Difference between revisions of "MBV-INFX410 2018"

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To be announced
 
To be announced
{| class="wikitable"
 
|+Tentative schedule for MBV-INFX410 2017
 
!Week
 
!Monday
 
!Tuesday
 
!Wednesday
 
!Thursday
 
!Friday
 
|-
 
|<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 15
 
| style="background: white; text-align: center;" |Nov 16
 
| style="background: white; text-align: center;" |Nov 17
 
|-
 
|
 
| style="background: #cefdce; vertical-align: top;" |'''Room 4613'''
 
09:15 - 10:00
 
 
 
Course introduction ([http://folk.uio.no/jonbra/MBV-INF4410_2017/lectures/2017-11-13_01_Introduction.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
 
 
Lunch 
 
 
 
13:15 - 14:00
 
 
Setting up laptops 
 
 
 
14:15 - 16:00
 
 
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 3213'''
 
09:15 - 11:00
 
 
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]) 
 
 
 
11:15 - 12:00
 
 
Working with sequences
 
 
and databases ([http://folk.uio.no/jonbra/MBV-INF4410_2017/lectures/2017-11-14_03_Working_with_sequences.pdf lecture])
 
 
 
12:00 - 13:00
 
 
Lunch   
 
 
 
13:15 - 16:00
 
 
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'''
 
09:15 - 12:00
 
 
UiO LifePortal ([http://folk.uio.no/jonbra/MBV-INF4410_2017/lectures/2017-11-15_01_Lifeportal_course.pdf lecture])
 
 
 
12:00 - 13:00
 
 
Lunch       
 
 
 
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 4424'''
 
09:15 - 16:00
 
 
[[Lectures / exercises|Python workshop]]
 
 
| 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])'''
 
 
09:15 - 16:00
 
 
[[Lectures / exercises|Python workshop]]
 
 
|-
 
|<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 22
 
| style="background: white; text-align: center;" |Nov 23
 
| style="background: white; text-align: center;" |Nov 24
 
|-
 
|
 
| style="background: #cefdce; vertical-align: top;" |'''Room 4613'''
 
09:15 - 16:00
 
 
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])
 
 
| style="background: #cefdce; vertical-align: top;" |'''Room 4613'''
 
09:15 - 16:00
 
 
[[Structural Bioinformatics 2017|Structural Bioinformatics]]
 
 
| style="background: #cefdce; vertical-align: top;" |'''Room 4613'''
 
09:15 - 16:00
 
 
[[Structural Bioinformatics 2017|Structural Bioinformatics]]
 
 
| style="background: #cefdce; vertical-align: top;" |'''Room 4424'''
 
 
09:15 - 12:00
 
 
[[Docking and drug discovery]]
 
 
 
13:15 - 14:00
 
 
[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)
 
 
<span style="color:red">Hand out oblig</span>
 
 
|-
 
|<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 29
 
| style="background: white; text-align: center;" |Nov 30
 
| style="background: white; text-align: center;" |Dec 1
 
|-
 
|
 
| 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;" |Obligatory home assignment
 
|-
 
|<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 6
 
| style="background: white; text-align: center;" |Dec 7
 
| style="background: white; text-align: center;" |Dec 8
 
|-
 
|
 
| style="background: #cefdce; vertical-align: top;" |'''Room 4613'''
 
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])
 
 
10:15 - ca. 14:00
 
 
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 4613'''
 
09:15 - ca. 12:00
 
 
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])
 
 
13:00 - ca. 14:30
 
 
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'''
 
09:15 - 11:00
 
 
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>
 
 
|-
 
|<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 13
 
| style="background: white; text-align: center;" |Dec 14
 
| style="background: white; text-align: center;" |Dec 15
 
|-
 
|
 
| 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
 
|}
 
  
 
===Recommended reading material / curriculum ===
 
===Recommended reading material / curriculum ===

Revision as of 11:16, 29 August 2018

Bioinformatics for Molecular Biology - 2018

Messages

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. All of the teaching will take place in room 4424 on the 4th floor of Biology Buiding (Kristine Bonnevies Hus, KB).

Detailed program

To be announced


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