Difference between revisions of "MBV-INFX410 2018"

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(Bioinformatics for Molecular Biology - 2018)
 
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== Bioinformatics for Molecular Biology - 2018 ==
 
== Bioinformatics for Molecular Biology - 2018 ==
 
=== Messages ===
 
=== Messages ===
 +
* '''December 7: Everyone should have gotten the exam by email. If you haven't received it, please send me a mail ASAP.'''
 +
* '''You can find the home assignment [http://folk.uio.no/jonbra/MBV-INF4410_2018/Home_assignment/Oblig_MBV-INFx410-2018.pdf here] and a useful python script [http://folk.uio.no/jonbra/MBV-INF4410_2018/Home_assignment/print_lengths.py here].'''
 +
* '''November 21: We will be in room 4613 all day.'''
 +
* '''November 22 will be a short summary of the Unix and Python material we have learned so far, including a short exercise showing what you are expected to accomplish. The material is made available so you can take a look and if it is very easy it is not so important to attend that day.'''
 +
* '''Notice that some days we will use a different room than 4424. See the [[MBV-INFX410 2018|Detailed program]]'''
 +
 
* '''You need to install the following software on your laptops:'''
 
* '''You need to install the following software on your laptops:'''
 
** PyMOL (https://www.pymol.org/). PyMOL is free for students but you have to register for a license. Go to "New users" and "Buy license" and click on Student/Teacher ([https://pymol.org/edu/?q=educational or click here])
 
** PyMOL (https://www.pymol.org/). PyMOL is free for students but you have to register for a license. Go to "New users" and "Buy license" and click on Student/Teacher ([https://pymol.org/edu/?q=educational or click here])
 
** R (https://www.r-project.org/)
 
** R (https://www.r-project.org/)
 
** RStudio (https://www.rstudio.com/)
 
** RStudio (https://www.rstudio.com/)
** Windows users only: PuTTY (http://www.putty.org/). Optional: In addition to PuTTY, windows users can also install [https://www.cygwin.com/ Cygwin] if you want to have a Unix-style environment also locally on your computer.
+
** Windows users only: PuTTY (http://www.putty.org/). Optional: In addition to PuTTY, windows users can also install [https://www.cygwin.com/ Cygwin] if you want to have a Unix-style environment also locally on your computer. [https://gitforwindows.org/ Git Bash] can be a nice alternative to Cygwin.
 
**'''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)]
  
Line 97: Line 103:
  
 
=== Time and place (Rooms) ===
 
=== Time and place (Rooms) ===
The teaching starts at 09:15 and we will end at latest 16:00. All of the teaching will take place in '''room 4424 on the 4th floor of [https://www.uio.no/om/finn-fram/omrader/blindern/bl18/ Biology Buiding]''' [https://www.uio.no/om/finn-fram/omrader/blindern/bl18/ (Kristine Bonnevies Hus, KB).]   
+
The teaching starts at 09:15 and we will end at latest 16:00. Most of the teaching will take place in '''room 4424 on the 4th floor of [https://www.uio.no/om/finn-fram/omrader/blindern/bl18/ Biology Buiding]''' [https://www.uio.no/om/finn-fram/omrader/blindern/bl18/ (Kristine Bonnevies Hus, KB).]But check the program because changes will happen..    
  
 
=== Detailed program ===
 
=== Detailed program ===
Line 122: Line 128:
 
09:15 - 10:00  
 
09:15 - 10:00  
 
    
 
    
Course introduction  
+
Course introduction ([http://folk.uio.no/jonbra/MBV-INF4410_2018/lectures/2018-11-12_01_Introduction.pdf lecture])
 +
       
  
10:15 - 11:00  
+
10:15 - 11:00
 +
Sequence databases ([http://folk.uio.no/jonbra/MBV-INF4410_2018/lectures/2018-11-12_02_Databases.pdf lecture])   
  
 
Sequence databases
 
  
 
11:15 - 12:00
 
11:15 - 12:00
 
+
Basic Unix ([http://folk.uio.no/jonbra/MBV-INF4410_2018/lectures/2018-11-12_03_Basic_Unix.pdf lecture])
 
 
Basic Unix  
 
  
  
Line 147: Line 151:
 
14:15 - 16:00  
 
14:15 - 16:00  
  
Basic Unix   
+
Basic Unix ([http://folk.uio.no/jonbra/MBV-INF4410_2018/exercises/2018-11-12_UNIXBasics-exercise.pdf excercises])  
 
| style="background: #cefdce; vertical-align: top;" |  
 
| style="background: #cefdce; vertical-align: top;" |  
 
09:15 - 11:00  
 
09:15 - 11:00  
  
Genome browsers  
+
Genome browsers ([http://folk.uio.no/jonbra/MBV-INF4410_2018/lectures/2018-11-13_01_GenomeBrowsers.pdf lecture] / [http://folk.uio.no/jonbra/MBV-INF4410_2018/exercises/2018-11-13-01_UCSC.pdf exercises]) and Jalview ([http://folk.uio.no/jonbra/MBV-INF4410_2018/lectures/2018-11-13_02_JalView.pdf lecture]) 
 
   
 
   
  
Line 158: Line 162:
 
Working with sequences  
 
Working with sequences  
  
and databases  
+
and databases ([http://folk.uio.no/jonbra/MBV-INF4410_2018/lectures/2018-11-13_03_Working_with_sequences.pdf lecture])
  
  
Line 168: Line 172:
 
13:15 - 16:00
 
13:15 - 16:00
  
Applied sequence bioinformatics   
+
Applied sequence bioinformatics ([http://folk.uio.no/jonbra/MBV-INF4410_2018/exercises/2018-11-13-02_Applied_seq_bioinf.pdf exercises])  
 
| style="background: #cefdce; vertical-align: top;" |
 
| style="background: #cefdce; vertical-align: top;" |
09:15 - 12:00
+
10:15 - 11:00 ('''NB! Note start time''')
 
 
UiO LifePortal
 
 
 
  
12:00 - 13:00
+
More Unix ([http://folk.uio.no/jonbra/MBV-INF4410_2018/lectures/2018-11-14_01_MoreUnix.pdf lecture])
  
Lunch       
 
  
 +
11:15 - 15:00
  
13:15 - 14:00   
+
Introduction to R,             
  
More Unix 
+
Basic R commands and exercises. ([http://folk.uio.no/jonbra/MBV-INF4410_2018/lectures/2018-11-14_02_R_introduction.pdf lecture], [http://folk.uio.no/jonbra/MBV-INF4410_2018/exercises/2018-11-14_Basic_R_Exercises.html exercises])           
  
 
| style="background: #cefdce; vertical-align: top;" |
 
| style="background: #cefdce; vertical-align: top;" |
 
09:15 - 16:00  
 
09:15 - 16:00  
  
Python workshop
+
[[Python workshop 2018|Python workshop]]
  
 
| style="background: #cefdce; vertical-align: top;" |
 
| style="background: #cefdce; vertical-align: top;" |
 
09:15 - 16:00
 
09:15 - 16:00
  
Python workshop
+
[[Python workshop 2018|Python workshop]]
  
 
|-
 
|-
Line 204: Line 205:
 
|
 
|
 
| style="background: #cefdce; vertical-align: top;" |
 
| 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_2018/lectures/2018-11-19_01_Rognes_mbvinf4410-bioinf-2018.pdf lecture], [http://folk.uio.no/jonbra/MBV-INF4410_2018/exercises/2018-11-19_AlignmentsAndMSAs.pdf exercises])  
  
 
| style="background: #cefdce; vertical-align: top;" |
 
| style="background: #cefdce; vertical-align: top;" |
 +
'''Room 3213'''
 +
 
09:15 - 16:00
 
09:15 - 16:00
  
Structural Bioinformatics
+
[[Structural Bioinformatics 2018|Structural Bioinformatics]]
  
 
| style="background: #cefdce; vertical-align: top;" |
 
| style="background: #cefdce; vertical-align: top;" |
 +
'''Room 4424 09:15 - 11:00'''
 +
 +
'''Room 3213 11:15 - 16:00'''
 +
 
09:15 - 16:00
 
09:15 - 16:00
  
Structural Bioinformatics
+
[[Structural Bioinformatics 2018|Structural Bioinformatics]]
  
 
| style="background: #cefdce; vertical-align: top;" |
 
| style="background: #cefdce; vertical-align: top;" |
To be announced
+
'''Room 4424'''
 +
 
 +
09:15 - 12:00
 +
 
 +
Short summary of Unix/Python ([http://folk.uio.no/jonbra/MBV-INF4410_2018/lectures/2018-11-22_UnixPythonSummary.pdf lecture])
 +
 
 +
[http://folk.uio.no/jonbra/MBV-INF4410_2018/exercises/2018-11-22_UNIX2-exercise.pdf Brief practical exercise]
  
 
| style="background: #cefdce; vertical-align: top;" |
 
| style="background: #cefdce; vertical-align: top;" |
To be announced
+
'''Rom 3213'''
 +
 
 +
09:15 - 16:00
 +
 
 +
Statistical epigenomics ([http://folk.uio.no/jonbra/MBV-INF4410_2018/lectures/2018-11-23_Statistical_genomics_Grytten.pdf lecture])
  
 
<span style="color:red">Hand out oblig</span>
 
<span style="color:red">Hand out oblig</span>
Line 250: Line 269:
 
|
 
|
 
| style="background: #cefdce; vertical-align: top;" |
 
| style="background: #cefdce; vertical-align: top;" |
To be announced
+
'''Room 4613'''
 +
 
 +
09:15 - 12:00
 +
 
 +
Docking and drug discovery ([http://folk.uio.no/jonbra/MBV-INF4410_2018/lectures/2018-12-03_MBV-INF-x410-Fall2018-handout.pdf lecture], [http://folk.uio.no/jonbra/MBV-INF4410_2018/exercises/2018-12-03_Tutorial.pdf tutorial/exercises]). [http://folk.uio.no/jonkl/StuffForMBV-INFx410/DockingFiles.tar.gz pdb-files]. ([http://folk.uio.no/jonbra/MBV-INF4410_2018/DockingFiles.zip zip files]) [http://folk.uio.no/jonbra/MBV-INF4410_2018/Tutorial-fasit.pdf Tutorial] answers.
 +
 
 +
13:00 - 16:00
 +
 
 +
Briefly about packages and RStudio ([http://folk.uio.no/jonbra/MBV-INF4410_2018/lectures/2018-12-03_01_RStudio_more.pdf lecture]).
 +
 
 +
[http://folk.uio.no/jonbra/MBV-INF4410_2018/R/2018-12-03_Setting_up_RStudio.html Installing RStudio and necessary packages].
 +
 
 +
[http://folk.uio.no/jonbra/MBV-INF4410_2018/R/More_on_csv.html Importing and writing data files].
 +
 
 +
[[Installing R packages on Freebee]]
  
 
| style="background: #cefdce; vertical-align: top;" |
 
| style="background: #cefdce; vertical-align: top;" |
Next Generation Sequencing, genomics, transcriptomics, Basic R
+
'''Room 4613'''
 +
 
 +
09:15 - 10:00
 +
 
 +
Introduction to Next Generation Sequencing ([http://folk.uio.no/jonbra/MBV-INF4410_2018/lectures/2018-12-04_01_HTSintro-UiO-Dec2018-v1.pdf lecture])
 +
 
 +
10:15 - 11:00
 +
 
 +
NGS applications + Fastq format ([http://folk.uio.no/jonbra/MBV-INF4410_2018/lectures/2018-12-04_02_NGS_Applications_Fastq.pdf lecture])
 +
 
 +
11:15 - 16:00
 +
 
 +
Introduction to Variant Calling ([http://folk.uio.no/jonbra/MBV-INF4410_2018/lectures/2018-12-04_03_VariantCalling.pdf lecture]) + ([https://github.com/jonbra/MBV-INFx410/blob/master/2017-variant_calling_exercise.md exercises]).
  
 
| style="background: #cefdce; vertical-align: top;" |
 
| style="background: #cefdce; vertical-align: top;" |
Next Generation Sequencing, genomics, transcriptomics, Basic R
+
'''Room 4613'''
 +
 
 +
09:15 - 10:00
 +
 
 +
Introduction to RNA-seq ([http://folk.uio.no/jonbra/MBV-INF4410_2018/lectures/2018-12-05_01_transcriptomics.pdf lecture])
 +
 
 +
10:15 - 14:00 (maybe)
 +
 
 +
A general RNA-seq pipeline ([http://folk.uio.no/jonbra/MBV-INF4410_2018/lectures/2018-12-05_02_transcriptomics.pdf lecture] + [https://github.com/jonbra/MBV-INFx410/blob/master/2018-transcriptomics_exercise.md exercises])
  
 
| style="background: #cefdce; vertical-align: top;" |
 
| style="background: #cefdce; vertical-align: top;" |
Next Generation Sequencing, genomics, transcriptomics, Basic R
+
'''Room 4613'''
 +
 
 +
09:15 - 11:00
 +
 
 +
RNA-seq: Experimental design and differential gene expression ([http://folk.uio.no/jonbra/MBV-INF4410_2018/lectures/2018-12-06_trancriptomics.pdf lecture/demo]).
 +
 
 +
11:15 - ca. 14:00
 +
 
 +
Analysing RNA-seq data in R and DEseq2 ([http://folk.uio.no/jonbra/MBV-INF4410_2018/exercises/2018-12-06_R_DESeq2_exercises_without_results.html exercises])
  
 
| style="background: #cefdce; vertical-align: top;" |
 
| style="background: #cefdce; vertical-align: top;" |
To be announced
+
'''Room 4613'''
 +
 
 +
09:15 - 12:00
 +
 
 +
UiO LifePortal ([http://folk.uio.no/sabryr/MBV-INF4410_2018.pdf slides])
 +
 
 +
13:00 - 14:00
 +
 
 +
Catch-up ("Snublegruppe")
  
 
<span style="color:red">Hand out exam</span>
 
<span style="color:red">Hand out exam</span>
Line 283: Line 352:
  
 
===Recommended 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. The articles listed below are only recommended but not mandatory:
 
*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)].
 
*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)]
Line 316: Line 385:
  
 
=== Useful links ===
 
=== Useful links ===
 +
 +
[https://swirlstats.com/ Learn R, using R (swirl)]
  
 
[http://swcarpentry.github.io/shell-novice/reference/ Very useful reference guide on the Unix shell (created by Software Carpentry)]
 
[http://swcarpentry.github.io/shell-novice/reference/ Very useful reference guide on the Unix shell (created by Software Carpentry)]

Latest revision as of 15:24, 7 December 2018

Bioinformatics for Molecular Biology - 2018

Messages

  • December 7: Everyone should have gotten the exam by email. If you haven't received it, please send me a mail ASAP.
  • You can find the home assignment here and a useful python script here.
  • November 21: We will be in room 4613 all day.
  • November 22 will be a short summary of the Unix and Python material we have learned so far, including a short exercise showing what you are expected to accomplish. The material is made available so you can take a look and if it is very easy it is not so important to attend that day.
  • Notice that some days we will use a different room than 4424. See the Detailed program

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 (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 username/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 4424 on the 4th floor of Biology Buiding (Kristine Bonnevies Hus, KB).But check the program because changes will happen..

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 2018
Week Monday Tuesday Wednesday Thursday Friday
46 Nov 12 Nov 13 Nov 14 Nov 15 Nov 16

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 (excercises)

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)

10:15 - 11:00 (NB! Note start time)

More Unix (lecture)


11:15 - 15:00

Introduction to R,

Basic R commands and exercises. (lecture, exercises)

09:15 - 16:00

Python workshop

09:15 - 16:00

Python workshop

47 Nov 19 Nov 20 Nov 21 Nov 22 Nov 23

Room 4613

09:15 - 16:00

Sequence searching and alignments (lecture, exercises)

Room 3213

09:15 - 16:00

Structural Bioinformatics

Room 4424 09:15 - 11:00

Room 3213 11:15 - 16:00

09:15 - 16:00

Structural Bioinformatics

Room 4424

09:15 - 12:00

Short summary of Unix/Python (lecture)

Brief practical exercise

Rom 3213

09:15 - 16:00

Statistical epigenomics (lecture)

Hand out oblig

48 Nov 26 Nov 27 Nov 28 Nov 29 Nov 30
Obligatory home assignment Obligatory home assignment Obligatory home assignment Obligatory home assignment Obligatory home assignment
49 Dec 3 Dec 4 Dec 5 Dec 6 Dec 7

Room 4613

09:15 - 12:00

Docking and drug discovery (lecture, tutorial/exercises). pdb-files. (zip files) Tutorial answers.

13:00 - 16:00

Briefly about packages and RStudio (lecture).

Installing RStudio and necessary packages.

Importing and writing data files.

Installing R packages on Freebee

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 (lecture) + (exercises).

Room 4613

09:15 - 10:00

Introduction to RNA-seq (lecture)

10:15 - 14:00 (maybe)

A general RNA-seq pipeline (lecture + exercises)

Room 4613

09:15 - 11:00

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

11:15 - ca. 14:00

Analysing RNA-seq data in R and DEseq2 (exercises)

Room 4613

09:15 - 12:00

UiO LifePortal (slides)

13:00 - 14:00

Catch-up ("Snublegruppe")

Hand out exam

50 Dec 10 Dec 11 Dec 12 Dec 13 Dec 14
Home exam Home exam Home exam Home exam Hand in exam

Recommended reading material / curriculum

The curriculum comprises all lectures, lecture handouts and exercises. The articles listed below are only recommended but not mandatory:

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

Learn R, using R (swirl)

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

Nice introductory eBook about statistics for biology and introduction to R (including downloadable R scripts)