Difference between revisions of "MBV-INFX410 2017"

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=== 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.
 
{| class="wikitable"
 
|+Detailed schedule for MBV-INFX410 2016
 
!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 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 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 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 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;" |Hand in 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 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 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
 
|}
 
  
 
=== Required reading material / Curriculum ===
 
=== Required reading material / Curriculum ===

Revision as of 08:13, 20 September 2017

NB!! NOT UPDATED YET!! Bioinformatics for Molecular Biology - 2017

NB!!!! Not updated for 2017!!!!

Messages

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 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

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