Difference between revisions of "INF-BIOX120"

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== High Throughput Sequencing technologies and bioinformatics analysis ==
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== High Throughput Sequencing technologies and bioinformatics analysis ==
  
This is the wiki for the courses [http://www.uio.no/studier/emner/matnat/ifi/INF-BIO9120 INF-BIO9120] and [http://www.uio.no/studier/emner/matnat/ifi/INF-BIO5120 INF-BIO5120] offered by the Department of Informatics and the Department of Biosciences at the University of Oslo (UiO).
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The wiki for the courses [http://www.uio.no/studier/emner/matnat/ifi/INF-BIO9121 INF-BIO9121] and [http://www.uio.no/studier/emner/matnat/ifi/INF-BIO5121 INF-BIO5121] is now located [[INF-BIOX121|here]].
 
 
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 [http://www.uio.no/om/finn-fram/omrader/gaustad/ga06 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 (a day and a half, about two weeks before the course), to be announced later.
 
 
 
 
 
 
 
<span style="font-size: 26px; font-weight: bold; line-height: 1.5em;">Contacts</span>
 
 
 
Lex Nederbragt (Course coordinator) - e-mail: lex.nederbragt - at - ibv.uio.no
 
 
 
Karin Lagesen&nbsp;(Course co-coordinator) - e-mail: karin.lagesen - at - ibv.uio.no
 
 
 
NN (Course administrator, registration) - e-mail: &nbsp;to be announced<br>
 
 
 
=== 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)<br>
 
 
 
<span style="font-size: 26px; font-weight: bold; line-height: 1.5em;">Programme</span>
 
 
 
To be announced
 
 
 
=== Exam  ===
 
 
 
'''########'''
 
 
 
<span style="line-height: 1.5em;">The exam for this course will be a one week, take-home exam</span>
 
 
 
The exam will be handed out to all participants at&nbsp;on the last course day.<br>
 
 
 
=== 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 https://sympa.uio.no/usit.uio.no/info/cbo-all]  
 
 
 
by following the link termed "Subscribe".  
 
 
 
=== Useful links  ===
 
 
 
Trond Hasle Amundsen's [http://www.uio.no/tjenester/it/maskin/linux/hjelp/tips/guide.html Local guide to Linux and Unix]
 
 
 
More to be added
 

Latest revision as of 09:42, 19 June 2015

High Throughput Sequencing technologies and bioinformatics analysis

The wiki for the courses INF-BIO9121 and INF-BIO5121 is now located here.