Difference between revisions of "MBV-INFX410 2017"

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This is the wiki for 2017
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== [https://wiki.uio.no/projects/clsi/index.php/MBV-INFX410 Bioinformatics for Molecular Biology] - 2016 ==
 +
 
 +
=== Messages ===
 +
* '''9 December: The exam will be handed out by email at 15:00 today to the ones who passed the home exam. Let me know if you did not receive it! The exam must be handed in by 15:00 on December 16 by email to torill.rortveit@ibv.uio.no. Do not write your name in the actual document, but you can write your name in the email subject header. If you log in to StudentWeb you can find your candidate number. This you can include in the document as well as in the email subject header. The answers should be handed in as a PDF document, if the file is very large (above 8 MB) you should divide it and make sure the parts are properly labeled.'''
 +
* '''25 Nov: I have written two different time points for handing in the home assignment. But it should be handed in ''latest'' before the class on Monday Dec. 5. But the sooner the better!'''
 +
* '''25 Nov: The extra home assignment for the PhD students will be to write a short essay (min. 2500 words) describing how two or more of the methods/topics in this course can be used in your own research project - be specific! (about types of analyses and research project).'''
 +
* '''NB! Tuesday and Wednesday November 22 and 23 (Structural Biology) we will be in the Python room at Ole Johan Dahls Hus.'''
 +
* '''Tutorials for working with LifePortal/Galaxy:''' [https://usegalaxy.org/ usegalaxy.org]
 +
* '''You need to install the following software on your laptops:'''
 +
** PyMOL (https://www.pymol.org/)
 +
** JalView Desktop (http://www.jalview.org/) - could maybe also run by pressing the "Launch Jalview Desktop" button
 +
** PuTTY (http://www.putty.org/)
 +
** R (https://www.r-project.org/)
 +
** RStudio (https://www.rstudio.com/)
 +
**'''Optional:''' It could also be wise to have Fetch (for Mac) (http://fetchsoftworks.com/) and WinSCP (Windows) ([https://winscp.net/eng/index.php https://winscp.net/eng/index.php)]
 +
 
 +
* '''''All students must be present at the start of the course, on November 14 at 09:15 in room 1250 in [https://www.uio.no/om/finn-fram/omrader/blindern/bl18/ Kristine Bonnevies (KB) Hus (biology building)]. Missing students will not be allowed to follow the course or to take the exam. If you for some reason are not able to attend, please contact Jon Bråte (See [https://wiki.uio.no/projects/clsi/index.php/MBV-INFX410_2016#Contacts contact details] below).'''''
 +
 
 +
=== Course information ===
 +
This is the wiki for the courses [http://www.uio.no/studier/emner/matnat/ibv/MBV-INF4410 MBV-INF4410] and [http://www.uio.no/studier/emner/matnat/ibv/MBV-INF9410 MBV-INF9410] offered by the Department of Biosciences and Department of Informatics at the University of Oslo (UiO). Both MBV-INF4410 (M.Sc. level) and MBV-INF9410 (Ph.D. level) are 10 study point courses. The 8 study points variant of the course (MBV-INF9410A) will not be given after 2013.
 +
 
 +
The course consists of five weeks of lectures, exercises, obligatory assignments, and a take-home exam (one week). Obligatory assignments must be completed and approved before the exam and in the same semester. An additional, limited, oral examination may be arranged in cases where this is necessary for the student evaluation. The course is open also for non-UiO students. It is only necessary to be physically present in Oslo for certain parts of the course.
 +
{| class="wikitable"
 +
|+General schedule for MBV-INFX410
 +
!
 +
!Mon
 +
!Tue
 +
!Wed
 +
!Thu
 +
!Fri
 +
|-
 +
!Week 46
 +
| style="background: white;" |Lectures/
 +
exercises
 +
| style="background: white;" |Lectures/
 +
exercises
 +
| style="background: white;" |Lectures/
 +
exercises
 +
| style="background: white;" |Lectures/
 +
exercises
 +
| style="background: white;" |Lectures/
 +
exercises
 +
|-
 +
!Week 47
 +
| style="background: white;" |Lectures/
 +
exercises
 +
| style="background: white;" |Lectures/
 +
exercises
 +
| style="background: white;" |Lectures/
 +
exercises
 +
| style="background: white;" |Lectures/
 +
exercises
 +
| style="background: white;" |Lectures/
 +
exercises
 +
|-
 +
!Week 48
 +
| style="background: white;" |Obligatory
 +
home assignment
 +
| style="background: white;" |Obligatory
 +
home assignment
 +
| style="background: white;" |Obligatory
 +
home assignment
 +
| style="background: white;" |Obligatory
 +
home assignment
 +
| style="background: white;" |Hand in
 +
home assignment
 +
|-
 +
!Week 49
 +
| style="background: white;" |Lectures/
 +
exercises
 +
| style="background: white;" |Lectures/
 +
exercises
 +
| style="background: white;" |Lectures/
 +
exercises
 +
| style="background: white;" |Lectures/
 +
exercises
 +
| style="background: white;" |Exam start
 +
(home assignment)
 +
|-
 +
!Week 50
 +
| style="background: white;" |Exam
 +
(home assignment)
 +
| style="background: white;" |Exam
 +
(home assignment)
 +
| style="background: white;" |Exam
 +
(home assignment)
 +
| style="background: white;" |Exam
 +
(home assignment)
 +
| style="background: white;" |Exam end
 +
(home assignment)
 +
|}
 +
 
 +
=== Computers/laptops, internet access, and UiO user account ===
 +
'''All students are strongly encouraged to bring their own laptops.'''
 +
 
 +
* It should be possible to connect the computer to the UiO wireless network
 +
* You must have a root/administrator password that gives you access to installing new software on the computer
 +
* Please bring an '''external mouse''', and do not rely on touchpad/trackpad only
 +
* You must have a '''valid UiO user account''' and must be able to log onto a computer on the UiO network
 +
* Instructions on how to find your username and get a new password can be found [http://www.uio.no/english/services/it/username-password/no-password.html here]. '''''To get a UiO username/password at the UiO helpdesk you need valid ID.'''''
 +
'''''If you are struggling with anything of the above, in particular<nowiki> </nowiki>if you have forgotten your UiO user name/password or you do not have one, you must contact Jon (see [https://wiki.uio.no/projects/clsi/index.php/MBV-INFX410_2016#Contacts contact details]) as soon as possible, and at least one week before the start of the course.'''''
 +
 
 +
On the first day of the course we will set up your laptop so that<nowiki> </nowiki>it can be used for the exercises/tutorials, the home exam and hopefully<nowiki> </nowiki>in your future work. How to get a reasonable setup is described [https://wiki.uio.no/projects/clsi/index.php/Laptop_Setup here].
 +
 
 +
If you already are an expert programmer and Unix guru, go [https://wiki.uio.no/projects/clsi/index.php/Biology_for_Informatics here].
 +
 
 +
=== Time and place (Rooms) ===
 +
The teaching starts at 09:15 and we will end at latest 16:00. Most of the teaching will take place in room 1250 on the 1st floor of Biology Buiding (Kristine Bonnevies Hus, KB). This is a computer room with Desktop machines you can use. Some days we have to change rooms and use a seminar room without desktops. Therefore you have to bring your own laptops (or share with someone else) those days (see the detailed program). NB: November 17 and 18 we will be at [https://www.uio.no/om/finn-fram/omrader/gaustad/ga06/ Ole Johan Dahls hus] (OJD) on the other side of the subway line in the Python seminar room on the second floor. 
 +
 
 +
=== Detailed program ===
 +
The times listed here are only tentative and may likely change. We will mix in small breaks here and there and try to have a lunch break between 12:00 - 13:00.
 +
{| class="wikitable"
 +
|+Detailed schedule for MBV-INFX410 2016
 +
!Week
 +
!Monday
 +
!Tuesday
 +
!Wednesday
 +
!Thursday
 +
!Friday
 +
|-
 +
|<b>46</b>
 +
| style="background: white; text-align: center;" |Nov 14
 +
| style="background: white; text-align: center;" |Nov 15
 +
| style="background: white; text-align: center;" |Nov 16
 +
| style="background: white; text-align: center;" |Nov 17
 +
| style="background: white; text-align: center;" |Nov 18
 +
|-
 +
|
 +
| style="background: #cefdce; vertical-align: top;" |'''Room 1250 KB'''
 +
09:15 - 12:00
 +
 
 +
Course introduction. [[Media:2016-11-14 01 Introduction reduced.pdf|(lecture)]]
 +
 
 +
Introduction to bioinformatics and sequence databases [[Media:2016-11-14_02_Databases.pdf|(lecture)]]
 +
 
 +
 
 +
12:00 - 13:00
 +
 
 +
Lunch   
 +
 
 +
13:15 - 14:00
 +
 
 +
Setting up laptops
 +
 
 +
Basic Unix [[Media:BasicUNIXLecture-15.pdf|(lecture (slides by Jon K. Lærdahl))]]   
 +
 
 +
14:15 - 16:00
 +
 
 +
Basic Unix [[Media:14_nov_UNIXBasics-exercise_JKL.docx|(exercises)]]
 +
| style="background: #cefdce; vertical-align: top;" |'''Room 1250 KB'''
 +
09:15 - 11:00
 +
 
 +
Genome browsers ([[Media:2016-11-15_01_GenomeBrowsers.pdf|lecture]]/ [[Media:UCSC-GB Exercise-15.pdf|exercise]])
 +
 
 +
and Jalview ([[Media:2016-11-15_JalView.pdf|lecture]] /demo)
 +
 
 +
11:15 - 12:00
 +
 
 +
Working with sequences
 +
 
 +
and databases (lectures)
 +
 
 +
12:00 - 13:00
 +
 
 +
Lunch 
 +
 
 +
13:15 - 16:00
 +
 
 +
Applied sequence bioinformatics [[Media:FerretTutorial-15.pdf|(exercise)]]
 +
| style="background: #cefdce; vertical-align: top;" |'''Room 4613 KB'''
 +
09:15 - 12:00
 +
 
 +
Galaxy/Life Portal ([http://www.uio.no/english/services/it/research/events/2016/april/galaxy2016-course-week.pdf lectures]/[[Media:Sabryr_MBV-INF4410.pdf|exercises]])
 +
 
 +
12:00 - 13:00
 +
 
 +
Lunch (we might have to skip this and finish early)   
 +
 
 +
13:15 - 14:00
 +
 
 +
More Unix ([[Media:2016-11-16_01_MoreUnix.pdf|lecture]])
 +
 
 +
| style="background: #cefdce; vertical-align: top;" |'''Room Python OJD'''
 +
09:15 - 16:00
 +
 
 +
Python workshop
 +
 
 +
([[lectures / exercises]])
 +
| style="background: #cefdce; vertical-align: top;" |'''Room Python OJD'''
 +
09:15 - 16:00
 +
 
 +
Python workshop
 +
 
 +
([[lectures / exercises]])
 +
|-
 +
|<b>47</b>
 +
| style="background: white; text-align: center;" |Nov 21
 +
| style="background: white; text-align: center;" |Nov 22
 +
| style="background: white; text-align: center;" |Nov 23
 +
| style="background: white; text-align: center;" |Nov 24
 +
| style="background: white; text-align: center;" |Nov 25
 +
|-
 +
|
 +
| style="background: #cefdce; vertical-align: top;" |'''Room 1250 KB'''
 +
09:15 - 16:00
 +
 +
Sequence searching and alignments
 +
 
 +
(lectures [[Media:2016-11-21_01_mbvinf4410-bioinf-2016.pdf|part1]] [[Media:2016-11-21_02_mbvinf4410-bioinf-2016.pdf|part2]], [[Media:2016-11-21_AlignmentsAndMSAs.pdf|exercises]] ([[Media:2016-11-21_AlignmentsAndMSAs_Task32.pdf|New exercise 32]]))
 +
 
 +
| style="background: #cefdce; vertical-align: top;" |'''Room Python OJD'''
 +
09:15 - 16:00
 +
 
 +
[[Structural Bioinformatics 2016|Structural Bioinformatics]]
 +
 
 +
(lectures and exercises)
 +
| style="background: #cefdce; vertical-align: top;" |'''Room Python OJD'''
 +
09:15 - 16:00
 +
 
 +
[[Structural Bioinformatics 2016|Structural Bioinformatics]]
 +
 
 +
(lectures and exercises)
 +
| style="background: #cefdce; vertical-align: top;" |'''Room 4613 KB 9:15-12'''
 +
'''Room 1250 KB 13:15-16'''
 +
 
 +
09:15 - 12:00
 +
 
 +
[[Docking and drug discovery]]
 +
 
 +
13:15 - 16:00
 +
 
 +
[[Practical Unix/Python 2015|Practical Unix/Python exercise]]
 +
| style="background: #cefdce; vertical-align: top;" |'''Room 2203a KB 9:15 - 12'''
 +
'''Room 1250 KB 13:15-16'''
 +
 
 +
[[Media:Statistical_genomics_2016.pdf|Statistical epigenomics (& reproducibility)]].
 +
 
 +
Lectures / exercises
 +
|-
 +
|<b>48</b>
 +
| style="background: white; text-align: center;" |Nov 28
 +
| style="background: white; text-align: center;" |Nov 29
 +
| style="background: white; text-align: center;" |Nov 30
 +
| style="background: white; text-align: center;" |Dec 1
 +
| style="background: white; text-align: center;" |Dec 2
 +
|-
 +
|
 +
| style="background: #87CEFA; vertical-align: top;" |Obligatory home assignment
 +
| style="background: #87CEFA; vertical-align: top;" |Obligatory home assignment
 +
| style="background: #87CEFA; vertical-align: top;" |Obligatory home assignment
 +
| style="background: #87CEFA; vertical-align: top;" |Obligatory home assignment
 +
| style="background: #87CEFA; vertical-align: top;" |Hand in home assignment
 +
|-
 +
|<b>49</b>
 +
| style="background: white; text-align: center;" |Dec 5
 +
| style="background: white; text-align: center;" |Dec 6
 +
| style="background: white; text-align: center;" |Dec 7
 +
| style="background: white; text-align: center;" |Dec 8
 +
| style="background: white; text-align: center;" |Dec 9
 +
|-
 +
|
 +
| style="background: #cefdce; vertical-align: top;" |'''Room 1250 KB'''
 +
09:15 - 16:00
 +
 
 +
[[Transcriptomics 2016|Analysing transcriptome data]]
 +
 
 +
[[Transcriptomics 2016|(including R)]]
 +
| style="background: #cefdce; vertical-align: top;" |'''Room 1250 KB'''
 +
09:15 - 16:00
 +
 
 +
[[Transcriptomics 2016|Analysing transcriptome data]]
 +
 
 +
[[Transcriptomics 2016|(including R)]]
 +
 
 +
| style="background: #cefdce; vertical-align: top;" |'''Room 1250 KB'''
 +
09:15 - 16:00
 +
 
 +
[[Next Generation Sequencing & variant calling]]
 +
| style="background: #cefdce; vertical-align: top;" |'''Room 4613 KB'''
 +
Last course day
 +
 
 +
09:15 - 11:00
 +
 
 +
[[Media:161208 MBV-INFX410 LexNederbragt final red.pdf|What does it mean to do bioinformatics?]]
 +
 
 +
[[Media:2016-12-08 Summary.pdf|Summary]]
 +
| style="background: salmon; vertical-align: top;" |Hand out exam
 +
|-
 +
|<b>50</b>
 +
| style="background: white; text-align: center;" |Dec 12
 +
| style="background: white; text-align: center;" |Dec 13
 +
| style="background: white; text-align: center;" |Dec 14
 +
| style="background: white; text-align: center;" |Dec 15
 +
| style="background: white; text-align: center;" |Dec 16
 +
|-
 +
|
 +
| style="background: salmon; vertical-align: top;" |Home exam
 +
| style="background: salmon; vertical-align: top;" |Home exam
 +
| style="background: salmon; vertical-align: top;" |Home exam
 +
| style="background: salmon; vertical-align: top;" |Home exam
 +
| style="background: salmon; vertical-align: top;" |Hand in exam
 +
|}
 +
 
 +
=== Required reading material / Curriculum ===
 +
The curriculum comprises all lectures, lecture handouts and exercises, in addition to the articles listed below:
 +
 
 +
*R.F. Service, "Biology's dry future", [http://dx.doi.org/10.1126/science.342.6155.186 Science <b>342</b>, 186 (2013)]
 +
*EMBnet, [http://www.embnet.org/sites/default/files/quickguides/guideUNIX.pdf A Quick Guide to UNIX]
 +
*NCBI Resource Coordinators, "Database resources of the National Center for Biotechnology Information", [http://dx.doi.org/10.1093/nar/gku1130 Nucleic Acids Res. <b>43</b>, D6 (2015)]
 +
*The UniProt Consortium, "UniProt: a hub for protein information", [http://dx.doi.org/10.1093/nar/gku989 Nucleic Acids Res. <b>43</b>, D204 (2015)]
 +
*P. Flicek ''et al.'', "Ensembl 2015", [http://dx.doi.org/10.1093/nar/gku1010 Nucleic Acids Res. <b>43</b>, D662 (2015)]
 +
*P.W. Rose ''et al.'', "The RCSB Protein Data Bank: new resources for research and education", [http://dx.doi.org/10.1093/nar/gks1200 Nucleic Acids Res. <b>41</b>, D475 (2013)]
 +
*P.J.A. Cock ''et al.'', "Biopython: freely available Python tools for computational molecular biology and bioinformatics", [http://dx.doi.org/10.1093/bioinformatics/btp163 Bioinformatics <b>25</b>, 1422 (2009)]
 +
*A.M. Waterhouse ''et al''., "Jalview Version 2--a multiple sequence alignment editor and analysis workbench", [http://dx.doi.org/10.1093/bioinformatics/btp033 Bioinformatics <b>25</b>, 1189 (2009)]
 +
*G.M. Boratyn ''et al.'', "BLAST: a more efficient report with usability improvements", [http://dx.doi.org/10.1093/nar/gkt282 Nucleic Acids Res. <b>41</b>, W29 (2013)]
 +
*J.-F. Taly ''et al.'', "Using the T-Coffee package to build multiple sequence alignments of protein, RNA, DNA sequences and 3D structures", [http://dx.doi.org/10.1038/nprot.2011.393 Nat. Protoc. <b>6</b>, 1669 (2011)]
 +
*L. Bordoli ''et al.'', "Protein structure homology modeling using SWISS-MODEL workspace", [http://dx.doi.org/10.1038/nprot.2008.197 Nat. Protoc. <b>4</b>, 1 (2009)]
 +
*J. Carlsson ''et al.'', "Ligand discovery from a dopamine D<sub>3</sub> receptor homology model and crystal structure", [http://dx.doi.org/10.1038/nchembio.662 Nat. Chem. Biol. <b>7</b>, 769 (2011)]
 +
*R.M. Kuhn ''et al.'', "The UCSC genome browser and associated tools", [http://dx.doi.org/10.1093/bib/bbs038 Brief. Bioinform. <b>14</b>, 144 (2013)]
 +
*J. Goecks ''et al''., "Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences", [http://dx.doi.org/10.1186/gb-2010-11-8-r86 Genome Biol. <b>11</b>, R86 (2010)]
 +
*G.K. Sandve ''et al.'', "Ten Simple Rules for reproducible computational Research", [http://dx.doi.org/10.1371/journal.pcbi.1003285 PLoS Comput. Biol. <b>9</b>, e1003285 (2013)]
 +
*G.K. Sandve ''et al.'', "The Genomic HyperBrowser: an analysis web server for genome-scale data", [http://dx.doi.org/10.1093/nar/gkt342 Nucleic Acids Res. <b>41</b>, W133 (2013)]
 +
*M.L. Mertzker, "Sequencing technologies - the next generation", [http://dx.doi.org/10.1038/nrg2626 Nat. Rev. Genet. <b>11</b>, 31 (2010)]
 +
*A. Altmann ''et al.'', "A beginners guide to SNP calling from high-throughput DNA-sequencing data", [http://dx.doi.org/10.1007/s00439-012-1213-z Hum. Genet. <b>131</b>, 1541 (2012)]
 +
*N. Nagarajan & M. Pop, "Sequence assembly demystified", [http://dx.doi.org/10.1038/nrg3367 Nat. Rev. Genet. <b>14</b>, 157 (2013)]
 +
*D.W. Huang ''et al.'', "Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources", [http://dx.doi.org/10.1038/nprot.2008.211 Nat. Protoc. <b>4</b>, 44 (2009)]
 +
 
 +
Other good articles (''not ''curriculum)
 +
*Z. Yang & B. Rannala, "Molecular phylogenetics: principles and practice", [http://dx.doi.org/doi:10.1038/nrg3186 Nat. Rev. Genet. <b>13</b>, 303 (2012)]
 +
 
 +
=== Contacts ===
 +
Jon Bråte (Course coordinator) - e-mail: jon.brate@ibv.uio.no, phone: +47 922 44 582
 +
 
 +
Torill Rørtveit (Course administrator, registration) - e-mail: torill.rortveit@ibv.uio.no
 +
 
 +
=== Useful links ===
 +
 
 +
Trond Hasle Amundsen's [http://www.uio.no/tjenester/it/maskin/linux/hjelp/tips/guide.html Local guide to Linux and Unix]
 +
 
 +
EMBnet [http://www.embnet.org/sites/default/files/quickguides/guideUNIX.pdf Quick guide Unix]
 +
 
 +
[https://github.com/stephenturner/oneliners Useful command line one-liners] by Stephen Turner
 +
 
 +
[http://www.jalview.org Jalview] and Jalview [http://www.jalview.org/refcard.pdf refcard]
 +
 
 +
UCSC [http://genome.ucsc.edu Genome browser]
 +
 
 +
Free [http://www.openhelix.com/ucsc UCSC Genome browser tutorial]&nbsp;&nbsp; from OpenHelix
 +
 
 +
Portal to [http://galaxyproject.org Galaxy]
 +
 
 +
[http://wiki.galaxyproject.org/Learn Galaxy 101 and other Galaxy screencasts/tutorials]
 +
 
 +
UiO [http://lifeportal.uio.no Lifeportal] and more [http://www.uio.no/english/services/it/research/hpc/lifeportal information on the Lifeportal]
 +
 
 +
The Genomic [http://hyperbrowser.uio.no/hb HyperBrowser]
 +
 
 +
[http://bioinformatics.ca/links_directory Links Directory] from bioinformatics.ca
 +
 
 +
The 2015 Nucleic Acids Research [http://nar.oxfordjournals.org/content/43/D1.toc Database Issue]
 +
 
 +
The 2015 Nucleic Acids Research [http://nar.oxfordjournals.org/content/43/W1.toc Web Server Issue]
 +
 
 +
UiO and OUS [http://core.rr-research.no/bioinformatics Bioinformatics Core Facility]

Revision as of 13:00, 5 September 2017

Bioinformatics for Molecular Biology - 2016

Messages

  • 9 December: The exam will be handed out by email at 15:00 today to the ones who passed the home exam. Let me know if you did not receive it! The exam must be handed in by 15:00 on December 16 by email to torill.rortveit@ibv.uio.no. Do not write your name in the actual document, but you can write your name in the email subject header. If you log in to StudentWeb you can find your candidate number. This you can include in the document as well as in the email subject header. The answers should be handed in as a PDF document, if the file is very large (above 8 MB) you should divide it and make sure the parts are properly labeled.
  • 25 Nov: I have written two different time points for handing in the home assignment. But it should be handed in latest before the class on Monday Dec. 5. But the sooner the better!
  • 25 Nov: The extra home assignment for the PhD students will be to write a short essay (min. 2500 words) describing how two or more of the methods/topics in this course can be used in your own research project - be specific! (about types of analyses and research project).
  • NB! Tuesday and Wednesday November 22 and 23 (Structural Biology) we will be in the Python room at Ole Johan Dahls Hus.
  • Tutorials for working with LifePortal/Galaxy: usegalaxy.org
  • You need to install the following software on your laptops:
  • All students must be present at the start of the course, on November 14 at 09:15 in room 1250 in Kristine Bonnevies (KB) Hus (biology building). Missing students will not be allowed to follow the course or to take the exam. If you for some reason are not able to attend, please contact Jon Bråte (See contact details below).

Course information

This is the wiki for the courses MBV-INF4410 and MBV-INF9410 offered by the Department of Biosciences and Department of Informatics at the University of Oslo (UiO). Both MBV-INF4410 (M.Sc. level) and MBV-INF9410 (Ph.D. level) are 10 study point courses. The 8 study points variant of the course (MBV-INF9410A) will not be given after 2013.

The course consists of five weeks of lectures, exercises, obligatory assignments, and a take-home exam (one week). Obligatory assignments must be completed and approved before the exam and in the same semester. An additional, limited, oral examination may be arranged in cases where this is necessary for the student evaluation. The course is open also for non-UiO students. It is only necessary to be physically present in Oslo for certain parts of the course.

General schedule for MBV-INFX410
Mon Tue Wed Thu Fri
Week 46 Lectures/

exercises

Lectures/

exercises

Lectures/

exercises

Lectures/

exercises

Lectures/

exercises

Week 47 Lectures/

exercises

Lectures/

exercises

Lectures/

exercises

Lectures/

exercises

Lectures/

exercises

Week 48 Obligatory

home assignment

Obligatory

home assignment

Obligatory

home assignment

Obligatory

home assignment

Hand in

home assignment

Week 49 Lectures/

exercises

Lectures/

exercises

Lectures/

exercises

Lectures/

exercises

Exam start

(home assignment)

Week 50 Exam

(home assignment)

Exam

(home assignment)

Exam

(home assignment)

Exam

(home assignment)

Exam end

(home assignment)

Computers/laptops, internet access, and UiO user account

All students are strongly encouraged to bring their own laptops.

  • It should be possible to connect the computer to the UiO wireless network
  • You must have a root/administrator password that gives you access to installing new software on the computer
  • Please bring an external mouse, and do not rely on touchpad/trackpad only
  • You must have a valid UiO user account and must be able to log onto a computer on the UiO network
  • Instructions on how to find your username and get a new password can be found here. To get a UiO username/password at the UiO helpdesk you need valid ID.

If you are struggling with anything of the above, in particular if you have forgotten your UiO user name/password or you do not have one, you must contact Jon (see contact details) as soon as possible, and at least one week before the start of the course.

On the first day of the course we will set up your laptop so that it can be used for the exercises/tutorials, the home exam and hopefully in your future work. How to get a reasonable setup is described here.

If you already are an expert programmer and Unix guru, go here.

Time and place (Rooms)

The teaching starts at 09:15 and we will end at latest 16:00. Most of the teaching will take place in room 1250 on the 1st floor of Biology Buiding (Kristine Bonnevies Hus, KB). This is a computer room with Desktop machines you can use. Some days we have to change rooms and use a seminar room without desktops. Therefore you have to bring your own laptops (or share with someone else) those days (see the detailed program). NB: November 17 and 18 we will be at Ole Johan Dahls hus (OJD) on the other side of the subway line in the Python seminar room on the second floor.

Detailed program

The times listed here are only tentative and may likely change. We will mix in small breaks here and there and try to have a lunch break between 12:00 - 13:00.

Detailed schedule for MBV-INFX410 2016
Week Monday Tuesday Wednesday Thursday Friday
46 Nov 14 Nov 15 Nov 16 Nov 17 Nov 18
Room 1250 KB

09:15 - 12:00

Course introduction. (lecture)

Introduction to bioinformatics and sequence databases (lecture)


12:00 - 13:00

Lunch

13:15 - 14:00

Setting up laptops

Basic Unix (lecture (slides by Jon K. Lærdahl))

14:15 - 16:00

Basic Unix (exercises)

Room 1250 KB

09:15 - 11:00

Genome browsers (lecture/ exercise)

and Jalview (lecture /demo)

11:15 - 12:00

Working with sequences

and databases (lectures)

12:00 - 13:00

Lunch

13:15 - 16:00

Applied sequence bioinformatics (exercise)

Room 4613 KB

09:15 - 12:00

Galaxy/Life Portal (lectures/exercises)

12:00 - 13:00

Lunch (we might have to skip this and finish early)

13:15 - 14:00

More Unix (lecture)

Room Python OJD

09:15 - 16:00

Python workshop

(lectures / exercises)

Room Python OJD

09:15 - 16:00

Python workshop

(lectures / exercises)

47 Nov 21 Nov 22 Nov 23 Nov 24 Nov 25
Room 1250 KB

09:15 - 16:00

Sequence searching and alignments

(lectures part1 part2, exercises (New exercise 32))

Room Python OJD

09:15 - 16:00

Structural Bioinformatics

(lectures and exercises)

Room Python OJD

09:15 - 16:00

Structural Bioinformatics

(lectures and exercises)

Room 4613 KB 9:15-12

Room 1250 KB 13:15-16

09:15 - 12:00

Docking and drug discovery

13:15 - 16:00

Practical Unix/Python exercise

Room 2203a KB 9:15 - 12

Room 1250 KB 13:15-16

Statistical epigenomics (& reproducibility).

Lectures / exercises

48 Nov 28 Nov 29 Nov 30 Dec 1 Dec 2
Obligatory home assignment Obligatory home assignment Obligatory home assignment Obligatory home assignment Hand in home assignment
49 Dec 5 Dec 6 Dec 7 Dec 8 Dec 9
Room 1250 KB

09:15 - 16:00

Analysing transcriptome data

(including R)

Room 1250 KB

09:15 - 16:00

Analysing transcriptome data

(including R)

Room 1250 KB

09:15 - 16:00

Next Generation Sequencing & variant calling

Room 4613 KB

Last course day

09:15 - 11:00

What does it mean to do bioinformatics?

Summary

Hand out exam
50 Dec 12 Dec 13 Dec 14 Dec 15 Dec 16
Home exam Home exam Home exam Home exam Hand in exam

Required reading material / Curriculum

The curriculum comprises all lectures, lecture handouts and exercises, in addition to the articles listed below:

Other good articles (not curriculum)

Contacts

Jon Bråte (Course coordinator) - e-mail: jon.brate@ibv.uio.no, phone: +47 922 44 582

Torill Rørtveit (Course administrator, registration) - e-mail: torill.rortveit@ibv.uio.no

Useful links

Trond Hasle Amundsen's Local guide to Linux and Unix

EMBnet Quick guide Unix

Useful command line one-liners by Stephen Turner

Jalview and Jalview refcard

UCSC Genome browser

Free UCSC Genome browser tutorial   from OpenHelix

Portal to Galaxy

Galaxy 101 and other Galaxy screencasts/tutorials

UiO Lifeportal and more information on the Lifeportal

The Genomic HyperBrowser

Links Directory from bioinformatics.ca

The 2015 Nucleic Acids Research Database Issue

The 2015 Nucleic Acids Research Web Server Issue

UiO and OUS Bioinformatics Core Facility