Difference between revisions of "MBV-INFX410 2017"

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== [https://wiki.uio.no/projects/clsi/index.php/MBV-INFX410 Bioinformatics for Molecular Biology] - 2016 ==
+
== [https://wiki.uio.no/projects/clsi/index.php/MBV-INFX410 Bioinformatics for Molecular Biology] - 2017 ==
 
 
 
=== Messages ===
 
=== 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.'''  
+
* 8 dec: Everyone should have received the exam by email. If not, you need to contact me (Jon). Good luck!
* '''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!'''  
+
* 24 nov: You should all have received the home assignment by email. If not you can also find the material [http://folk.uio.no/jonbra/MBV-INF4410_2017/Home_assignment/ here]
* '''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).'''
+
* 24 nov: See [http://folk.uio.no/jonbra/MBV-INF4410_2017/copy_files_ToFrom_freebee.txt here] for a short description on how to copy files between your local computer and Freebee using the command line.
* '''NB! Tuesday and Wednesday November 22 and 23 (Structural Biology) we will be in the Python room at Ole Johan Dahls Hus.'''
+
* '''20 nov: NB! In order to get everybody at an acceptable level in structural biology, before we start the Structural Bioinformatics lectures/exercises on Tuesday Nov 21, there will be a Structural Biology Review lecture in the morning, at 09:15. See handouts/slides  [[Structural Bioinformatics 2017|here]]. Take a look at these and decide if you need to follow the Structural Biology Review lecture. If you decide that you do not need this and that you already know ''everything'' we will go through in this lecture, come at 10:45 on Tuesday Nov 21.'''
* '''Tutorials for working with LifePortal/Galaxy:''' [https://usegalaxy.org/ usegalaxy.org]
+
* '''16 nov: NB! Notice room change for Python workshop 17 nov: Seminarrom U30 in [https://www.uio.no/om/finn-fram/omrader/blindern/bl20/ Helga Enghs Hus.] Go in the main door and down one floor.'''
* '''You need to install the following software on your laptops:'''
+
* '''''All students must be present at the start of the course, on November 13 at 09:15 in room 4613 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).'''''
 +
* '''All students must bring their own laptops, including an external mouse.'''
 +
* '''You need to install the following software on your laptops (we will help you with this):'''
 +
** Anaconda (https://www.anaconda.com/download/)
 
** PyMOL (https://www.pymol.org/)
 
** PyMOL (https://www.pymol.org/)
 
** JalView Desktop (http://www.jalview.org/) - could maybe also run by pressing the "Launch Jalview Desktop" button
 
** JalView Desktop (http://www.jalview.org/) - could maybe also run by pressing the "Launch Jalview Desktop" button
 
** PuTTY (http://www.putty.org/)
 
** PuTTY (http://www.putty.org/)
** R (https://www.r-project.org/)
+
** R (https://www.r-project.org/) '''Install''' '''inside Anaconda instead'''
** RStudio (https://www.rstudio.com/)
+
** RStudio (https://www.rstudio.com/) '''Install''' '''inside Anaconda instead'''
 
**'''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)]
 
**'''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 ===
 
=== 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.
+
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 (IBV) at the University of Oslo (UiO). Both MBV-INF4410 (M.Sc. level) and MBV-INF9410 (Ph.D. level) are 10 study point courses.  
  
 
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.
 
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.
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'''All students are strongly encouraged to bring their own laptops.'''  
 
'''All students are strongly encouraged to bring their own laptops.'''  
  
* It should be possible to connect the computer to the UiO wireless network
+
* It should be possible to connect the computer to the UiO wireless network (probably Eduroam)
 
* You must have a root/administrator password that gives you access to installing new software on the computer
 
* 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
 
* Please bring an '''external mouse''', and do not rely on touchpad/trackpad only
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=== Time and place (Rooms) ===
 
=== 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.
+
The teaching starts at 09:15 and we will end at latest 16:00. Most of the teaching will take place in room 4613 on the 4th floor of Biology Buiding (Kristine Bonnevies Hus, KB). Some days we have to change rooms so check the detailed program regularly.  
  
 
=== Detailed program ===
 
=== 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.
 
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"
 
{| class="wikitable"
|+Detailed schedule for MBV-INFX410 2016
+
|+Tentative schedule for MBV-INFX410 2017
 
!Week
 
!Week
 
!Monday
 
!Monday
Line 120: Line 121:
 
|-
 
|-
 
|<b>46</b>
 
|<b>46</b>
 +
| style="background: white; text-align: center;" |Nov 13
 
| style="background: white; text-align: center;" |Nov 14
 
| style="background: white; text-align: center;" |Nov 14
 
| style="background: white; text-align: center;" |Nov 15
 
| style="background: white; text-align: center;" |Nov 15
 
| style="background: white; text-align: center;" |Nov 16
 
| style="background: white; text-align: center;" |Nov 16
 
| style="background: white; text-align: center;" |Nov 17
 
| 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'''
+
| style="background: #cefdce; vertical-align: top;" |'''Room 4613'''  
09:15 - 12:00  
+
09:15 - 10:00  
 
    
 
    
Course introduction. [[Media:2016-11-14 01 Introduction reduced.pdf|(lecture)]]
+
Course introduction ([http://folk.uio.no/jonbra/MBV-INF4410_2017/lectures/2017-11-13_01_Introduction.pdf lecture])  
  
Introduction to bioinformatics and sequence databases [[Media:2016-11-14_02_Databases.pdf|(lecture)]]
+
10:15 - 11:00
 +
 
 +
 
 +
Sequence databases ([http://folk.uio.no/jonbra/MBV-INF4410_2017/lectures/2017-11-13_02_Databases.pdf lecture])
 +
 
 +
11:15 - 12:00
 +
 
 +
 
 +
Basic Unix ([http://folk.uio.no/jonbra/MBV-INF4410_2017/lectures/2017-11-13_03_Basic_Unix.pdf lecture])  
  
  
 
12:00 - 13:00  
 
12:00 - 13:00  
  
Lunch  
+
Lunch
 +
 
  
 
13:15 - 14:00  
 
13:15 - 14:00  
  
Setting up laptops  
+
Setting up laptops
  
Basic Unix [[Media:BasicUNIXLecture-15.pdf|(lecture (slides by Jon K. Lærdahl))]]   
 
  
 
14:15 - 16:00  
 
14:15 - 16:00  
  
Basic Unix [[Media:14_nov_UNIXBasics-exercise_JKL.docx|(exercises)]]
+
Basic Unix ([http://folk.uio.no/jonbra/MBV-INF4410_2017/exercises/2017-11-13_UNIXBasics-exercise.pdf exercises])  
| style="background: #cefdce; vertical-align: top;" |'''Room 1250 KB'''
+
| style="background: #cefdce; vertical-align: top;" |'''Room 3213'''  
 
09:15 - 11:00  
 
09:15 - 11:00  
  
Genome browsers ([[Media:2016-11-15_01_GenomeBrowsers.pdf|lecture]]/ [[Media:UCSC-GB Exercise-15.pdf|exercise]])  
+
Genome browsers ([http://folk.uio.no/jonbra/MBV-INF4410_2017/lectures/2017-11-14_01_GenomeBrowsers.pdf lecture] / [http://folk.uio.no/jonbra/MBV-INF4410_2017/exercises/2017-11-14-01_UCSC.pdf exercises]) and Jalview ([http://folk.uio.no/jonbra/MBV-INF4410_2017/lectures/2017-11-14_02_JalView.pdf lecture])  
 
+
and Jalview ([[Media:2016-11-15_JalView.pdf|lecture]] /demo)  
 
  
 
11:15 - 12:00
 
11:15 - 12:00
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Working with sequences  
 
Working with sequences  
  
and databases (lectures)
+
and databases ([http://folk.uio.no/jonbra/MBV-INF4410_2017/lectures/2017-11-14_03_Working_with_sequences.pdf lecture])
 +
 
  
 
12:00 - 13:00
 
12:00 - 13:00
  
Lunch
+
Lunch  
 +
 
  
 
13:15 - 16:00
 
13:15 - 16:00
  
Applied sequence bioinformatics [[Media:FerretTutorial-15.pdf|(exercise)]]
+
Applied sequence bioinformatics ([http://folk.uio.no/jonbra/MBV-INF4410_2017/exercises/2017-11-14-02_Applied_seq_bioinf.pdf exercises])  
| style="background: #cefdce; vertical-align: top;" |'''Room 4613 KB'''
+
| style="background: #cefdce; vertical-align: top;" |'''Room 4613'''
 
09:15 - 12:00
 
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]])
+
UiO LifePortal ([http://folk.uio.no/jonbra/MBV-INF4410_2017/lectures/2017-11-15_01_Lifeportal_course.pdf lecture])
 +
 
  
 
12:00 - 13:00
 
12:00 - 13:00
  
Lunch (we might have to skip this and finish early)   
+
Lunch        
  
13:15 - 14:00
 
  
More Unix ([[Media:2016-11-16_01_MoreUnix.pdf|lecture]])  
+
13:15 - 14:00   
 +
 
 +
More Unix ([http://folk.uio.no/jonbra/MBV-INF4410_2017/lectures/2017-11-15_02_MoreUnix.pdf lecture])  
  
| style="background: #cefdce; vertical-align: top;" |'''Room Python OJD'''
+
| style="background: #cefdce; vertical-align: top;" |'''Room 4424'''
 
09:15 - 16:00  
 
09:15 - 16:00  
  
Python workshop
+
[[Lectures / exercises|Python workshop]]
  
([[lectures / exercises]])
+
| style="background: #cefdce; vertical-align: top;" |'''NB! Notice room change: Seminarrom U30 Helga Enghs Hus (see [https://wiki.uio.no/projects/clsi/index.php?title=MBV-INFX410_2017#Messages Messages])'''
| style="background: #cefdce; vertical-align: top;" |'''Room Python OJD'''
+
 
09:15 - 16:00  
+
09:15 - 16:00
  
Python workshop
+
[[Lectures / exercises|Python workshop]]
  
([[lectures / exercises]])
 
 
|-
 
|-
 
|<b>47</b>
 
|<b>47</b>
 +
| style="background: white; text-align: center;" |Nov 20
 
| style="background: white; text-align: center;" |Nov 21
 
| style="background: white; text-align: center;" |Nov 21
 
| style="background: white; text-align: center;" |Nov 22
 
| style="background: white; text-align: center;" |Nov 22
 
| style="background: white; text-align: center;" |Nov 23
 
| style="background: white; text-align: center;" |Nov 23
 
| style="background: white; text-align: center;" |Nov 24
 
| 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'''
+
| style="background: #cefdce; vertical-align: top;" |'''Room 4613'''
 
09:15 - 16:00
 
09:15 - 16:00
 
   
 
   
Sequence searching and alignments  
+
Sequence searching and alignments ([http://folk.uio.no/jonbra/MBV-INF4410_2017/lectures/2017-11-20_mbvinf4410-bioinf.pdf lecture] / [http://folk.uio.no/jonbra/MBV-INF4410_2017/exercises/2017-11-20_AlignmentsAndMSAs.pdf exercises])
  
(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 4613'''
 
 
| style="background: #cefdce; vertical-align: top;" |'''Room Python OJD'''
 
 
09:15 - 16:00
 
09:15 - 16:00
  
[[Structural Bioinformatics 2016|Structural Bioinformatics]]
+
[[Structural Bioinformatics 2017|Structural Bioinformatics]]
  
(lectures and exercises)
+
| style="background: #cefdce; vertical-align: top;" |'''Room 4613'''
| style="background: #cefdce; vertical-align: top;" |'''Room Python OJD'''
 
 
09:15 - 16:00
 
09:15 - 16:00
  
[[Structural Bioinformatics 2016|Structural Bioinformatics]]
+
[[Structural Bioinformatics 2017|Structural Bioinformatics]]
  
(lectures and exercises)
+
| style="background: #cefdce; vertical-align: top;" |'''Room 4424'''
| style="background: #cefdce; vertical-align: top;" |'''Room 4613 KB 9:15-12'''
 
'''Room 1250 KB 13:15-16'''
 
  
 
09:15 - 12:00
 
09:15 - 12:00
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[[Docking and drug discovery]]
 
[[Docking and drug discovery]]
  
13:15 - 16:00
 
  
[[Practical Unix/Python 2015|Practical Unix/Python exercise]]
+
13:15 - 14:00
| style="background: #cefdce; vertical-align: top;" |'''Room 2203a KB 9:15 - 12'''
+
 
'''Room 1250 KB 13:15-16'''
+
[http://folk.uio.no/jonbra/MBV-INF4410_2017/exercises/2017-11-23_UNIX2-exercise.pdf Practical Unix/Python]
 +
 
 +
| style="background: #cefdce; vertical-align: top;" |'''Room 2203a'''
 +
 
 +
09:15 - 12:00
 +
 
 +
"Catch-up" / "Snublegruppe" (You can ask questions from the first two weeks)
  
[[Media:Statistical_genomics_2016.pdf|Statistical epigenomics (& reproducibility)]].
+
<span style="color:red">Hand out oblig</span>
  
Lectures / exercises
 
 
|-
 
|-
 
|<b>48</b>
 
|<b>48</b>
 +
| style="background: white; text-align: center;" |Nov 27
 
| style="background: white; text-align: center;" |Nov 28
 
| style="background: white; text-align: center;" |Nov 28
 
| style="background: white; text-align: center;" |Nov 29
 
| style="background: white; text-align: center;" |Nov 29
 
| style="background: white; text-align: center;" |Nov 30
 
| style="background: white; text-align: center;" |Nov 30
 
| style="background: white; text-align: center;" |Dec 1
 
| style="background: white; text-align: center;" |Dec 1
| style="background: white; text-align: center;" |Dec 2
 
 
|-
 
|-
 
|
 
|
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| 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
+
| style="background: #87CEFA; vertical-align: top;" |Obligatory home assignment
 
|-
 
|-
 
|<b>49</b>
 
|<b>49</b>
 +
| style="background: white; text-align: center;" |Dec 4
 
| style="background: white; text-align: center;" |Dec 5
 
| style="background: white; text-align: center;" |Dec 5
 
| style="background: white; text-align: center;" |Dec 6
 
| style="background: white; text-align: center;" |Dec 6
 
| style="background: white; text-align: center;" |Dec 7
 
| style="background: white; text-align: center;" |Dec 7
 
| style="background: white; text-align: center;" |Dec 8
 
| 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'''
+
| style="background: #cefdce; vertical-align: top;" |'''Room 4613'''
09:15 - 16:00
+
09:15 - 10:00
 +
 
 +
Introduction to Next Generation Sequencing ([http://folk.uio.no/jonbra/MBV-INF4410_2017/lectures/2017-12-04_HTSintro-Gregor.pdf lecture]) 
 +
 
 +
10:15 - 11:00
 +
 
 +
NGS applications + Fastq format ([http://folk.uio.no/jonbra/MBV-INF4410_2017/lectures/2017-12-04_02_NGS_Applications_Fastq.pdf lecture])
 +
 
 +
11:15 - 16:00
 +
 
 +
Introduction to Variant Calling + exercises ([http://folk.uio.no/jonbra/MBV-INF4410_2017/lectures/2017-12-04_03_VariantCalling.pdf lectures] / [https://github.com/jonbra/MBV-INFx410/blob/master/2017-variant_calling_exercise.md exercises])
 +
 
 +
| style="background: #cefdce; vertical-align: top;" |'''Room 4613'''
 +
09:15 - 10:00
 +
 
 +
Introduction to RNA-seq ([http://folk.uio.no/jonbra/MBV-INF4410_2017/lectures/2017-12-05_01_trancriptomics.pdf lecture])
  
[[Transcriptomics 2016|Analysing transcriptome data]]
+
10:15 - ca. 14:00
  
[[Transcriptomics 2016|(including R)]]
+
A general RNA-seq pipeline ([http://folk.uio.no/jonbra/MBV-INF4410_2017/lectures/2017-12-05_02_trancriptomics.pdf lectures] + [https://github.com/jonbra/MBV-INFx410/blob/master/2017-transcriptomics_exercise.md exercises])
| style="background: #cefdce; vertical-align: top;" |'''Room 1250 KB'''
 
09:15 - 16:00
 
  
[[Transcriptomics 2016|Analysing transcriptome data]]
+
| style="background: #cefdce; vertical-align: top;" |'''Room 4613'''
 +
09:15 - ca. 12:00
  
[[Transcriptomics 2016|(including R)]]
+
Introduction to R. Basic R commands and exercises. ([http://folk.uio.no/jonbra/MBV-INF4410_2017/lectures/2017-12-06_01_R_introduction.pdf lecture] / [http://folk.uio.no/jonbra/MBV-INF4410_2017/exercises/2017-12-06_Basic_R_Exercises.html exercises])
  
| style="background: #cefdce; vertical-align: top;" |'''Room 1250 KB'''
+
13:00 - ca. 14:30
09:15 - 16:00
 
  
[[Next Generation Sequencing & variant calling]]
+
Briefly about packages and RStudio ([http://folk.uio.no/jonbra/MBV-INF4410_2017/lectures/2017-12-06_02_RStudio_more.pdf lecture]). Installing RStudio and [http://folk.uio.no/jonbra/MBV-INF4410_2017/R/2017-11-06_Setting_up_RStudio.html necessary packages].
| style="background: #cefdce; vertical-align: top;" |'''Room 4613 KB'''
 
Last course day
 
  
 +
| style="background: #cefdce; vertical-align: top;" |'''Room 4613'''
 
09:15 - 11:00
 
09:15 - 11:00
  
[[Media:161208 MBV-INFX410 LexNederbragt final red.pdf|What does it mean to do bioinformatics?]]
+
RNA-seq: Experimental design and differential gene expression ([http://folk.uio.no/jonbra/MBV-INF4410_2017/lectures/2017-12-07_trancriptomics.pdf lecture]).
 +
 
 +
11:15 - ca. 14:00
 +
 
 +
Analysing RNA-seq data in R and DEseq2 ([http://folk.uio.no/jonbra/MBV-INF4410_2017/exercises/2017-12-07_R_DESeq2_exercises_without_results.html demo/exercises] - [http://folk.uio.no/jonbra/MBV-INF4410_2017/exercises/2017-12-07_R_DESeq2_exercises_with_results.html today's DESeq2 commands with solutions and comments])
 +
| style="background: #cefdce; vertical-align: top;" |'''Room 4613'''
 +
09:15 - 16:00
 +
 
 +
[http://folk.uio.no/jonbra/MBV-INF4410_2017/lectures/2017-12-08_Statistical_epigenomics.pdf Statistical epigenomics]
 +
 
 +
<span style="color:red">Hand out exam</span>
  
[[Media:2016-12-08 Summary.pdf|Summary]]
 
| style="background: salmon; vertical-align: top;" |Hand out exam
 
 
|-
 
|-
 
|<b>50</b>
 
|<b>50</b>
 +
| style="background: white; text-align: center;" |Dec 11
 
| style="background: white; text-align: center;" |Dec 12
 
| style="background: white; text-align: center;" |Dec 12
 
| style="background: white; text-align: center;" |Dec 13
 
| style="background: white; text-align: center;" |Dec 13
 
| style="background: white; text-align: center;" |Dec 14
 
| style="background: white; text-align: center;" |Dec 14
 
| style="background: white; text-align: center;" |Dec 15
 
| style="background: white; text-align: center;" |Dec 15
| style="background: white; text-align: center;" |Dec 16
 
 
|-
 
|-
 
|
 
|
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|}
 
|}
  
=== Required reading material / Curriculum ===
+
=== Recommended reading material / curriculum ===
 
The curriculum comprises all lectures, lecture handouts and exercises, in addition to the articles listed below:
 
The curriculum comprises all lectures, lecture handouts and exercises, in addition to the articles listed below:
 
+
*J. R. A. Hutchins, "Genomic Database Searching", in [https://link.springer.com/protocol/10.1007%2F978-1-4939-6622-6_10 Bioinformatics pp 225-269. Springer (2017)].
 
*R.F. Service, "Biology's dry future", [http://dx.doi.org/10.1126/science.342.6155.186 Science <b>342</b>, 186 (2013)]
 
*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]
 
*EMBnet, [http://www.embnet.org/sites/default/files/quickguides/guideUNIX.pdf A Quick Guide to UNIX]
Line 322: Line 352:
 
*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)]
 
*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)]
 
*M.L. Mertzker, "Sequencing technologies - the next generation", [http://dx.doi.org/10.1038/nrg2626 Nat. Rev. Genet. <b>11</b>, 31 (2010)]
 +
*Nielsen, R. ''et al''., "Genotype and SNP calling from next-generation sequencing data", [https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3593722/ Nat Rev Genet. (2011)].
 
*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)]
 
*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)]
 
*N. Nagarajan & M. Pop, "Sequence assembly demystified", [http://dx.doi.org/10.1038/nrg3367 Nat. Rev. Genet. <b>14</b>, 157 (2013)]
Line 335: Line 366:
  
 
=== Useful links ===
 
=== Useful links ===
 +
 +
[http://swcarpentry.github.io/shell-novice/reference/ Very useful reference guide on the Unix shell (created by Software Carpentry)]
  
 
Trond Hasle Amundsen's [http://www.uio.no/tjenester/it/maskin/linux/hjelp/tips/guide.html Local guide to Linux and Unix]
 
Trond Hasle Amundsen's [http://www.uio.no/tjenester/it/maskin/linux/hjelp/tips/guide.html Local guide to Linux and Unix]
 +
 +
[https://github.com/EbookFoundation/free-programming-books/blob/master/free-programming-books.md#python Tons of free e-books on Python]
  
 
EMBnet [http://www.embnet.org/sites/default/files/quickguides/guideUNIX.pdf Quick guide 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
 
[https://github.com/stephenturner/oneliners Useful command line one-liners] by Stephen Turner
 +
 +
[https://github.com/mcandre/cheatsheets/blob/master/nano.md Nano text editor cheat sheet]
 +
 +
[https://github.com/EbookFoundation/free-programming-books/blob/master/free-programming-books.md Tons of free programming books, about anything really.]
  
 
[http://www.jalview.org Jalview] and Jalview [http://www.jalview.org/refcard.pdf refcard]
 
[http://www.jalview.org Jalview] and Jalview [http://www.jalview.org/refcard.pdf refcard]
Line 358: Line 397:
 
[http://bioinformatics.ca/links_directory Links Directory] from bioinformatics.ca
 
[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 2017 Nucleic Acids Research [https://academic.oup.com/nar/issue/45/D1 Database Issue]
  
The 2015 Nucleic Acids Research [http://nar.oxfordjournals.org/content/43/W1.toc Web Server Issue]
+
The 2015 Nucleic Acids Research [https://academic.oup.com/nar/issue/45/W1 Web Server Issue]
  
 
UiO and OUS [http://core.rr-research.no/bioinformatics Bioinformatics Core Facility]
 
UiO and OUS [http://core.rr-research.no/bioinformatics Bioinformatics Core Facility]

Latest revision as of 15:54, 8 December 2017

Bioinformatics for Molecular Biology - 2017

Messages

  • 8 dec: Everyone should have received the exam by email. If not, you need to contact me (Jon). Good luck!
  • 24 nov: You should all have received the home assignment by email. If not you can also find the material here
  • 24 nov: See here for a short description on how to copy files between your local computer and Freebee using the command line.
  • 20 nov: NB! In order to get everybody at an acceptable level in structural biology, before we start the Structural Bioinformatics lectures/exercises on Tuesday Nov 21, there will be a Structural Biology Review lecture in the morning, at 09:15. See handouts/slides here. Take a look at these and decide if you need to follow the Structural Biology Review lecture. If you decide that you do not need this and that you already know everything we will go through in this lecture, come at 10:45 on Tuesday Nov 21.
  • 16 nov: NB! Notice room change for Python workshop 17 nov: Seminarrom U30 in Helga Enghs Hus. Go in the main door and down one floor.
  • All students must be present at the start of the course, on November 13 at 09:15 in room 4613 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).
  • All students must bring their own laptops, including an external mouse.
  • You need to install the following software on your laptops (we will help you with this):

Course information

This is the wiki for the courses MBV-INF4410 and MBV-INF9410 offered by the Department of Biosciences (IBV) at the University of Oslo (UiO). Both MBV-INF4410 (M.Sc. level) and MBV-INF9410 (Ph.D. level) are 10 study point courses.

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 (probably Eduroam)
  • 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 4613 on the 4th floor of Biology Buiding (Kristine Bonnevies Hus, KB). Some days we have to change rooms so check the detailed program regularly.

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.

Tentative schedule for MBV-INFX410 2017
Week Monday Tuesday Wednesday Thursday Friday
46 Nov 13 Nov 14 Nov 15 Nov 16 Nov 17
Room 4613

09:15 - 10:00

Course introduction (lecture)

10:15 - 11:00


Sequence databases (lecture)

11:15 - 12:00


Basic Unix (lecture)


12:00 - 13:00

Lunch


13:15 - 14:00

Setting up laptops


14:15 - 16:00

Basic Unix (exercises)

Room 3213

09:15 - 11:00

Genome browsers (lecture / exercises) and Jalview (lecture)


11:15 - 12:00

Working with sequences

and databases (lecture)


12:00 - 13:00

Lunch


13:15 - 16:00

Applied sequence bioinformatics (exercises)

Room 4613

09:15 - 12:00

UiO LifePortal (lecture)


12:00 - 13:00

Lunch


13:15 - 14:00

More Unix (lecture)

Room 4424

09:15 - 16:00

Python workshop

NB! Notice room change: Seminarrom U30 Helga Enghs Hus (see Messages)

09:15 - 16:00

Python workshop

47 Nov 20 Nov 21 Nov 22 Nov 23 Nov 24
Room 4613

09:15 - 16:00

Sequence searching and alignments (lecture / exercises)

Room 4613

09:15 - 16:00

Structural Bioinformatics

Room 4613

09:15 - 16:00

Structural Bioinformatics

Room 4424

09:15 - 12:00

Docking and drug discovery


13:15 - 14:00

Practical Unix/Python

Room 2203a

09:15 - 12:00

"Catch-up" / "Snublegruppe" (You can ask questions from the first two weeks)

Hand out oblig

48 Nov 27 Nov 28 Nov 29 Nov 30 Dec 1
Obligatory home assignment Obligatory home assignment Obligatory home assignment Obligatory home assignment Obligatory home assignment
49 Dec 4 Dec 5 Dec 6 Dec 7 Dec 8
Room 4613

09:15 - 10:00

Introduction to Next Generation Sequencing (lecture)

10:15 - 11:00

NGS applications + Fastq format (lecture)

11:15 - 16:00

Introduction to Variant Calling + exercises (lectures / exercises)

Room 4613

09:15 - 10:00

Introduction to RNA-seq (lecture)

10:15 - ca. 14:00

A general RNA-seq pipeline (lectures + exercises)

Room 4613

09:15 - ca. 12:00

Introduction to R. Basic R commands and exercises. (lecture / exercises)

13:00 - ca. 14:30

Briefly about packages and RStudio (lecture). Installing RStudio and necessary packages.

Room 4613

09:15 - 11:00

RNA-seq: Experimental design and differential gene expression (lecture).

11:15 - ca. 14:00

Analysing RNA-seq data in R and DEseq2 (demo/exercises - today's DESeq2 commands with solutions and comments)

Room 4613

09:15 - 16:00

Statistical epigenomics

Hand out exam

50 Dec 11 Dec 12 Dec 13 Dec 14 Dec 15
Home exam Home exam Home exam Home exam Hand in exam

Recommended 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

Very useful reference guide on the Unix shell (created by Software Carpentry)

Trond Hasle Amundsen's Local guide to Linux and Unix

Tons of free e-books on Python

EMBnet Quick guide Unix

Useful command line one-liners by Stephen Turner

Nano text editor cheat sheet

Tons of free programming books, about anything really.

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 2017 Nucleic Acids Research Database Issue

The 2015 Nucleic Acids Research Web Server Issue

UiO and OUS Bioinformatics Core Facility