Difference between revisions of "INF-BIOX120 H13"

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== High Throughput Sequencing technologies and bioinformatics analysis  ==
 
== High Throughput Sequencing technologies and bioinformatics analysis  ==
  
This is the wiki for the fall 2013 edition of 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). Click [http://www.mn.uio.no/ifi/english/research/networks/clsi/bioinformatics_courses.html here] for other courses in Computational Life Science/Bioinformatics at UiO.
+
This is the wiki for the fall 2013 edition of the credited 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]&nbsp;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.&nbsp;''Participants not taking the course for credits ''should&nbsp;'''''register&nbsp;'''''<b>[http://collect.limequery.com/index.php/981717/lang-en '''here''']&nbsp;before August 13&nbsp;</b>and&nbsp;read this wiki.
 +
 
 +
Click [http://www.mn.uio.no/ifi/english/research/networks/clsi/bioinformatics_courses.html here] for other courses in Computational Life Science/Bioinformatics at UiO.  
  
 
The High Throughput Sequencing technologies and bioinformatics analysis&nbsp;course consists of two weeks of lectures and practicals, and a final take-home exam (one week), plus reading material  
 
The High Throughput Sequencing technologies and bioinformatics analysis&nbsp;course consists of two weeks of lectures and practicals, and a final take-home exam (one week), plus reading material  
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== Course description  ==
 
== 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. SUbjects are control of quantity and quality of data, analysis of small RNA-seq and mRNA-seq, ''de novo'' genome assembly, and variant calling.  
+
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 students should have a basic understanding of molecular biology,&nbsp;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.''  
+
All participants should have a basic understanding of molecular biology,&nbsp;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. Students without this knowledge need to take the '''introductory unix course''' on Tuesday September 3rd - details will be provided upon registration.<br>  
+
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.<br>  
  
 
== Fall 2013 schedule  ==
 
== Fall 2013 schedule  ==
  
To be announced. Monday - Friday from 9:00 to 17:00, some lectures, mostly hands-on exercises  
+
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 [[INF-BIOX120 H13 course material|here]].
  
 
<br>  
 
<br>  
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|-
 
|-
 
| Tuesday September 3rd  
 
| Tuesday September 3rd  
| Unix pre-course for people new to the unix command-line  
+
| [[Unix pre-course H13|Unix pre-course for people new to the unix command-line]]&nbsp;(teacher: KM)
| Unix pre-course for people new to the unix command-line
+
| [[Unix pre-course H13|Unix pre-course for people new to the unix command-line]]&nbsp;(KM)
 
|-
 
|-
 
|  
 
|  
 
|-
 
|-
 
| Monday September 16th  
 
| Monday September 16th  
| Introduction to High-throughput sequencing technologies and applications
 
 
|  
 
|  
File formats
+
[https://wiki.uio.no/projects/clsi/index.php/INF-BIOX120_H13_course_material Introduction to High-throughput sequencing technologies and applications] (LMZ)
  
Quality control of sequencing data  
+
|
 +
[[INF-BIOX120 H13 course material|File formats]] (DV)
 +
 
 +
[[INF-BIOX120 H13 course material|Quality control of sequencing data]] (LN)
  
 
|-
 
|-
 
| Tuesday September 17th  
 
| Tuesday September 17th  
| miRNA  
+
| [[INF-BIOX120 H13 course material|miRNA]] (MMW, DV)
| miRNA
+
| [[INF-BIOX120 H13 course material|miRNA]]&nbsp;(MMW, DV)<br>
 
|-
 
|-
 
| Wednesday September 18th  
 
| Wednesday September 18th  
| RNA-seq  
+
| [[INF-BIOX120 H13 course material|RNA-seq ]](LMZ, SL, JCB)
| RNA-seq
+
| [[INF-BIOX120 H13 course material|RNA-seq]] (LMZ, SL, JCB)
 
|-
 
|-
 
| Thursday September 19th  
 
| Thursday September 19th  
| RNA-seq  
+
| [[INF-BIOX120 H13 course material|RNA-seq]] (LMZ, SL, JCB)
| RNA-seq
+
| [[INF-BIOX120 H13 course material|RNA-seq]] (LMZ, SL, JCB)
 
|-
 
|-
 
| Friday September 20th  
 
| Friday September 20th  
| Variant calling  
+
| [https://wiki.uio.no/projects/clsi/index.php/INF-BIOX120_H13_course_material Variant calling] (TH)
| Variant calling
+
| [https://wiki.uio.no/projects/clsi/index.php/INF-BIOX120_H13_course_material Variant calling] (TH)
 
|-
 
|-
 
| &nbsp;  
 
| &nbsp;  
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|-
 
|-
 
| Monday September 23  
 
| Monday September 23  
| Variant calling  
+
| [https://wiki.uio.no/projects/clsi/index.php/INF-BIOX120_H13_course_material Variant calling] (TH)
| Variant calling
+
| [https://wiki.uio.no/projects/clsi/index.php/INF-BIOX120_H13_course_material Variant calling] (TH)
 
|-
 
|-
 
| Tuesday September 24  
 
| Tuesday September 24  
| de novo Assembly  
+
| [https://wiki.uio.no/projects/clsi/index.php/INF-BIOX120_H13_course_material de novo Assembly] (LN)
| de novo Assembly
+
| [https://wiki.uio.no/projects/clsi/index.php/INF-BIOX120_H13_course_material de novo Assembly] (LN)
 
|-
 
|-
 
| Wednesday September 25  
 
| Wednesday September 25  
| de novo Assembly  
+
| [https://wiki.uio.no/projects/clsi/index.php/INF-BIOX120_H13_course_material de novo Assembly] (LN)
| de novo Assembly
+
| [https://wiki.uio.no/projects/clsi/index.php/INF-BIOX120_H13_course_material de novo Assembly] (LN)
 
|-
 
|-
 
| Thursday September 26  
 
| Thursday September 26  
| Statistical genomics (Galaxy, Hyperbrowser)  
+
| [https://wiki.uio.no/projects/clsi/index.php/INF-BIOX120_H13_course_material Statistical genomics] (Galaxy, Hyperbrowser) (GKS, SG)  
| Statistical genomics (Galaxy, Hyperbrowser)
+
| [https://wiki.uio.no/projects/clsi/index.php/INF-BIOX120_H13_course_material Statistical genomics] (Galaxy, Hyperbrowser)(GKS, SG)
 
|-
 
|-
 
| Friday September 27  
 
| Friday September 27  
 
|  
 
|  
Wrap-up and conclusions  
+
Wrap-up and conclusions (all)
  
Handout of exam exercises  
+
Handout of exam exercises (all)
  
Course evaluation  
+
Course evaluation (all)
  
| Installation of programs on your own laptop
+
| Installation of programs on your own laptop (MMW, DV, KM)
 +
|-
 +
| &nbsp;
 +
|
 +
|
 +
|-
 +
| Monday October 21
 +
| Examination
 +
| Examination
 
|}
 
|}
  
== Contact information<br> ==
+
== Contact information<br> ==
  
Lex Nederbragt (Course coordinator) - e-mail: lex.nederbragt - at - ibv.uio.no
+
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
+
Karin Lagesen (Course co-coordinator) - e-mail: karin.lagesen - at - medisin.uio.no  
  
NN (Course administrator, registration) - e-mail: to be announced
+
Course administration/registration - e-mail: studieinfo@ifi.uio.no
  
 
== Teachers  ==
 
== Teachers  ==
  
Lex Nederbragt (Norwegian Sequencing Centre, Dept. of Biosciences/Dept. of Informatics)<br>Karin Lagesen (Norwegian Sequencing Centre, Oslo Univ. Hospital/Dept. of Informatics)<br>Daniel Vodák (Bioinformatics core facility, Dept. of Tumor Biology, Norwegian Radium Hospital, Oslo University Hospital)<br>Geir Kjetil Sandve (Dept. of Informatics)<br>Jan Christian Bryne (Northern Genomics AS)<br>Leonardo A. Meza-Zepeda (Genomics Core Facility, Dept. of Tumor Biology, Norwegian Radium Hospital, Oslo University Hospital)<br>Merete Molton Worren (Bioinformatics core facility, Dept. of Tumor Biology, Norwegian Radium Hospital, Oslo University Hospital)<br>Susanne Lorenz (Genomics Core Facility, Dept. of Tumor Biology, Norwegian Radium Hospital, Oslo University Hospital)<br>Sveinung Gundersen (Dept. of Tumor Biology, Norwegian Radium Hospital, Oslo University Hospital)<br>Timothy Hughes (Norwegian Sequencing Centre, Oslo Univ. Hospital)<br>  
+
Lex Nederbragt (LN, Norwegian Sequencing Centre, Dept. of Biosciences/Dept. of Informatics, University of Oslo)<br>Karin Lagesen (KL, Norwegian Sequencing Centre, Oslo Univ. Hospital/Dept. of Informatics)<br>Daniel Vodák (DV, Bioinformatics core facility, Dept. of Tumor Biology, Norwegian Radium Hospital, Oslo University Hospital)<br>Geir Kjetil Sandve (GKJ, Dept. of Informatics, University of Oslo)<br>Jan Christian Bryne (JCB, Northern Genomics AS)<br>Leonardo A. Meza-Zepeda (LMZ, Genomics Core Facility, Dept. of Tumor Biology, Norwegian Radium Hospital, Oslo University Hospital)<br>Merete Molton Worren (MMW, Bioinformatics core facility, Dept. of Tumor Biology, Norwegian Radium Hospital, Oslo University Hospital)<br>Susanne Lorenz (SL, Genomics Core Facility, Dept. of Tumor Biology, Norwegian Radium Hospital, Oslo University Hospital)<br>Sveinung Gundersen (SG, Dept. of Tumor Biology, Norwegian Radium Hospital, Oslo University Hospital)<br>Timothy Hughes (TH, Norwegian Sequencing Centre, Oslo Univ. Hospital)<br>Katerina Michalickova (KM, Research Computing Services Group, USIT, University of Oslo)<br>
  
 
== Computers/laptops, internet access, and UiO user account  ==
 
== 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).  
+
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).
 +
 
 +
[https://wiki.uio.no/projects/clsi/index.php/VM_use Connect to virtual machines]
 +
 
 +
== Curriculum and suggested reading<br>  ==
 +
 
 +
<span style="line-height: 1.5em;">
 +
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.
 +
</span>
 +
 
 +
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: [[INF-BIOX120 H13 curriculum|this page]].  
  
 
== Exam<br>  ==
 
== Exam<br>  ==
  
<span style="line-height: 1.5em;">The exam for this course will be a one week, individual, take-home exam.</span><span style="line-height: 1.5em;">&nbsp;Students will</span><span style="line-height: 1.5em;">&nbsp;present their work to two-three teachers, followed by some questioning (20-30 minutes in total).</span>  
+
<span style="line-height: 1.5em;">For students taking the course for 5 study points, the exam for this course will be an ''individual'', take-home exam '''on October 21st'''.</span><span style="line-height: 1.5em;">&nbsp;Students will</span><span style="line-height: 1.5em;">&nbsp;present their work to two-three teachers, followed by some questioning (20-30 minutes in total).</span>  
  
 
The exam will be handed out to all participants during the last course day.<br>  
 
The exam will be handed out to all participants during the last course day.<br>  
 
Watch this space for more detail.
 
  
 
== Bioinformatics mailing list for the Oslo region  ==
 
== Bioinformatics mailing list for the Oslo region  ==
Line 138: Line 160:
 
Trond Hasle Amundsen's "[http://www.uio.no/tjenester/it/maskin/linux/hjelp/tips/guide.html Local guide to Linux and Unix]"  
 
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<br>
+
Community resources:
 +
 
 +
*[http://seqanswers.com/wiki/SEQanswers seqwiki]:&nbsp;overview of HTS analysis software, providers, etc
 +
*the 'Next Generation Sequencing' [http://en.wikibooks.org/wiki/Next_Generation_Sequencing_(NGS) wikibook]
 +
*[http://seqanswers.com/ seqanswers]: helpful forums
 +
*[http://www.biostars.org/ biostars]: Q&amp;A site for general bioinformatics<br>
 +
 
 +
<br>
 +
 
 +
== Messages  ==
 +
 
 +
Follow [[INF BIOX120 H13 messages|this page]] for updates during and after the course.

Latest revision as of 09:03, 27 September 2013

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.

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. 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.



Morning

9:00 - 12:00

Afternoon

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

Introduction to High-throughput sequencing technologies and applications (LMZ)

File formats (DV)

Quality control of sequencing data (LN)

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

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)
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).

Connect to virtual machines

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.

Exam

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 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.