis

This is the wiki for the fall 2013 edition of the courses INF-BIO9120 and INF-BIO5120 offered by the Department of Informatics and the Department of Biosciences at the University of Oslo (UiO).

The 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 [confirmation pending] 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 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. Control of quantity and quality of data, analysis of small RNA-seq and mRNA-seq, de novo genome assembly, and variant calling.

All students 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 Lex or Karin (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. Students without this knowledge need to take the introductory unix course on Monday September 2nd - details will be provided upon registration.

Fall 2013 schedule

To be announced. Monday - Friday from 9:00 to 17:00, some lectures, mostly hands-on exercises



Morning

9:00 - 12:00

Afternoon

12:30 - 17:00

Monday September 16th Introduction to Hight-throughput sequencing technologies and applications

File formats

Quality control of sequencing data

Tuesday September 17th
Wednesday September 18th
Thursday September 19th
Friday September 20th

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 NN (Course administrator, registration) - e-mail:  to be announced

Teachers

Lex Nederbragt (Norwegian Sequencing Centre, Dept. of Biosciences/Dept. of Informatics)
Karin Lagesen (Norwegian Sequencing Centre, Oslo Univ. Hospital/Dept. of Informatics)
Daniel Vodák (Bioinformatics core facility)
Geir Kjetil Sandve (Dept. of Informatics)
Jan Christian Bryne (Institute for Cancer Research, Oslo University Hospital)
Leonardo Meza-Zepeda (Genomics Core Facility , Oslo University Hospital)
Merete Molton Worren Bioinformatics core facility
Susanne Lorenz (Genomics Core Facility, Oslo University Hospital)
Sveinung Gundersen (Dept. of Informatics)
Timothy Hughes (Norwegian Sequencing Centre, Oslo Univ. Hospital)

Computers/laptops, internet access, and UiO user account

All students will be provided with a PC 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).

Exam

The exam for this course will be a one week, take-home exam.

The exam will be handed out to all participants at on the last course day.

Watch this space for more detail.

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

https://sympa.uio.no/usit.uio.no/info/cbo-all

by following the link termed "Subscribe".

Useful links

Trond Hasle Amundsen's Local guide to Linux and Unix

More to be added