https://wiki.uio.no/projects/clsi/api.php?action=feedcontributions&user=Katerim%40uio.no&feedformat=atomprojects/clsi - User contributions [en]2024-03-29T08:55:22ZUser contributionsMediaWiki 1.27.4https://wiki.uio.no/projects/clsi/index.php?title=INF-BIOX120_H13&diff=282INF-BIOX120 H132013-09-24T09:02:15Z<p>Katerim@uio.no: /* Teachers */</p>
<hr />
<div>== High Throughput Sequencing technologies and bioinformatics analysis ==<br />
<br />
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. <br />
<br />
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. <br />
<br />
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 <br />
<br />
Both INF-BIO5120 (M.Sc. level) and INF-BIO9120 (Ph.D. level) are 5 study point courses. <br />
<br />
<br> <br />
<br />
'''''Please bookmark this page. All future changes or announcements for the 2013 course will be posted&nbsp;on this page.''''' <br />
<br />
== '''Time and place''' ==<br />
<br />
'''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&nbsp;and 13:00. You will&nbsp;have to bring your own lunch or buy lunch in the local cantina.&nbsp; <br />
<br />
'''Lecture room:''' All lectures/exercises will be given in&nbsp;lecture room&nbsp;'''Cobol'''&nbsp;(room 3452) in&nbsp;Ole-Johan Dahls hus (IFI2). A map showing&nbsp;the location of the building is found [http://www.uio.no/om/finn-fram/omrader/gaustad/ga06 here]. The building is located&nbsp;next to&nbsp;the Forskningsparken metro and tram stations. <br />
<br />
== Course description ==<br />
<br />
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. <br />
<br />
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.'' <br />
<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> <br />
<br />
== Fall 2013 schedule ==<br />
<br />
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 />
<br> <br />
<br />
{| width="600" border="1" cellpadding="1" cellspacing="1"<br />
|-<br />
! scope="col" | <br> <br />
! scope="col" | <br />
Morning <br />
<br />
9:00 - 12:00 <br />
<br />
! scope="col" | <br />
Afternoon <br />
<br />
13:00 - 17:00 <br />
<br />
|-<br />
| Tuesday September 3rd <br />
| [[Unix pre-course H13|Unix pre-course for people new to the unix command-line]]&nbsp;(teacher: KM) <br />
| [[Unix pre-course H13|Unix pre-course for people new to the unix command-line]]&nbsp;(KM)<br />
|-<br />
| <br />
|-<br />
| Monday September 16th <br />
| <br />
[https://wiki.uio.no/projects/clsi/index.php/INF-BIOX120_H13_course_material Introduction to High-throughput sequencing technologies and applications] (LMZ) <br />
<br />
| <br />
[[INF-BIOX120 H13 course material|File formats]] (DV) <br />
<br />
[[INF-BIOX120 H13 course material|Quality control of sequencing data]] (LN) <br />
<br />
|-<br />
| Tuesday September 17th <br />
| [[INF-BIOX120 H13 course material|miRNA]] (MMW, DV) <br />
| [[INF-BIOX120 H13 course material|miRNA]]&nbsp;(MMW, DV)<br><br />
|-<br />
| Wednesday September 18th <br />
| [[INF-BIOX120 H13 course material|RNA-seq ]](LMZ, SL, JCB) <br />
| [[INF-BIOX120 H13 course material|RNA-seq]] (LMZ, SL, JCB)<br />
|-<br />
| Thursday September 19th <br />
| [[INF-BIOX120 H13 course material|RNA-seq]] (LMZ, SL, JCB) <br />
| [[INF-BIOX120 H13 course material|RNA-seq]] (LMZ, SL, JCB)<br />
|-<br />
| Friday September 20th <br />
| Variant calling (TH) <br />
| Variant calling (TH)<br />
|-<br />
| &nbsp; <br />
| <br />
| <br />
|-<br />
| Monday September 23 <br />
| Variant calling (TH) <br />
| Variant calling (TH)<br />
|-<br />
| Tuesday September 24 <br />
| [https://wiki.uio.no/projects/clsi/index.php/INF-BIOX120_H13_course_material de novo Assembly] (LN) <br />
| [https://wiki.uio.no/projects/clsi/index.php/INF-BIOX120_H13_course_material de novo Assembly] (LN) <br />
|-<br />
| Wednesday September 25 <br />
| [https://wiki.uio.no/projects/clsi/index.php/INF-BIOX120_H13_course_material de novo Assembly] (LN) <br />
| [https://wiki.uio.no/projects/clsi/index.php/INF-BIOX120_H13_course_material de novo Assembly] (LN) <br />
|-<br />
| Thursday September 26 <br />
| Statistical genomics (Galaxy, Hyperbrowser) (GKS, SG) <br />
| Statistical genomics (Galaxy, Hyperbrowser)(GKS, SG)<br />
|-<br />
| Friday September 27 <br />
| <br />
Wrap-up and conclusions (all) <br />
<br />
Handout of exam exercises (all) <br />
<br />
Course evaluation (all) <br />
<br />
| Installation of programs on your own laptop (MMW, DV, KM)<br />
|-<br />
| &nbsp; <br />
| <br />
| <br />
|-<br />
| Monday October 21 <br />
| Examination <br />
| Examination<br />
|}<br />
<br />
== Contact information<br> ==<br />
<br />
Lex Nederbragt (Course coordinator) - e-mail: lex.nederbragt - at - ibv.uio.no <br />
<br />
Karin Lagesen (Course co-coordinator) - e-mail: karin.lagesen - at - medisin.uio.no <br />
<br />
Course administration/registration - e-mail: studieinfo@ifi.uio.no <br />
<br />
== Teachers ==<br />
<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><br />
<br />
== Computers/laptops, internet access, and UiO user account ==<br />
<br />
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). <br />
<br />
[https://wiki.uio.no/projects/clsi/index.php/VM_use Connect to virtual machines] <br />
<br />
== Curriculum and suggested reading<br> ==<br />
<br />
<span style="line-height: 1.5em;"> <br />
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.<br />
</span> <br />
<br />
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. <br />
<br />
Specific details of the curriculum, and a list of further suggested papers, can be found here: [[INF-BIOX120 H13 curriculum|this page]]. <br />
<br />
== Exam<br> ==<br />
<br />
<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> <br />
<br />
The exam will be handed out to all participants during the last course day.<br> <br />
<br />
== Bioinformatics mailing list for the Oslo region ==<br />
<br />
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 [https://sympa.uio.no/usit.uio.no/info/cbo-all here]&nbsp;by following the link termed "Subscribe". <br />
<br />
== Useful links ==<br />
<br />
Trond Hasle Amundsen's "[http://www.uio.no/tjenester/it/maskin/linux/hjelp/tips/guide.html Local guide to Linux and Unix]" <br />
<br />
Community resources: <br />
<br />
*[http://seqanswers.com/wiki/SEQanswers seqwiki]:&nbsp;overview of HTS analysis software, providers, etc <br />
*the 'Next Generation Sequencing' [http://en.wikibooks.org/wiki/Next_Generation_Sequencing_(NGS) wikibook] <br />
*[http://seqanswers.com/ seqanswers]: helpful forums <br />
*[http://www.biostars.org/ biostars]: Q&amp;A site for general bioinformatics<br><br />
<br />
<br> <br />
<br />
== Messages ==<br />
<br />
Follow [[INF BIOX120 H13 messages|this page]] for updates during and after the course.</div>Katerim@uio.nohttps://wiki.uio.no/projects/clsi/index.php?title=VM_use&diff=253VM use2013-09-18T09:14:42Z<p>Katerim@uio.no: /* Connecting to virtual machines using a remote desktop */</p>
<hr />
<div>=VM number=<br />
Each course participant will work on a virtual machine (VM) that has been taylored for the course purpose.<br />
<br />
The virtual machines are named from hts01.uio.no to hts32.uio.no. Each student was assigned a virtual machine number at the course. This number is used instead of "XX" in the machine address below.<br />
<br />
UiO username can be used to log into the VMs. External course participants use a guest account. <br />
<br />
<br />
=Connecting to virtual machines using a remote desktop=<br />
During the course, the preferred way to connect to the VM is via a remote desktop. This allows full use of various graphical programs on the VM.<br />
<br />
[https://www.uio.no/english/services/it/network/home-and-away/rdp/ Read more about Remote Desktop]<br />
<br />
==Login to machines at Cobol==<br />
There is a mix of Linux, Windows and Mac computers in Cobol. Use your uio username to log into Windows and Macs. Linux machines require use of a guest username (their use is limited only to IFI students and employees).<br />
<br />
<br />
==Using temote desktop on Linux==<br />
Open a terminal and type "xfreerdp -k no htsXX.uio.no" (replace the "XX" with your VM number).<br />
<br />
<br />
You will get prompted for username and password. Fill them in and press OK.<br />
<br />
[[File: image002.jpg]]<br />
<br />
<br />
==Using remote desktop on Windows==<br />
Press the start button and select "Remote Desktop Connection" application.<br />
<br />
Type in the VM name and press "Connect". <br />
<br />
<br />
[[File: image004.jpg]]<br />
<br />
The next screen is the same as the remote login screen in the Linux section above.<br />
<br />
<br />
==Using remote desktop on a Mac==<br />
Press Applications icon in the task bar. Find "CoRD" application and fill in the VM name in the dialog box. Proceed the same as in the Linux section.<br />
<br />
=Using virtual machines via ssh=<br />
<br />
If there is no need for a graphical interface, you can use a ssh connection to the VM. The advantage is that is requires less resources and configuration on the VM side.<br />
<br />
<br />
==VM login and password==<br />
Use your UiO credentials to log into the VM. If you do not have UiO login name, use the guest account that you have been given at the course.<br />
<br />
==Log in==<br />
<br />
===Windows===<br />
Open 'PuTTy'. Fill 'htsxx.uio.no' in the host name dialog box. Click "Open".<br />
<br />
[[File:putty.jpg]]<br />
<br />
<br />
===Mac===<br />
Use 'Terminal'. Type:<br />
<br />
<pre>ssh htsxx.uio.no</pre><br />
<br />
<br />
===Linux===<br />
Open a terminal. Type: <br />
<br />
<pre>ssh htsxx.uio.no</pre> <br />
<br><br></div>Katerim@uio.nohttps://wiki.uio.no/projects/clsi/index.php?title=VM_use&diff=252VM use2013-09-18T09:14:30Z<p>Katerim@uio.no: /* Connecting to virtual machines using a remote desktop */</p>
<hr />
<div>=VM number=<br />
Each course participant will work on a virtual machine (VM) that has been taylored for the course purpose.<br />
<br />
The virtual machines are named from hts01.uio.no to hts32.uio.no. Each student was assigned a virtual machine number at the course. This number is used instead of "XX" in the machine address below.<br />
<br />
UiO username can be used to log into the VMs. External course participants use a guest account. <br />
<br />
<br />
=Connecting to virtual machines using a remote desktop=<br />
During the course, the preferred way to connect to the VM is via a remote desktop. This allows full use of various graphical programs on the VM.<br />
<br />
[https://www.uio.no/english/services/it/network/home-and-away/rdp/ | Read more about Remote Desktop]<br />
<br />
==Login to machines at Cobol==<br />
There is a mix of Linux, Windows and Mac computers in Cobol. Use your uio username to log into Windows and Macs. Linux machines require use of a guest username (their use is limited only to IFI students and employees).<br />
<br />
<br />
==Using temote desktop on Linux==<br />
Open a terminal and type "xfreerdp -k no htsXX.uio.no" (replace the "XX" with your VM number).<br />
<br />
<br />
You will get prompted for username and password. Fill them in and press OK.<br />
<br />
[[File: image002.jpg]]<br />
<br />
<br />
==Using remote desktop on Windows==<br />
Press the start button and select "Remote Desktop Connection" application.<br />
<br />
Type in the VM name and press "Connect". <br />
<br />
<br />
[[File: image004.jpg]]<br />
<br />
The next screen is the same as the remote login screen in the Linux section above.<br />
<br />
<br />
==Using remote desktop on a Mac==<br />
Press Applications icon in the task bar. Find "CoRD" application and fill in the VM name in the dialog box. Proceed the same as in the Linux section.<br />
<br />
=Using virtual machines via ssh=<br />
<br />
If there is no need for a graphical interface, you can use a ssh connection to the VM. The advantage is that is requires less resources and configuration on the VM side.<br />
<br />
<br />
==VM login and password==<br />
Use your UiO credentials to log into the VM. If you do not have UiO login name, use the guest account that you have been given at the course.<br />
<br />
==Log in==<br />
<br />
===Windows===<br />
Open 'PuTTy'. Fill 'htsxx.uio.no' in the host name dialog box. Click "Open".<br />
<br />
[[File:putty.jpg]]<br />
<br />
<br />
===Mac===<br />
Use 'Terminal'. Type:<br />
<br />
<pre>ssh htsxx.uio.no</pre><br />
<br />
<br />
===Linux===<br />
Open a terminal. Type: <br />
<br />
<pre>ssh htsxx.uio.no</pre> <br />
<br><br></div>Katerim@uio.nohttps://wiki.uio.no/projects/clsi/index.php?title=VM_use&diff=251VM use2013-09-18T09:14:09Z<p>Katerim@uio.no: /* Connecting to virtual machines using a remote desktop */</p>
<hr />
<div>=VM number=<br />
Each course participant will work on a virtual machine (VM) that has been taylored for the course purpose.<br />
<br />
The virtual machines are named from hts01.uio.no to hts32.uio.no. Each student was assigned a virtual machine number at the course. This number is used instead of "XX" in the machine address below.<br />
<br />
UiO username can be used to log into the VMs. External course participants use a guest account. <br />
<br />
<br />
=Connecting to virtual machines using a remote desktop=<br />
During the course, the preferred way to connect to the VM is via a remote desktop. This allows full use of various graphical programs on the VM.<br />
<br />
[https://www.uio.no/english/services/it/network/home-and-away/rdp/| Read more about Remote Desktop]<br />
<br />
==Login to machines at Cobol==<br />
There is a mix of Linux, Windows and Mac computers in Cobol. Use your uio username to log into Windows and Macs. Linux machines require use of a guest username (their use is limited only to IFI students and employees).<br />
<br />
<br />
==Using temote desktop on Linux==<br />
Open a terminal and type "xfreerdp -k no htsXX.uio.no" (replace the "XX" with your VM number).<br />
<br />
<br />
You will get prompted for username and password. Fill them in and press OK.<br />
<br />
[[File: image002.jpg]]<br />
<br />
<br />
==Using remote desktop on Windows==<br />
Press the start button and select "Remote Desktop Connection" application.<br />
<br />
Type in the VM name and press "Connect". <br />
<br />
<br />
[[File: image004.jpg]]<br />
<br />
The next screen is the same as the remote login screen in the Linux section above.<br />
<br />
<br />
==Using remote desktop on a Mac==<br />
Press Applications icon in the task bar. Find "CoRD" application and fill in the VM name in the dialog box. Proceed the same as in the Linux section.<br />
<br />
=Using virtual machines via ssh=<br />
<br />
If there is no need for a graphical interface, you can use a ssh connection to the VM. The advantage is that is requires less resources and configuration on the VM side.<br />
<br />
<br />
==VM login and password==<br />
Use your UiO credentials to log into the VM. If you do not have UiO login name, use the guest account that you have been given at the course.<br />
<br />
==Log in==<br />
<br />
===Windows===<br />
Open 'PuTTy'. Fill 'htsxx.uio.no' in the host name dialog box. Click "Open".<br />
<br />
[[File:putty.jpg]]<br />
<br />
<br />
===Mac===<br />
Use 'Terminal'. Type:<br />
<br />
<pre>ssh htsxx.uio.no</pre><br />
<br />
<br />
===Linux===<br />
Open a terminal. Type: <br />
<br />
<pre>ssh htsxx.uio.no</pre> <br />
<br><br></div>Katerim@uio.nohttps://wiki.uio.no/projects/clsi/index.php?title=VM_use&diff=250VM use2013-09-18T09:13:38Z<p>Katerim@uio.no: /* Connecting to virtual machines using a remote desktop */</p>
<hr />
<div>=VM number=<br />
Each course participant will work on a virtual machine (VM) that has been taylored for the course purpose.<br />
<br />
The virtual machines are named from hts01.uio.no to hts32.uio.no. Each student was assigned a virtual machine number at the course. This number is used instead of "XX" in the machine address below.<br />
<br />
UiO username can be used to log into the VMs. External course participants use a guest account. <br />
<br />
<br />
=Connecting to virtual machines using a remote desktop=<br />
During the course, the preferred way to connect to the VM is via a remote desktop. This allows full use of various graphical programs on the VM.<br />
<br />
[http://www.uio.no/english/services/it/network/home-and-away/rdp/| Read more about Remote Desktop]<br />
<br />
==Login to machines at Cobol==<br />
There is a mix of Linux, Windows and Mac computers in Cobol. Use your uio username to log into Windows and Macs. Linux machines require use of a guest username (their use is limited only to IFI students and employees).<br />
<br />
<br />
==Using temote desktop on Linux==<br />
Open a terminal and type "xfreerdp -k no htsXX.uio.no" (replace the "XX" with your VM number).<br />
<br />
<br />
You will get prompted for username and password. Fill them in and press OK.<br />
<br />
[[File: image002.jpg]]<br />
<br />
<br />
==Using remote desktop on Windows==<br />
Press the start button and select "Remote Desktop Connection" application.<br />
<br />
Type in the VM name and press "Connect". <br />
<br />
<br />
[[File: image004.jpg]]<br />
<br />
The next screen is the same as the remote login screen in the Linux section above.<br />
<br />
<br />
==Using remote desktop on a Mac==<br />
Press Applications icon in the task bar. Find "CoRD" application and fill in the VM name in the dialog box. Proceed the same as in the Linux section.<br />
<br />
=Using virtual machines via ssh=<br />
<br />
If there is no need for a graphical interface, you can use a ssh connection to the VM. The advantage is that is requires less resources and configuration on the VM side.<br />
<br />
<br />
==VM login and password==<br />
Use your UiO credentials to log into the VM. If you do not have UiO login name, use the guest account that you have been given at the course.<br />
<br />
==Log in==<br />
<br />
===Windows===<br />
Open 'PuTTy'. Fill 'htsxx.uio.no' in the host name dialog box. Click "Open".<br />
<br />
[[File:putty.jpg]]<br />
<br />
<br />
===Mac===<br />
Use 'Terminal'. Type:<br />
<br />
<pre>ssh htsxx.uio.no</pre><br />
<br />
<br />
===Linux===<br />
Open a terminal. Type: <br />
<br />
<pre>ssh htsxx.uio.no</pre> <br />
<br><br></div>Katerim@uio.nohttps://wiki.uio.no/projects/clsi/index.php?title=VM_use&diff=249VM use2013-09-18T09:10:26Z<p>Katerim@uio.no: </p>
<hr />
<div>=VM number=<br />
Each course participant will work on a virtual machine (VM) that has been taylored for the course purpose.<br />
<br />
The virtual machines are named from hts01.uio.no to hts32.uio.no. Each student was assigned a virtual machine number at the course. This number is used instead of "XX" in the machine address below.<br />
<br />
UiO username can be used to log into the VMs. External course participants use a guest account. <br />
<br />
<br />
=Connecting to virtual machines using a remote desktop=<br />
During the course, the preferred way to connect to the VM is via a remote desktop. This allows full use of various graphical programs on the VM.<br />
<br />
<br />
==Login to machines at Cobol==<br />
There is a mix of Linux, Windows and Mac computers in Cobol. Use your uio username to log into Windows and Macs. Linux machines require use of a guest username (their use is limited only to IFI students and employees).<br />
<br />
<br />
==Using temote desktop on Linux==<br />
Open a terminal and type "xfreerdp -k no htsXX.uio.no" (replace the "XX" with your VM number).<br />
<br />
<br />
You will get prompted for username and password. Fill them in and press OK.<br />
<br />
[[File: image002.jpg]]<br />
<br />
<br />
==Using remote desktop on Windows==<br />
Press the start button and select "Remote Desktop Connection" application.<br />
<br />
Type in the VM name and press "Connect". <br />
<br />
<br />
[[File: image004.jpg]]<br />
<br />
The next screen is the same as the remote login screen in the Linux section above.<br />
<br />
<br />
==Using remote desktop on a Mac==<br />
Press Applications icon in the task bar. Find "CoRD" application and fill in the VM name in the dialog box. Proceed the same as in the Linux section.<br />
<br />
<br />
<br />
<br />
<br />
=Using virtual machines via ssh=<br />
<br />
If there is no need for a graphical interface, you can use a ssh connection to the VM. The advantage is that is requires less resources and configuration on the VM side.<br />
<br />
<br />
==VM login and password==<br />
Use your UiO credentials to log into the VM. If you do not have UiO login name, use the guest account that you have been given at the course.<br />
<br />
==Log in==<br />
<br />
===Windows===<br />
Open 'PuTTy'. Fill 'htsxx.uio.no' in the host name dialog box. Click "Open".<br />
<br />
[[File:putty.jpg]]<br />
<br />
<br />
===Mac===<br />
Use 'Terminal'. Type:<br />
<br />
<pre>ssh htsxx.uio.no</pre><br />
<br />
<br />
===Linux===<br />
Open a terminal. Type: <br />
<br />
<pre>ssh htsxx.uio.no</pre> <br />
<br><br></div>Katerim@uio.nohttps://wiki.uio.no/projects/clsi/index.php?title=VM_use&diff=248VM use2013-09-18T09:07:24Z<p>Katerim@uio.no: /* Using virtual machines via ssh */</p>
<hr />
<div>=VM number=<br />
Each course participant will work on a virtual machine (VM) that has been taylored for the course purpose.<br />
<br />
The virtual machines are named from hts01.uio.no to hts32.uio.no. Each student was assigned a virtual machine number at the course. This number is used instead of "XX" in the machine address below.<br />
<br />
UiO username can be used to log into the VMs. External course participants use a guest account. <br />
<br />
<br />
=Connecting to virtual machines using a remote desktop=<br />
During the course, the preferred way to connect to the VM is via a remote desktop.<br />
<br />
==Log into machines at Cobol==<br />
There is a mix of Linux, Windows and Mac computers in Cobol. Use your uio username to log into Windows and Macs. Linux machines require use of a guest username since their use is limited only to IFI students and employees.<br />
<br />
==Using temote desktop on Linux==<br />
Open a terminal and type "xfreerdp -k no htsXX.uio.no" (replace the "XX" with your VM number).<br />
<br />
<br />
You will get prompted for username and password. Fill them in and press OK.<br />
<br />
[[File: image002.jpg]]<br />
<br />
==Using remote desktop on Windows==<br />
Press the start button and select "Remote Desktop Connection" application.<br />
<br />
Type in the VM name and press "Connect". <br />
<br />
<br />
[[File: image004.jpg]]<br />
<br />
The next screen is the same as the remote login screen in the Linux section above.<br />
<br />
==Using remote desktop on a Mac==<br />
Press Applications icon in the task bar. Find "CoRD" application and fill in the VM name in the dialog box. Proceed the same as in the Linux section.<br />
<br />
<br />
=Using virtual machines via ssh=<br />
<br />
If there is no need for a graphical interface, you can use a ssh connection to the VM. The advantage is that is requires less resources and configuration on the VM side.<br />
<br />
==VM login and password==<br />
Use your UiO credentials to log into the VM. If you do not have UiO login name, use the guest account that you have been given at the course.<br />
<br />
==Log in==<br />
<br />
<br />
===Windows===<br />
Open 'PuTTy'. Fill 'htsxx.uio.no' in the host name dialog box. Click "Open".<br />
<br />
[[File:putty.jpg]]<br />
<br />
===Mac===<br />
Use 'Terminal'. Type:<br />
<br />
<pre>ssh htsxx.uio.no</pre><br />
<br />
===Linux===<br />
Open a terminal. Type: <br />
<br />
<pre>ssh htsxx.uio.no</pre> <br />
<br><br></div>Katerim@uio.nohttps://wiki.uio.no/projects/clsi/index.php?title=File:Image004.jpg&diff=247File:Image004.jpg2013-09-18T09:06:51Z<p>Katerim@uio.no: </p>
<hr />
<div></div>Katerim@uio.nohttps://wiki.uio.no/projects/clsi/index.php?title=File:Image002.jpg&diff=246File:Image002.jpg2013-09-18T09:06:35Z<p>Katerim@uio.no: </p>
<hr />
<div></div>Katerim@uio.nohttps://wiki.uio.no/projects/clsi/index.php?title=VM_use&diff=245VM use2013-09-18T09:06:04Z<p>Katerim@uio.no: </p>
<hr />
<div>=VM number=<br />
Each course participant will work on a virtual machine (VM) that has been taylored for the course purpose.<br />
<br />
The virtual machines are named from hts01.uio.no to hts32.uio.no. Each student was assigned a virtual machine number at the course. This number is used instead of "XX" in the machine address below.<br />
<br />
UiO username can be used to log into the VMs. External course participants use a guest account. <br />
<br />
<br />
=Connecting to virtual machines using a remote desktop=<br />
During the course, the preferred way to connect to the VM is via a remote desktop.<br />
<br />
==Log into machines at Cobol==<br />
There is a mix of Linux, Windows and Mac computers in Cobol. Use your uio username to log into Windows and Macs. Linux machines require use of a guest username since their use is limited only to IFI students and employees.<br />
<br />
==Using temote desktop on Linux==<br />
Open a terminal and type "xfreerdp -k no htsXX.uio.no" (replace the "XX" with your VM number).<br />
<br />
<br />
You will get prompted for username and password. Fill them in and press OK.<br />
<br />
[[File: image002.jpg]]<br />
<br />
==Using remote desktop on Windows==<br />
Press the start button and select "Remote Desktop Connection" application.<br />
<br />
Type in the VM name and press "Connect". <br />
<br />
<br />
[[File: image004.jpg]]<br />
<br />
The next screen is the same as the remote login screen in the Linux section above.<br />
<br />
==Using remote desktop on a Mac==<br />
Press Applications icon in the task bar. Find "CoRD" application and fill in the VM name in the dialog box. Proceed the same as in the Linux section.<br />
<br />
<br />
=Using virtual machines via ssh=<br />
<br />
If there is no need for a graphical interface, you can use an ssh connection to the VM. The advantage is that is requires less resources and configuration on the VM side.<br />
<br />
==VM login and password==<br />
Use your UiO credentials to log into the VM. If you do not have UiO login name, use the guest account that you have been given at the course.<br />
<br />
==Log in==<br />
<br />
<br />
===Windows===<br />
Open 'PuTTy'. Fill 'htsxx.uio.no' in the host name dialog box. Click "Open".<br />
<br />
[[File:putty.jpg]]<br />
<br />
===Mac===<br />
Use 'Terminal'. Type:<br />
<br />
<pre>ssh htsxx.uio.no</pre><br />
<br />
===Linux===<br />
Open a terminal. Type: <br />
<br />
<pre>ssh htsxx.uio.no</pre> <br />
<br><br></div>Katerim@uio.nohttps://wiki.uio.no/projects/clsi/index.php?title=INF-BIOX120_H13&diff=225INF-BIOX120 H132013-09-16T14:07:34Z<p>Katerim@uio.no: /* Fall 2013 schedule */</p>
<hr />
<div>== High Throughput Sequencing technologies and bioinformatics analysis ==<br />
<br />
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. <br />
<br />
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. <br />
<br />
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 <br />
<br />
Both INF-BIO5120 (M.Sc. level) and INF-BIO9120 (Ph.D. level) are 5 study point courses. <br />
<br />
<br> <br />
<br />
'''''Please bookmark this page. All future changes or announcements for the 2013 course will be posted&nbsp;on this page.''''' <br />
<br />
== '''Time and place''' ==<br />
<br />
'''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&nbsp;and 13:00. You will&nbsp;have to bring your own lunch or buy lunch in the local cantina.&nbsp; <br />
<br />
'''Lecture room:''' All lectures/exercises will be given in&nbsp;lecture room&nbsp;'''Cobol'''&nbsp;(room 3452) in&nbsp;Ole-Johan Dahls hus (IFI2). A map showing&nbsp;the location of the building is found [http://www.uio.no/om/finn-fram/omrader/gaustad/ga06 here]. The building is located&nbsp;next to&nbsp;the Forskningsparken metro and tram stations. <br />
<br />
== Course description ==<br />
<br />
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. <br />
<br />
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.'' <br />
<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> <br />
<br />
== Fall 2013 schedule ==<br />
<br />
To be announced. Monday - Friday from 9:00 to 17:00, some lectures, mostly hands-on exercises <br />
<br />
<br> <br />
<br />
{| width="600" border="1" cellpadding="1" cellspacing="1"<br />
|-<br />
! scope="col" | <br> <br />
! scope="col" | <br />
Morning <br />
<br />
9:00 - 12:00 <br />
<br />
! scope="col" | <br />
Afternoon <br />
<br />
13:00 - 17:00 <br />
<br />
|-<br />
| Tuesday September 3rd <br />
| [[Unix pre-course H13|Unix pre-course for people new to the unix command-line]]&nbsp;(teacher: KM) <br />
| [[Unix pre-course H13|Unix pre-course for people new to the unix command-line]]&nbsp;(KM)<br />
|-<br />
| <br />
|-<br />
| Monday September 16th <br />
| <br />
Introduction to High-throughput sequencing technologies and applications (LMZ) <br />
| <br />
File formats (DV) <br />
<br />
Quality control of sequencing data (LN) <br />
<br />
|-<br />
| Tuesday September 17th <br />
| miRNA (MMW, DV) <br />
| miRNA&nbsp;(MMW, DV)<br><br />
|-<br />
| Wednesday September 18th <br />
| RNA-seq (LMZ, SL, JCB) <br />
| RNA-seq (LMZ, SL, JCB)<br />
|-<br />
| Thursday September 19th <br />
| RNA-seq (LMZ, SL, JCB) <br />
| RNA-seq (LMZ, SL, JCB)<br />
|-<br />
| Friday September 20th <br />
| Variant calling (TH) <br />
| Variant calling (TH)<br />
|-<br />
| &nbsp; <br />
| <br />
| <br />
|-<br />
| Monday September 23 <br />
| Variant calling (TH) <br />
| Variant calling (TH)<br />
|-<br />
| Tuesday September 24 <br />
| de novo Assembly (LN) <br />
| de novo Assembly (LN)<br />
|-<br />
| Wednesday September 25 <br />
| de novo Assembly (LN) <br />
| de novo Assembly (LN)<br />
|-<br />
| Thursday September 26 <br />
| Statistical genomics (Galaxy, Hyperbrowser) (GKS, SG) <br />
| Statistical genomics (Galaxy, Hyperbrowser)(GKS, SG)<br />
|-<br />
| Friday September 27 <br />
| <br />
Wrap-up and conclusions (all) <br />
<br />
Handout of exam exercises (all) <br />
<br />
Course evaluation (all) <br />
<br />
| Installation of programs on your own laptop (MMW, DV, KM)<br />
|-<br />
| &nbsp; <br />
| <br />
| <br />
|-<br />
| Monday October 21 <br />
| Examination <br />
| Examination<br />
|}<br />
<br />
== Contact information<br> ==<br />
<br />
Lex Nederbragt (Course coordinator) - e-mail: lex.nederbragt - at - ibv.uio.no <br />
<br />
Karin Lagesen (Course co-coordinator) - e-mail: karin.lagesen - at - medisin.uio.no <br />
<br />
Course administration/registration - e-mail: studieinfo@ifi.uio.no <br />
<br />
== Teachers ==<br />
<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 Support Services Group, USIT, University of Oslo)<br> <br />
<br />
== Computers/laptops, internet access, and UiO user account ==<br />
<br />
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). <br />
<br />
[https://wiki.uio.no/projects/clsi/index.php/VM_use Connect to virtual machines] <br />
<br />
== Curriculum and suggested reading<br> ==<br />
<br />
<span style="line-height: 1.5em;"> <br />
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.<br />
</span> <br />
<br />
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. <br />
<br />
Specific details of the curriculum, and a list of further suggested papers, can be found here: [[INF-BIOX120 H13 curriculum|this page]]. <br />
<br />
== Exam<br> ==<br />
<br />
<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> <br />
<br />
The exam will be handed out to all participants during the last course day.<br> <br />
<br />
== Bioinformatics mailing list for the Oslo region ==<br />
<br />
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 [https://sympa.uio.no/usit.uio.no/info/cbo-all here]&nbsp;by following the link termed "Subscribe". <br />
<br />
== Useful links ==<br />
<br />
Trond Hasle Amundsen's "[http://www.uio.no/tjenester/it/maskin/linux/hjelp/tips/guide.html Local guide to Linux and Unix]" <br />
<br />
Community resources: <br />
<br />
*[http://seqanswers.com/wiki/SEQanswers seqwiki]:&nbsp;overview of HTS analysis software, providers, etc <br />
*the 'Next Generation Sequencing' [http://en.wikibooks.org/wiki/Next_Generation_Sequencing_(NGS) wikibook] <br />
*[http://seqanswers.com/ seqanswers]: helpful forums <br />
*[http://www.biostars.org/ biostars]: Q&amp;A site for general bioinformatics<br><br />
<br />
<br> <br />
<br />
== Messages ==<br />
<br />
Follow [[INF BIOX120 H13 messages|this page]] for updates during and after the course.</div>Katerim@uio.nohttps://wiki.uio.no/projects/clsi/index.php?title=INF-BIOX120_H13&diff=224INF-BIOX120 H132013-09-16T13:51:09Z<p>Katerim@uio.no: /* Fall 2013 schedule */</p>
<hr />
<div>== High Throughput Sequencing technologies and bioinformatics analysis ==<br />
<br />
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. <br />
<br />
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. <br />
<br />
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 <br />
<br />
Both INF-BIO5120 (M.Sc. level) and INF-BIO9120 (Ph.D. level) are 5 study point courses. <br />
<br />
<br> <br />
<br />
'''''Please bookmark this page. All future changes or announcements for the 2013 course will be posted&nbsp;on this page.''''' <br />
<br />
== '''Time and place''' ==<br />
<br />
'''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&nbsp;and 13:00. You will&nbsp;have to bring your own lunch or buy lunch in the local cantina.&nbsp; <br />
<br />
'''Lecture room:''' All lectures/exercises will be given in&nbsp;lecture room&nbsp;'''Cobol'''&nbsp;(room 3452) in&nbsp;Ole-Johan Dahls hus (IFI2). A map showing&nbsp;the location of the building is found [http://www.uio.no/om/finn-fram/omrader/gaustad/ga06 here]. The building is located&nbsp;next to&nbsp;the Forskningsparken metro and tram stations. <br />
<br />
== Course description ==<br />
<br />
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. <br />
<br />
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.'' <br />
<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> <br />
<br />
== Fall 2013 schedule ==<br />
<br />
To be announced. Monday - Friday from 9:00 to 17:00, some lectures, mostly hands-on exercises <br />
<br />
<br> <br />
<br />
{| width="600" border="1" cellpadding="1" cellspacing="1"<br />
|-<br />
! scope="col" | <br> <br />
! scope="col" | <br />
Morning <br />
<br />
9:00 - 12:00 <br />
<br />
! scope="col" | <br />
Afternoon <br />
<br />
13:00 - 17:00 <br />
<br />
|-<br />
| Tuesday September 3rd <br />
| [[Unix pre-course H13|Unix pre-course for people new to the unix command-line]]&nbsp;(teacher: KM) <br />
| [[Unix pre-course H13|Unix pre-course for people new to the unix command-line]]&nbsp;(KM)<br />
|-<br />
| <br />
|-<br />
| Monday September 16th <br />
| <br />
Introduction to High-throughput sequencing technologies and applications (LMZ) <br />
[[Media:SequencingTech&Applic.pdf|slides]]<br />
| <br />
File formats (DV) <br />
<br />
Quality control of sequencing data (LN) <br />
<br />
|-<br />
| Tuesday September 17th <br />
| miRNA (MMW, DV) <br />
| miRNA&nbsp;(MMW, DV)<br><br />
|-<br />
| Wednesday September 18th <br />
| RNA-seq (LMZ, SL, JCB) <br />
| RNA-seq (LMZ, SL, JCB)<br />
|-<br />
| Thursday September 19th <br />
| RNA-seq (LMZ, SL, JCB) <br />
| RNA-seq (LMZ, SL, JCB)<br />
|-<br />
| Friday September 20th <br />
| Variant calling (TH) <br />
| Variant calling (TH)<br />
|-<br />
| &nbsp; <br />
| <br />
| <br />
|-<br />
| Monday September 23 <br />
| Variant calling (TH) <br />
| Variant calling (TH)<br />
|-<br />
| Tuesday September 24 <br />
| de novo Assembly (LN) <br />
| de novo Assembly (LN)<br />
|-<br />
| Wednesday September 25 <br />
| de novo Assembly (LN) <br />
| de novo Assembly (LN)<br />
|-<br />
| Thursday September 26 <br />
| Statistical genomics (Galaxy, Hyperbrowser) (GKS, SG) <br />
| Statistical genomics (Galaxy, Hyperbrowser)(GKS, SG)<br />
|-<br />
| Friday September 27 <br />
| <br />
Wrap-up and conclusions (all) <br />
<br />
Handout of exam exercises (all) <br />
<br />
Course evaluation (all) <br />
<br />
| Installation of programs on your own laptop (MMW, DV, KM)<br />
|-<br />
| &nbsp; <br />
| <br />
| <br />
|-<br />
| Monday October 21 <br />
| Examination <br />
| Examination<br />
|}<br />
<br />
== Contact information<br> ==<br />
<br />
Lex Nederbragt (Course coordinator) - e-mail: lex.nederbragt - at - ibv.uio.no <br />
<br />
Karin Lagesen (Course co-coordinator) - e-mail: karin.lagesen - at - medisin.uio.no <br />
<br />
Course administration/registration - e-mail: studieinfo@ifi.uio.no <br />
<br />
== Teachers ==<br />
<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 Support Services Group, USIT, University of Oslo)<br> <br />
<br />
== Computers/laptops, internet access, and UiO user account ==<br />
<br />
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). <br />
<br />
[https://wiki.uio.no/projects/clsi/index.php/VM_use Connect to virtual machines] <br />
<br />
== Curriculum and suggested reading<br> ==<br />
<br />
<span style="line-height: 1.5em;"> <br />
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.<br />
</span> <br />
<br />
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. <br />
<br />
Specific details of the curriculum, and a list of further suggested papers, can be found here: [[INF-BIOX120 H13 curriculum|this page]]. <br />
<br />
== Exam<br> ==<br />
<br />
<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> <br />
<br />
The exam will be handed out to all participants during the last course day.<br> <br />
<br />
== Bioinformatics mailing list for the Oslo region ==<br />
<br />
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 [https://sympa.uio.no/usit.uio.no/info/cbo-all here]&nbsp;by following the link termed "Subscribe". <br />
<br />
== Useful links ==<br />
<br />
Trond Hasle Amundsen's "[http://www.uio.no/tjenester/it/maskin/linux/hjelp/tips/guide.html Local guide to Linux and Unix]" <br />
<br />
Community resources: <br />
<br />
*[http://seqanswers.com/wiki/SEQanswers seqwiki]:&nbsp;overview of HTS analysis software, providers, etc <br />
*the 'Next Generation Sequencing' [http://en.wikibooks.org/wiki/Next_Generation_Sequencing_(NGS) wikibook] <br />
*[http://seqanswers.com/ seqanswers]: helpful forums <br />
*[http://www.biostars.org/ biostars]: Q&amp;A site for general bioinformatics<br><br />
<br />
<br> <br />
<br />
== Messages ==<br />
<br />
Follow [[INF BIOX120 H13 messages|this page]] for updates during and after the course.</div>Katerim@uio.nohttps://wiki.uio.no/projects/clsi/index.php?title=INF-BIOX120_H13&diff=223INF-BIOX120 H132013-09-16T13:49:18Z<p>Katerim@uio.no: /* Fall 2013 schedule */</p>
<hr />
<div>== High Throughput Sequencing technologies and bioinformatics analysis ==<br />
<br />
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. <br />
<br />
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. <br />
<br />
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 <br />
<br />
Both INF-BIO5120 (M.Sc. level) and INF-BIO9120 (Ph.D. level) are 5 study point courses. <br />
<br />
<br> <br />
<br />
'''''Please bookmark this page. All future changes or announcements for the 2013 course will be posted&nbsp;on this page.''''' <br />
<br />
== '''Time and place''' ==<br />
<br />
'''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&nbsp;and 13:00. You will&nbsp;have to bring your own lunch or buy lunch in the local cantina.&nbsp; <br />
<br />
'''Lecture room:''' All lectures/exercises will be given in&nbsp;lecture room&nbsp;'''Cobol'''&nbsp;(room 3452) in&nbsp;Ole-Johan Dahls hus (IFI2). A map showing&nbsp;the location of the building is found [http://www.uio.no/om/finn-fram/omrader/gaustad/ga06 here]. The building is located&nbsp;next to&nbsp;the Forskningsparken metro and tram stations. <br />
<br />
== Course description ==<br />
<br />
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. <br />
<br />
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.'' <br />
<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> <br />
<br />
== Fall 2013 schedule ==<br />
<br />
To be announced. Monday - Friday from 9:00 to 17:00, some lectures, mostly hands-on exercises <br />
<br />
<br> <br />
<br />
{| width="600" border="1" cellpadding="1" cellspacing="1"<br />
|-<br />
! scope="col" | <br> <br />
! scope="col" | <br />
Morning <br />
<br />
9:00 - 12:00 <br />
<br />
! scope="col" | <br />
Afternoon <br />
<br />
13:00 - 17:00 <br />
<br />
|-<br />
| Tuesday September 3rd <br />
| [[Unix pre-course H13|Unix pre-course for people new to the unix command-line]]&nbsp;(teacher: KM) <br />
| [[Unix pre-course H13|Unix pre-course for people new to the unix command-line]]&nbsp;(KM)<br />
|-<br />
| <br />
|-<br />
| Monday September 16th <br />
| <br />
Introduction to High-throughput sequencing technologies and applications (LMZ) <br />
[[ |slides]]<br />
| <br />
File formats (DV) <br />
<br />
Quality control of sequencing data (LN) <br />
<br />
|-<br />
| Tuesday September 17th <br />
| miRNA (MMW, DV) <br />
| miRNA&nbsp;(MMW, DV)<br><br />
|-<br />
| Wednesday September 18th <br />
| RNA-seq (LMZ, SL, JCB) <br />
| RNA-seq (LMZ, SL, JCB)<br />
|-<br />
| Thursday September 19th <br />
| RNA-seq (LMZ, SL, JCB) <br />
| RNA-seq (LMZ, SL, JCB)<br />
|-<br />
| Friday September 20th <br />
| Variant calling (TH) <br />
| Variant calling (TH)<br />
|-<br />
| &nbsp; <br />
| <br />
| <br />
|-<br />
| Monday September 23 <br />
| Variant calling (TH) <br />
| Variant calling (TH)<br />
|-<br />
| Tuesday September 24 <br />
| de novo Assembly (LN) <br />
| de novo Assembly (LN)<br />
|-<br />
| Wednesday September 25 <br />
| de novo Assembly (LN) <br />
| de novo Assembly (LN)<br />
|-<br />
| Thursday September 26 <br />
| Statistical genomics (Galaxy, Hyperbrowser) (GKS, SG) <br />
| Statistical genomics (Galaxy, Hyperbrowser)(GKS, SG)<br />
|-<br />
| Friday September 27 <br />
| <br />
Wrap-up and conclusions (all) <br />
<br />
Handout of exam exercises (all) <br />
<br />
Course evaluation (all) <br />
<br />
| Installation of programs on your own laptop (MMW, DV, KM)<br />
|-<br />
| &nbsp; <br />
| <br />
| <br />
|-<br />
| Monday October 21 <br />
| Examination <br />
| Examination<br />
|}<br />
<br />
== Contact information<br> ==<br />
<br />
Lex Nederbragt (Course coordinator) - e-mail: lex.nederbragt - at - ibv.uio.no <br />
<br />
Karin Lagesen (Course co-coordinator) - e-mail: karin.lagesen - at - medisin.uio.no <br />
<br />
Course administration/registration - e-mail: studieinfo@ifi.uio.no <br />
<br />
== Teachers ==<br />
<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 Support Services Group, USIT, University of Oslo)<br> <br />
<br />
== Computers/laptops, internet access, and UiO user account ==<br />
<br />
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). <br />
<br />
[https://wiki.uio.no/projects/clsi/index.php/VM_use Connect to virtual machines] <br />
<br />
== Curriculum and suggested reading<br> ==<br />
<br />
<span style="line-height: 1.5em;"> <br />
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.<br />
</span> <br />
<br />
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. <br />
<br />
Specific details of the curriculum, and a list of further suggested papers, can be found here: [[INF-BIOX120 H13 curriculum|this page]]. <br />
<br />
== Exam<br> ==<br />
<br />
<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> <br />
<br />
The exam will be handed out to all participants during the last course day.<br> <br />
<br />
== Bioinformatics mailing list for the Oslo region ==<br />
<br />
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 [https://sympa.uio.no/usit.uio.no/info/cbo-all here]&nbsp;by following the link termed "Subscribe". <br />
<br />
== Useful links ==<br />
<br />
Trond Hasle Amundsen's "[http://www.uio.no/tjenester/it/maskin/linux/hjelp/tips/guide.html Local guide to Linux and Unix]" <br />
<br />
Community resources: <br />
<br />
*[http://seqanswers.com/wiki/SEQanswers seqwiki]:&nbsp;overview of HTS analysis software, providers, etc <br />
*the 'Next Generation Sequencing' [http://en.wikibooks.org/wiki/Next_Generation_Sequencing_(NGS) wikibook] <br />
*[http://seqanswers.com/ seqanswers]: helpful forums <br />
*[http://www.biostars.org/ biostars]: Q&amp;A site for general bioinformatics<br><br />
<br />
<br> <br />
<br />
== Messages ==<br />
<br />
Follow [[INF BIOX120 H13 messages|this page]] for updates during and after the course.</div>Katerim@uio.nohttps://wiki.uio.no/projects/clsi/index.php?title=Unix_pre-course_H13&diff=209Unix pre-course H132013-09-10T09:01:02Z<p>Katerim@uio.no: </p>
<hr />
<div>This page can also be reached by going to&nbsp;<u>bit.ly/htscourse1</u> <br />
<br />
<br />
=Pre-course materials=<br />
<br><br><br />
[[Media:Unix_tutorial_sep2013.pdf| PDF file]] <br />
<br><br><br />
[http://folk.uio.no/katerim/unix_tutorial_sep2013b.htm HTML page] <br />
<br><br><br />
[https://wiki.uio.no/usit/suf/vd/hpc/index.php/Unix_precourse Wiki page]<br />
<br><br><br />
[https://wiki.uio.no/projects/clsi/index.php/VM_use How do I connect to virtual machines?]<br />
<br><br><br><br><br />
The works created for the course are released under a Creative Commons Attribution-NonCommercial-ShareAlike 3.0 license. See http://creativecommons.org/licenses/by-nc-sa/3.0/. This license lets you remix, tweak, and build upon our work non-commercially, as long as you credit us and license your new creations under the identical terms.<br />
<br><br><br />
Katerina Michalickova for The Research Computing Services at the University of Oslo ([https://uio.no/hpc uio.no/hpc])</div>Katerim@uio.nohttps://wiki.uio.no/projects/clsi/index.php?title=Unix_pre-course_H13&diff=208Unix pre-course H132013-09-06T13:39:23Z<p>Katerim@uio.no: /* Pre-course materials */</p>
<hr />
<div>This page can also be reached by going to&nbsp;<u>bit.ly/htscourse1</u> <br />
<br />
<br />
=Pre-course materials=<br />
<br><br><br />
[[Media:Unix_tutorial_sep2013.pdf| PDF file]] <br />
<br><br><br />
[http://folk.uio.no/katerim/unix_tutorial.htm HTML page] <br />
<br><br><br />
[https://wiki.uio.no/usit/suf/vd/hpc/index.php/Unix_precourse Wiki page]<br />
<br><br><br />
[https://wiki.uio.no/projects/clsi/index.php/VM_use How do I connect to virtual machines?]<br />
<br><br><br><br><br />
The works created for the course are released under a Creative Commons Attribution-NonCommercial-ShareAlike 3.0 license. See http://creativecommons.org/licenses/by-nc-sa/3.0/. This license lets you remix, tweak, and build upon our work non-commercially, as long as you credit us and license your new creations under the identical terms.<br />
<br><br><br />
Katerina Michalickova for The Research Computing Services at the University of Oslo ([https://uio.no/hpc uio.no/hpc])</div>Katerim@uio.nohttps://wiki.uio.no/projects/clsi/index.php?title=Unix_pre-course_H13&diff=207Unix pre-course H132013-09-06T13:37:42Z<p>Katerim@uio.no: /* Pre-course materials */</p>
<hr />
<div>This page can also be reached by going to&nbsp;<u>bit.ly/htscourse1</u> <br />
<br />
<br />
=Pre-course materials=<br />
<br><br><br />
[[Media:Unix_tutorial_sep2013.pdf| PDF file]] <br />
<br><br><br />
[http://folk.uio.no/katerim/unix_tutorial.htm HTML page] <br />
<br><br><br />
[https://wiki.uio.no/usit/suf/vd/hpc/index.php/Unix_precourse Wiki page]<br />
<br><br><br />
[https://wiki.uio.no/projects/clsi/index.php/VM_use How do I connect to virtual machines?]<br />
<br><br><br><br><br />
The works created for the course are released under a Creative Commons Attribution-NonCommercial-ShareAlike 3.0 license. See http://creativecommons.org/licenses/by-nc-sa/3.0/. This license lets you remix, tweak, and build upon our work non-commercially, as long as you credit us and license your new creations under the identical terms.<br />
<br><br><br />
Katerina Michalickova for The Research Computing Services at the University of Oslo (uio.no/hpc)</div>Katerim@uio.nohttps://wiki.uio.no/projects/clsi/index.php?title=VM_use&diff=199VM use2013-09-04T12:13:13Z<p>Katerim@uio.no: /* Login in */</p>
<hr />
<div>=Using virtual machines via ssh=<br />
==VM number==<br />
Each student was assigned a virtual machine (VM) number at the unix pre-course. Use this number instead of "xx" in the machine address.<br />
<br />
==VM login and password==<br />
Use your UiO credentials to log into the VM. If you do not have UiO login name, use the guest account that you have been given at the pre-course.<br />
<br />
==Log in==<br />
<br />
<br />
===Windows===<br />
Open 'PuTTy'. Fill 'htsxx.uio.no' in the host name dialog box. Click "Open".<br />
<br />
[[File:putty.jpg]]<br />
<br />
===Mac===<br />
Use 'Terminal'. Type:<br />
<br />
<pre>ssh htsxx.uio.no</pre><br />
<br />
===Linux===<br />
Open a terminal. Type: <br />
<br />
<pre>ssh htsxx.uio.no</pre> <br />
<br><br></div>Katerim@uio.nohttps://wiki.uio.no/projects/clsi/index.php?title=VM_use&diff=198VM use2013-09-04T12:12:52Z<p>Katerim@uio.no: </p>
<hr />
<div>=Using virtual machines via ssh=<br />
==VM number==<br />
Each student was assigned a virtual machine (VM) number at the unix pre-course. Use this number instead of "xx" in the machine address.<br />
<br />
==VM login and password==<br />
Use your UiO credentials to log into the VM. If you do not have UiO login name, use the guest account that you have been given at the pre-course.<br />
<br />
==Login in==<br />
===Windows===<br />
Open 'PuTTy'. Fill 'htsxx.uio.no' in the host name dialog box. Click "Open".<br />
<br />
[[File:putty.jpg]]<br />
<br />
===Mac===<br />
Use 'Terminal'. Type:<br />
<br />
<pre>ssh htsxx.uio.no</pre><br />
<br />
===Linux===<br />
Open a terminal. Type: <br />
<br />
<pre>ssh htsxx.uio.no</pre> <br />
<br><br></div>Katerim@uio.nohttps://wiki.uio.no/projects/clsi/index.php?title=VM_use&diff=197VM use2013-09-04T12:11:31Z<p>Katerim@uio.no: /* Mac */</p>
<hr />
<div>=Using virtual machines via ssh=<br />
Each student was assigned a virtual machine (VM) number at the unix pre-course. Use this number instead of "xx" in the machine address.<br />
<br />
Use your UiO credentials to log into the VM. If you do not have UiO login name, use the guest account that you have been given at the pre-course.<br />
<br />
==Windows==<br />
Open 'PuTTy'. Fill 'htsxx.uio.no' in the host name dialog box. Click "Open".<br />
<br />
[[File:putty.jpg]]<br />
<br />
==Mac ==<br />
Use 'Terminal'. Type:<br />
<br />
<pre>ssh htsxx.uio.no</pre><br />
<br />
==Linux==<br />
Open a terminal. Type: <br />
<br />
<pre>ssh htsxx.uio.no</pre> <br />
<br><br></div>Katerim@uio.nohttps://wiki.uio.no/projects/clsi/index.php?title=VM_use&diff=196VM use2013-09-04T12:11:22Z<p>Katerim@uio.no: /* Linux: open a terminal */</p>
<hr />
<div>=Using virtual machines via ssh=<br />
Each student was assigned a virtual machine (VM) number at the unix pre-course. Use this number instead of "xx" in the machine address.<br />
<br />
Use your UiO credentials to log into the VM. If you do not have UiO login name, use the guest account that you have been given at the pre-course.<br />
<br />
==Windows==<br />
Open 'PuTTy'. Fill 'htsxx.uio.no' in the host name dialog box. Click "Open".<br />
<br />
[[File:putty.jpg]]<br />
<br />
==Mac ==<br />
Use 'Terminal'. Type<br />
<br />
<pre>ssh htsxx.uio.no</pre> <br />
<br />
<br />
==Linux==<br />
Open a terminal. Type: <br />
<br />
<pre>ssh htsxx.uio.no</pre> <br />
<br><br></div>Katerim@uio.nohttps://wiki.uio.no/projects/clsi/index.php?title=Unix_pre-course_H13&diff=195Unix pre-course H132013-09-04T12:09:39Z<p>Katerim@uio.no: /* Pre-course materials */</p>
<hr />
<div>This page can also be reached by going to&nbsp;<u>bit.ly/htscourse1</u> <br />
<br />
<br />
=Pre-course materials=<br />
<br><br><br />
[[Media:Unix_tutorial_sep2013.pdf| PDF file]] <br />
<br><br><br />
[http://folk.uio.no/katerim/unix_tutorial.htm HTML page] <br />
<br><br><br />
[https://wiki.uio.no/usit/suf/vd/hpc/index.php/Unix_precourse Wiki page]<br />
<br><br><br />
[https://wiki.uio.no/projects/clsi/index.php/VM_use How do I connect to virtual machines?]<br />
<br><br><br><br></div>Katerim@uio.nohttps://wiki.uio.no/projects/clsi/index.php?title=Unix_pre-course_H13&diff=194Unix pre-course H132013-09-04T12:09:23Z<p>Katerim@uio.no: /* Pre-course materials */</p>
<hr />
<div>This page can also be reached by going to&nbsp;<u>bit.ly/htscourse1</u> <br />
<br />
<br />
=Pre-course materials=<br />
<br />
[[Media:Unix_tutorial_sep2013.pdf| PDF file]] <br />
<br><br><br />
[http://folk.uio.no/katerim/unix_tutorial.htm HTML page] <br />
<br><br><br />
[https://wiki.uio.no/usit/suf/vd/hpc/index.php/Unix_precourse Wiki page]<br />
<br><br><br />
[https://wiki.uio.no/projects/clsi/index.php/VM_use How do I connect to virtual machines?]<br />
<br><br><br><br></div>Katerim@uio.nohttps://wiki.uio.no/projects/clsi/index.php?title=INF-BIOX120_H13&diff=193INF-BIOX120 H132013-09-04T12:08:37Z<p>Katerim@uio.no: /* Computers/laptops, internet access, and UiO user account */</p>
<hr />
<div>== High Throughput Sequencing technologies and bioinformatics analysis ==<br />
<br />
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. <br />
<br />
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. <br />
<br />
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 <br />
<br />
Both INF-BIO5120 (M.Sc. level) and INF-BIO9120 (Ph.D. level) are 5 study point courses. <br />
<br />
<br> <br />
<br />
'''''Please bookmark this page. All future changes or announcements for the 2013 course will be posted&nbsp;on this page.''''' <br />
<br />
== '''Time and place''' ==<br />
<br />
'''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&nbsp;and 13:00. You will&nbsp;have to bring your own lunch or buy lunch in the local cantina.&nbsp; <br />
<br />
'''Lecture room:''' All lectures/exercises will be given in&nbsp;lecture room&nbsp;'''Cobol'''&nbsp;(room 3452) in&nbsp;Ole-Johan Dahls hus (IFI2). A map showing&nbsp;the location of the building is found [http://www.uio.no/om/finn-fram/omrader/gaustad/ga06 here]. The building is located&nbsp;next to&nbsp;the Forskningsparken metro and tram stations. <br />
<br />
== Course description ==<br />
<br />
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. <br />
<br />
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.'' <br />
<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> <br />
<br />
== Fall 2013 schedule ==<br />
<br />
To be announced. Monday - Friday from 9:00 to 17:00, some lectures, mostly hands-on exercises <br />
<br />
<br> <br />
<br />
{| width="600" border="1" cellpadding="1" cellspacing="1"<br />
|-<br />
! scope="col" | <br> <br />
! scope="col" | <br />
Morning <br />
<br />
9:00 - 12:00 <br />
<br />
! scope="col" | <br />
Afternoon <br />
<br />
13:00 - 17:00 <br />
<br />
|-<br />
| Tuesday September 3rd <br />
| [[Unix_pre-course_H13|Unix pre-course for people new to the unix command-line]]<br />
| [[Unix_pre-course_H13|Unix pre-course for people new to the unix command-line]]<br />
|-<br />
| <br />
|-<br />
| Monday September 16th <br />
| Introduction to High-throughput sequencing technologies and applications <br />
| <br />
File formats <br />
<br />
Quality control of sequencing data <br />
<br />
|-<br />
| Tuesday September 17th <br />
| miRNA <br />
| miRNA<br />
|-<br />
| Wednesday September 18th <br />
| RNA-seq <br />
| RNA-seq<br />
|-<br />
| Thursday September 19th <br />
| RNA-seq <br />
| RNA-seq<br />
|-<br />
| Friday September 20th <br />
| Variant calling <br />
| Variant calling<br />
|-<br />
| &nbsp; <br />
| <br />
| <br />
|-<br />
| Monday September 23 <br />
| Variant calling <br />
| Variant calling<br />
|-<br />
| Tuesday September 24 <br />
| de novo Assembly <br />
| de novo Assembly<br />
|-<br />
| Wednesday September 25 <br />
| de novo Assembly <br />
| de novo Assembly<br />
|-<br />
| Thursday September 26 <br />
| Statistical genomics (Galaxy, Hyperbrowser) <br />
| Statistical genomics (Galaxy, Hyperbrowser)<br />
|-<br />
| Friday September 27 <br />
| <br />
Wrap-up and conclusions <br />
<br />
Handout of exam exercises <br />
<br />
Course evaluation <br />
<br />
| Installation of programs on your own laptop<br />
|-<br />
| &nbsp; <br />
| <br />
| <br />
|-<br />
| Monday October 21 <br />
| Examination <br />
| Examination<br />
|}<br />
<br />
== Contact information<br> ==<br />
<br />
Lex Nederbragt (Course coordinator) - e-mail: lex.nederbragt - at - ibv.uio.no <br />
<br />
Karin Lagesen (Course co-coordinator) - e-mail: karin.lagesen - at - medisin.uio.no <br />
<br />
Course administration/registration - e-mail: studieinfo@ifi.uio.no <br />
<br />
== Teachers ==<br />
<br />
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> <br />
<br />
== Computers/laptops, internet access, and UiO user account ==<br />
<br />
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).<br />
<br />
[https://wiki.uio.no/projects/clsi/index.php/VM_use Connect to virtual machines]<br />
<br />
== Curriculum and suggested reading<br> ==<br />
<br />
<span style="line-height: 1.5em;"> <br />
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.<br />
</span><br />
<br />
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. <br />
<br />
Specific details of the curriculum, and a list of further suggested papers, can be found here: [[INF-BIOX120 H13 curriculum|this page]].<br />
<br />
== Exam<br> ==<br />
<br />
<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> <br />
<br />
The exam will be handed out to all participants during the last course day.<br><br />
<br />
== Bioinformatics mailing list for the Oslo region ==<br />
<br />
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 [https://sympa.uio.no/usit.uio.no/info/cbo-all here]&nbsp;by following the link termed "Subscribe". <br />
<br />
== Useful links ==<br />
<br />
Trond Hasle Amundsen's "[http://www.uio.no/tjenester/it/maskin/linux/hjelp/tips/guide.html Local guide to Linux and Unix]" <br />
<br />
Community resources:<br />
<br />
*[http://seqanswers.com/wiki/SEQanswers seqwiki]:&nbsp;overview of HTS analysis software, providers, etc<br />
*the 'Next Generation Sequencing' [http://en.wikibooks.org/wiki/Next_Generation_Sequencing_(NGS) wikibook]<br />
*[http://seqanswers.com/ seqanswers]: helpful forums<br />
*[http://www.biostars.org/ biostars]: Q&amp;A site for general bioinformatics<br></div>Katerim@uio.nohttps://wiki.uio.no/projects/clsi/index.php?title=Unix_pre-course_H13&diff=192Unix pre-course H132013-09-04T12:07:10Z<p>Katerim@uio.no: </p>
<hr />
<div>This page can also be reached by going to&nbsp;<u>bit.ly/htscourse1</u> <br />
<br />
<br />
=Pre-course materials=<br />
<br />
[[Media:Unix_tutorial_sep2013.pdf| PDF file]] <br />
<br><br><br />
[http://folk.uio.no/katerim/unix_tutorial.htm HTML page] <br />
<br><br><br />
[https://wiki.uio.no/usit/suf/vd/hpc/index.php/Unix_precourse Wiki page]<br />
<br><br><br />
[https://wiki.uio.no/projects/clsi/index.php/VM_use How do I connect to virtual machines?]</div>Katerim@uio.nohttps://wiki.uio.no/projects/clsi/index.php?title=VM_use&diff=191VM use2013-09-04T12:02:55Z<p>Katerim@uio.no: /* Using virtual machines via ssh */</p>
<hr />
<div>=Using virtual machines via ssh=<br />
Each student was assigned a virtual machine (VM) number at the unix pre-course. Use this number instead of "xx" in the machine address.<br />
<br />
Use your UiO credentials to log into the VM. If you do not have UiO login name, use the guest account that you have been given at the pre-course.<br />
<br />
==Windows==<br />
Open 'PuTTy'. Fill 'htsxx.uio.no' in the host name dialog box. Click "Open".<br />
<br />
[[File:putty.jpg]]<br />
<br />
==Mac ==<br />
Use 'Terminal'. Type<br />
<br />
<pre>ssh htsxx.uio.no</pre> <br />
<br />
<br />
==Linux: open a terminal ==<br />
Open a terminal. Type: <br />
<br />
<pre>ssh htsxx.uio.no</pre> <br />
<br><br></div>Katerim@uio.nohttps://wiki.uio.no/projects/clsi/index.php?title=VM_use&diff=190VM use2013-09-04T12:01:24Z<p>Katerim@uio.no: /* Windows */</p>
<hr />
<div>=Using virtual machines via ssh=<br />
Each student was assigned a virtual machine number at the unix pre-course. Use this number instead of "xx" in the machine address.<br />
<br />
==Windows==<br />
Open 'PuTTy'. Fill 'htsxx.uio.no' in the host name dialog box. Click "Open".<br />
<br />
[[File:putty.jpg]]<br />
<br />
==Mac ==<br />
Use 'Terminal'. Type<br />
<br />
<pre>ssh htsxx.uio.no</pre> <br />
<br />
<br />
==Linux: open a terminal ==<br />
Open a terminal. Type: <br />
<br />
<pre>ssh htsxx.uio.no</pre> <br />
<br><br></div>Katerim@uio.nohttps://wiki.uio.no/projects/clsi/index.php?title=VM_use&diff=189VM use2013-09-04T12:01:08Z<p>Katerim@uio.no: Created page with "=Using virtual machines via ssh= Each student was assigned a virtual machine number at the unix pre-course. Use this number instead of "xx" in the machine address. ==Windows== ..."</p>
<hr />
<div>=Using virtual machines via ssh=<br />
Each student was assigned a virtual machine number at the unix pre-course. Use this number instead of "xx" in the machine address.<br />
<br />
==Windows==<br />
Open 'PuTTy'. Fill 'htsxx.uio.no' in the host name dialog box. Click "Connect".<br />
<br />
[[File:putty.jpg]]<br />
<br />
<br />
==Mac ==<br />
Use 'Terminal'. Type<br />
<br />
<pre>ssh htsxx.uio.no</pre> <br />
<br />
<br />
==Linux: open a terminal ==<br />
Open a terminal. Type: <br />
<br />
<pre>ssh htsxx.uio.no</pre> <br />
<br><br></div>Katerim@uio.nohttps://wiki.uio.no/projects/clsi/index.php?title=File:Unix_tutorial_sep2013.pdf&diff=188File:Unix tutorial sep2013.pdf2013-09-04T11:32:44Z<p>Katerim@uio.no: uploaded a new version of &quot;File:Unix tutorial sep2013.pdf&quot;</p>
<hr />
<div></div>Katerim@uio.nohttps://wiki.uio.no/projects/clsi/index.php?title=Unix_pre-course_H13&diff=187Unix pre-course H132013-09-03T13:09:27Z<p>Katerim@uio.no: </p>
<hr />
<div>This page can also be reached by going to&nbsp;<u>bit.ly/htscourse1</u> <br />
<br />
==Using course virtual machines at home==<br />
<br />
<br />
*Windows: open 'PuTTy'<br><br />
*Mac: use 'Terminal'<br><br />
*Linux: open a terminal <br />
<br />
In terminals, type: <br />
<pre>ssh htsxx.uio.no</pre> <br />
<br><br><br />
<br />
In Putty: connect to 'htsxx.uio.no' <br />
<br />
[[File:putty.jpg]]<br />
<br />
<br />
<br />
<br />
==Pre-course materials==<br />
<br />
[[Media:Unix_tutorial_sep2013.pdf|PDF file]] <br />
<br />
[http://folk.uio.no/katerim/unix_tutorial.htm HTML page] <br />
<br> [https://wiki.uio.no/usit/suf/vd/hpc/index.php/Unix_precourse Wiki page] <br></div>Katerim@uio.nohttps://wiki.uio.no/projects/clsi/index.php?title=Unix_pre-course_H13&diff=186Unix pre-course H132013-09-03T13:09:07Z<p>Katerim@uio.no: /* Using course virtual machines at home */</p>
<hr />
<div>This page can also be reached by going to&nbsp;<u>bit.ly/htscourse1</u> <br />
<br />
==Using course virtual machines at home==<br />
<br />
<br />
*Windows: open 'PuTTy'<br><br />
*Mac: use 'Terminal'<br><br />
*Linux: open a terminal <br />
<br />
In terminals, type: <br />
<pre>ssh htsxx.uio.no</pre> <br />
<br><br><br />
<br />
In Putty: connect to 'htsxx.uio.no' <br />
<br />
[[File:putty.jpg]]<br />
<br />
==Pre-course materials==<br />
<br />
[[Media:Unix_tutorial_sep2013.pdf|PDF file]] <br />
<br />
[http://folk.uio.no/katerim/unix_tutorial.htm HTML page] <br />
<br> [https://wiki.uio.no/usit/suf/vd/hpc/index.php/Unix_precourse Wiki page] <br></div>Katerim@uio.nohttps://wiki.uio.no/projects/clsi/index.php?title=File:Putty.jpg&diff=185File:Putty.jpg2013-09-03T13:06:32Z<p>Katerim@uio.no: uploaded a new version of &quot;File:Putty.jpg&quot;</p>
<hr />
<div></div>Katerim@uio.nohttps://wiki.uio.no/projects/clsi/index.php?title=Unix_pre-course_H13&diff=184Unix pre-course H132013-09-03T13:03:34Z<p>Katerim@uio.no: /* Using course virtual machines at home */</p>
<hr />
<div>This page can also be reached by going to&nbsp;<u>bit.ly/htscourse1</u> <br />
<br />
==Using course virtual machines at home==<br />
<br />
<br />
*Windows: open 'PuTTy'<br><br />
*Mac: use 'Terminal'<br><br />
*Linux: open a terminal <br />
<br />
In terminals, type: <br />
<pre>ssh htsxx.uio.no</pre> <br />
<br><br><br />
<br />
In Putty: connect to 'htsxx.uio.no' <br />
<br />
[[File:putty.jpg]]<br />
<br />
<br />
<br />
[[Media:Unix_tutorial_sep2013.pdf|PDF file]] <br />
<br />
[http://folk.uio.no/katerim/unix_tutorial.htm HTML page] <br> [https://wiki.uio.no/usit/suf/vd/hpc/index.php/Unix_precourse Wiki page] <br></div>Katerim@uio.nohttps://wiki.uio.no/projects/clsi/index.php?title=Unix_pre-course_H13&diff=183Unix pre-course H132013-09-03T13:02:28Z<p>Katerim@uio.no: /* Using course virtual machines at home */</p>
<hr />
<div>This page can also be reached by going to&nbsp;<u>bit.ly/htscourse1</u> <br />
<br />
==Using course virtual machines at home==<br />
<u></u><u>ssh solution:</u> <br />
<br />
Windows: open 'PuTTy'<br>Mac: use 'Terminal'<br>Linux: open a terminal <br />
<br />
In terminals, type: <br />
<pre>ssh htsxx.uio.no</pre> <br />
<br><br><br />
<br />
In Putty: connect to 'htsxx.uio.no' <br />
<br />
[[File:putty.jpg]]<br />
<br />
<br />
<br />
[[Media:Unix_tutorial_sep2013.pdf|PDF file]] <br />
<br />
[http://folk.uio.no/katerim/unix_tutorial.htm HTML page] <br> [https://wiki.uio.no/usit/suf/vd/hpc/index.php/Unix_precourse Wiki page] <br></div>Katerim@uio.nohttps://wiki.uio.no/projects/clsi/index.php?title=File:Putty.jpg&diff=182File:Putty.jpg2013-09-03T13:01:49Z<p>Katerim@uio.no: </p>
<hr />
<div></div>Katerim@uio.nohttps://wiki.uio.no/projects/clsi/index.php?title=Unix_pre-course_H13&diff=181Unix pre-course H132013-09-03T13:00:04Z<p>Katerim@uio.no: /* Using course virtual machines at home */</p>
<hr />
<div>This page can also be reached by going to&nbsp;<u>bit.ly/htscourse1</u> <br />
<br />
==Using course virtual machines at home==<br />
<u></u><u>ssh solution:</u> <br />
<br />
Windows: open 'PuTTy'<br>Mac: use 'Terminal'<br>Linux: open a terminal <br />
<br />
In terminals, type: <br />
<pre>ssh htsxx.uio.no</pre> <br />
<p><p><br />
<br />
In Putty: connect to 'htsxx.uio.no' <br />
<br />
[[File:putty.jpg]]<br />
<br />
<br />
<br />
[[Media:Unix_tutorial_sep2013.pdf|PDF file]] <br />
<br />
[http://folk.uio.no/katerim/unix_tutorial.htm HTML page] <br> [https://wiki.uio.no/usit/suf/vd/hpc/index.php/Unix_precourse Wiki page] <br></div>Katerim@uio.nohttps://wiki.uio.no/projects/clsi/index.php?title=Unix_pre-course_H13&diff=180Unix pre-course H132013-09-03T12:58:19Z<p>Katerim@uio.no: </p>
<hr />
<div>This page can also be reached by going to&nbsp;<u>bit.ly/htscourse1</u> <br />
<br />
==Using course virtual machines at home==<br />
<u></u><u>ssh solution:</u> <br />
<br />
Windows: open 'PuTTy'<br>Mac: use 'Terminal'<br>Linux: open a terminal <br />
<br />
In terminals, type: <br />
<pre>ssh htsxx.uio.no</pre> <br />
In Putty: connect to 'htsxx.uio.no' <br />
<br />
<br />
<br />
<br />
<br />
[[Media:Unix_tutorial_sep2013.pdf|PDF file]] <br />
<br />
[http://folk.uio.no/katerim/unix_tutorial.htm HTML page] <br> [https://wiki.uio.no/usit/suf/vd/hpc/index.php/Unix_precourse Wiki page] <br></div>Katerim@uio.nohttps://wiki.uio.no/projects/clsi/index.php?title=Unix_pre-course_H13&diff=173Unix pre-course H132013-09-02T13:44:36Z<p>Katerim@uio.no: </p>
<hr />
<div>[[Media:unix_tutorial_sep2013.pdf| PDF file]] <p><br />
[http://folk.uio.no/katerim/unix_tutorial.htm HTML page] <br><br />
[https://wiki.uio.no/usit/suf/vd/hpc/index.php/Unix_precourse Wiki page] <br></div>Katerim@uio.nohttps://wiki.uio.no/projects/clsi/index.php?title=Unix_pre-course_H13&diff=172Unix pre-course H132013-09-02T12:51:33Z<p>Katerim@uio.no: </p>
<hr />
<div>[[Media:unix_tutorial_sep2013.pdf| PDF file]] <p><br />
[http://folk.uio.no/katerim/unix_tutorial.htm HTML page] <br><br />
Wiki page coming soon...</div>Katerim@uio.nohttps://wiki.uio.no/projects/clsi/index.php?title=Unix_pre-course_H13&diff=171Unix pre-course H132013-09-02T12:38:25Z<p>Katerim@uio.no: </p>
<hr />
<div>[[Media:unix_tutorial_sep2013.pdf| PDF file]] <p><br />
[http://folk.uio.no/katerim/unix_tutorial.htm HTML page] <p><p><br />
Wiki page coming soon...</div>Katerim@uio.nohttps://wiki.uio.no/projects/clsi/index.php?title=Unix_pre-course_H13&diff=170Unix pre-course H132013-09-02T12:38:04Z<p>Katerim@uio.no: </p>
<hr />
<div>[[Media:unix_tutorial_sep2013.pdf| PDF file]] <p><br />
[http://folk.uio.no/katerim/unix_tutorial.htm HTML page] <p><br />
Wiki page coming soon...</div>Katerim@uio.nohttps://wiki.uio.no/projects/clsi/index.php?title=Unix_pre-course_H13&diff=169Unix pre-course H132013-09-02T12:37:53Z<p>Katerim@uio.no: </p>
<hr />
<div>[[Media:unix_tutorial_sep2013.pdf| PDF file]] <p><br />
[http://folk.uio.no/katerim/unix_tutorial.htm HTML page]<br />
Wiki page coming soon...</div>Katerim@uio.nohttps://wiki.uio.no/projects/clsi/index.php?title=File:Unix_tutorial_sep2013.pdf&diff=168File:Unix tutorial sep2013.pdf2013-09-02T11:47:01Z<p>Katerim@uio.no: uploaded a new version of &quot;File:Unix tutorial sep2013.pdf&quot;</p>
<hr />
<div></div>Katerim@uio.nohttps://wiki.uio.no/projects/clsi/index.php?title=File:Unix_tutorial_sep2013.pdf&diff=167File:Unix tutorial sep2013.pdf2013-09-02T11:43:21Z<p>Katerim@uio.no: </p>
<hr />
<div></div>Katerim@uio.nohttps://wiki.uio.no/projects/clsi/index.php?title=Unix_pre-course_H13&diff=166Unix pre-course H132013-09-02T11:42:29Z<p>Katerim@uio.no: </p>
<hr />
<div>[[Media:unix_tutorial_sep2013.pdf| PDF file]] <p><br />
Wiki page coming soon...</div>Katerim@uio.nohttps://wiki.uio.no/projects/clsi/index.php?title=Unix_pre-course_H13&diff=165Unix pre-course H132013-09-02T11:41:56Z<p>Katerim@uio.no: Created page with " PDF file Wiki page coming soon..."</p>
<hr />
<div>[[Media:unix_tutorial_sep2013.pdf| PDF file]]<br />
Wiki page coming soon...</div>Katerim@uio.no