Difference between revisions of "MBV-INFX410 2016"

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(Bioinformatics for Molecular Biology - 2016)
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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] - 2016 ==
<span style="background:yellow">'''''UNDER CONSTRUCTION!!!!!'''''</span>
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<span style="background:yellow">'''''Under construction! Changes will happen'''''</span>
  
 
'''''All students must be present at the start of the course, at 09:15, on November 14. 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 be present at the start of the course, at 09:15, on November 14. 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).'''''
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|style="background: white; vertical-align: top;"|09:15 - 11:00:
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|style="background: white; vertical-align: top;"|09:15 - 10:00  
Course introduction (lecture)
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Course introduction  
  
11:15 - 13:00:
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<nowiki> </nowiki>10:15 - 12:00  
  
Biological databases,
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Sequence databases
  
Unix (lectures/exercises)
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12:00 - 13:00
  
14:15 - 16:00:
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Lunch 
  
Basic Unix (excercises)
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13:15 - 14:00
|style="background: white; vertical-align: top;"|09:15 - 11:00:
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 +
Setting up laptops
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 +
Basic Unix (lecture) 
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14:15 - 16:00
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Basic Unix (exercises)
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|style="background: white; vertical-align: top;"|09:15 - 10:00  
  
 
Ensembl genome browser  
 
Ensembl genome browser  
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and Jalview (lectures/demo)
 
and Jalview (lectures/demo)
  
11:15 - 13:00:
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10:15 - 11:00
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UCSC genome browser (lectures/exercises)
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11:15 - 12:00
  
 
Working with sequences  
 
Working with sequences  
  
and databases (lectures/exercises)
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and databases (lectures)
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 +
12:00 - 13:00
  
14:15 - 16:00:
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Lunch
  
Applied sequence bioinformatics
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13:15 - 16:00
|style="background: white; vertical-align: top;"|09:15 - 11:00:
 
  
More Unix and
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Applied sequence bioinformatics (exercise)
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|style="background: white; vertical-align: top;"|09:15 - 12:00
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Galaxy/Life Portal (lectures/demo)
  
UCSC genome browser (lectures/exercises)
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12:00 - 13:00
  
11:15 - 13:00:
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Lunch 
  
Galaxy / Life Portal (lectures/exercises)
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13:15 - 16:00
  
14:15 - 16:00:
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More Unix (lecture/exercises)
  
|style="background: white; vertical-align: top;"|09:15 - 16:00:
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|style="background: white; vertical-align: top;"|09:15 - 16:00  
 
Python workshop
 
Python workshop
  
 
(lectures / exercises)
 
(lectures / exercises)
|style="background: white; vertical-align: top;"|09:15 - 16:00:
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|style="background: white; vertical-align: top;"|09:15 - 16:00  
 
Python workshop
 
Python workshop
  

Revision as of 09:47, 6 October 2016

Bioinformatics for Molecular Biology - 2016

Under construction! Changes will happen

All students must be present at the start of the course, at 09:15, on November 14. 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).

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.

Course information

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

Most of the teaching will take place in room 1250 on the 1st floor of Biology Buiding (Kristine Bonnevies Hus). The teaching starts at 09:15 and we will end at latest 16:00.

Detailed program

The program is still under development and may be updated. The times listed here are only tentative and may likely change. We will mix in small breaks and try to have a lunch break between 13:00 - 14:00.

Detailed schedule for MBV-INFX410 2016
Week Monday Tuesday Wednesday Thursday Friday
46 Nov 14 Nov 15 Nov 16 Nov 17 Nov 18
09:15 - 10:00

Course introduction

10:15 - 12:00

Sequence databases

12:00 - 13:00

Lunch

13:15 - 14:00

Setting up laptops

Basic Unix (lecture)

14:15 - 16:00

Basic Unix (exercises)

09:15 - 10:00

Ensembl genome browser

and Jalview (lectures/demo)

10:15 - 11:00

UCSC genome browser (lectures/exercises)

11:15 - 12:00

Working with sequences

and databases (lectures)

12:00 - 13:00

Lunch

13:15 - 16:00

Applied sequence bioinformatics (exercise)

09:15 - 12:00

Galaxy/Life Portal (lectures/demo)

12:00 - 13:00

Lunch

13:15 - 16:00

More Unix (lecture/exercises)

09:15 - 16:00

Python workshop

(lectures / exercises)

09:15 - 16:00

Python workshop

(lectures / exercises)

47 Nov 21 Nov 22 Nov 23 Nov 24 Nov 25
09:15 - 16:00:

Sequence searching and alignments

(lectures and exercises)

09:15 - 16:00:

Structural bioinformatics

(lectures and exercises)

09:15 - 16:00:

Structural bioinformatics

(lectures and exercises)

Docking and drug discovery

Practical Unix/Python exercise

Reproducibility /

Statistical epigenomics

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
Introduction to statistical inference and R

Basic R and exploring your data

Analysis of gene expression using R NGS Last course day

What does it mean to do bioinformatics?

Gene lists and over-representation analysis

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

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