Difference between revisions of "MBV-INFX410 2018"

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== [https://wiki.uio.no/projects/clsi/index.php/MBV-INFX410 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 [http://folk.uio.no/jonbra/MBV-INF4410_2017/Home_assignment/ here]
 +
* 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.
 +
* '''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.'''
 +
* '''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.'''
 +
* '''''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/)
 +
** JalView Desktop (http://www.jalview.org/) - could maybe also run by pressing the "Launch Jalview Desktop" button
 +
** PuTTY (http://www.putty.org/)
 +
** R (https://www.r-project.org/) '''Install''' '''inside Anaconda instead'''
 +
** 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)]
 +
 
 +
=== 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 (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.
 +
{| class="wikitable"
 +
|+General schedule for MBV-INFX410
 +
!
 +
!Mon
 +
!Tue
 +
!Wed
 +
!Thu
 +
!Fri
 +
|-
 +
!Week 46
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| style="background: white;" |Lectures/
 +
exercises
 +
| style="background: white;" |Lectures/
 +
exercises
 +
| style="background: white;" |Lectures/
 +
exercises
 +
| style="background: white;" |Lectures/
 +
exercises
 +
| style="background: white;" |Lectures/
 +
exercises
 +
|-
 +
!Week 47
 +
| style="background: white;" |Lectures/
 +
exercises
 +
| style="background: white;" |Lectures/
 +
exercises
 +
| style="background: white;" |Lectures/
 +
exercises
 +
| style="background: white;" |Lectures/
 +
exercises
 +
| style="background: white;" |Lectures/
 +
exercises
 +
|-
 +
!Week 48
 +
| style="background: white;" |Obligatory
 +
home assignment
 +
| style="background: white;" |Obligatory
 +
home assignment
 +
| style="background: white;" |Obligatory
 +
home assignment
 +
| style="background: white;" |Obligatory
 +
home assignment
 +
| style="background: white;" |Hand in
 +
home assignment
 +
|-
 +
!Week 49
 +
| style="background: white;" |Lectures/
 +
exercises
 +
| style="background: white;" |Lectures/
 +
exercises
 +
| style="background: white;" |Lectures/
 +
exercises
 +
| style="background: white;" |Lectures/
 +
exercises
 +
| style="background: white;" |Exam start
 +
(home assignment)
 +
|-
 +
!Week 50
 +
| style="background: white;" |Exam
 +
(home assignment)
 +
| style="background: white;" |Exam
 +
(home assignment)
 +
| style="background: white;" |Exam
 +
(home assignment)
 +
| style="background: white;" |Exam
 +
(home assignment)
 +
| style="background: white;" |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 [http://www.uio.no/english/services/it/username-password/no-password.html 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<nowiki> </nowiki>if you have forgotten your UiO user name/password or you do not have one, you must contact Jon (see [https://wiki.uio.no/projects/clsi/index.php/MBV-INFX410_2016#Contacts 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<nowiki> </nowiki>it can be used for the exercises/tutorials, the home exam and hopefully<nowiki> </nowiki>in your future work. How to get a reasonable setup is described [https://wiki.uio.no/projects/clsi/index.php/Laptop_Setup here].
 +
 
 +
If you already are an expert programmer and Unix guru, go [https://wiki.uio.no/projects/clsi/index.php/Biology_for_Informatics 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.
 +
{| 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 ===
 +
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)]
 +
*EMBnet, [http://www.embnet.org/sites/default/files/quickguides/guideUNIX.pdf A Quick Guide to UNIX]
 +
*NCBI Resource Coordinators, "Database resources of the National Center for Biotechnology Information", [http://dx.doi.org/10.1093/nar/gku1130 Nucleic Acids Res. <b>43</b>, D6 (2015)]
 +
*The UniProt Consortium, "UniProt: a hub for protein information", [http://dx.doi.org/10.1093/nar/gku989 Nucleic Acids Res. <b>43</b>, D204 (2015)]
 +
*P. Flicek ''et al.'', "Ensembl 2015", [http://dx.doi.org/10.1093/nar/gku1010 Nucleic Acids Res. <b>43</b>, D662 (2015)]
 +
*P.W. Rose ''et al.'', "The RCSB Protein Data Bank: new resources for research and education", [http://dx.doi.org/10.1093/nar/gks1200 Nucleic Acids Res. <b>41</b>, D475 (2013)]
 +
*P.J.A. Cock ''et al.'', "Biopython: freely available Python tools for computational molecular biology and bioinformatics", [http://dx.doi.org/10.1093/bioinformatics/btp163 Bioinformatics <b>25</b>, 1422 (2009)]
 +
*A.M. Waterhouse ''et al''., "Jalview Version 2--a multiple sequence alignment editor and analysis workbench", [http://dx.doi.org/10.1093/bioinformatics/btp033 Bioinformatics <b>25</b>, 1189 (2009)]
 +
*G.M. Boratyn ''et al.'', "BLAST: a more efficient report with usability improvements", [http://dx.doi.org/10.1093/nar/gkt282 Nucleic Acids Res. <b>41</b>, W29 (2013)]
 +
*J.-F. Taly ''et al.'', "Using the T-Coffee package to build multiple sequence alignments of protein, RNA, DNA sequences and 3D structures", [http://dx.doi.org/10.1038/nprot.2011.393 Nat. Protoc. <b>6</b>, 1669 (2011)]
 +
*L. Bordoli ''et al.'', "Protein structure homology modeling using SWISS-MODEL workspace", [http://dx.doi.org/10.1038/nprot.2008.197 Nat. Protoc. <b>4</b>, 1 (2009)]
 +
*J. Carlsson ''et al.'', "Ligand discovery from a dopamine D<sub>3</sub> receptor homology model and crystal structure", [http://dx.doi.org/10.1038/nchembio.662 Nat. Chem. Biol. <b>7</b>, 769 (2011)]
 +
*R.M. Kuhn ''et al.'', "The UCSC genome browser and associated tools", [http://dx.doi.org/10.1093/bib/bbs038 Brief. Bioinform. <b>14</b>, 144 (2013)]
 +
*J. Goecks ''et al''., "Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences", [http://dx.doi.org/10.1186/gb-2010-11-8-r86 Genome Biol. <b>11</b>, R86 (2010)]
 +
*G.K. Sandve ''et al.'', "Ten Simple Rules for reproducible computational Research", [http://dx.doi.org/10.1371/journal.pcbi.1003285 PLoS Comput. Biol. <b>9</b>, e1003285 (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)]
 +
*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)]
 +
*N. Nagarajan & M. Pop, "Sequence assembly demystified", [http://dx.doi.org/10.1038/nrg3367 Nat. Rev. Genet. <b>14</b>, 157 (2013)]
 +
*D.W. Huang ''et al.'', "Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources", [http://dx.doi.org/10.1038/nprot.2008.211 Nat. Protoc. <b>4</b>, 44 (2009)]
 +
 
 +
Other good articles (''not ''curriculum)
 +
*Z. Yang & B. Rannala, "Molecular phylogenetics: principles and practice", [http://dx.doi.org/doi:10.1038/nrg3186 Nat. Rev. Genet. <b>13</b>, 303 (2012)]
 +
 
 +
=== 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 ===
 +
 
 +
[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]
 +
 
 +
[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]
 +
 
 +
[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]
 +
 
 +
UCSC [http://genome.ucsc.edu Genome browser]
 +
 
 +
Free [http://www.openhelix.com/ucsc UCSC Genome browser tutorial]&nbsp;&nbsp; from OpenHelix
 +
 
 +
Portal to [http://galaxyproject.org Galaxy]
 +
 
 +
[http://wiki.galaxyproject.org/Learn Galaxy 101 and other Galaxy screencasts/tutorials]
 +
 
 +
UiO [http://lifeportal.uio.no Lifeportal] and more [http://www.uio.no/english/services/it/research/hpc/lifeportal information on the Lifeportal]
 +
 
 +
The Genomic [http://hyperbrowser.uio.no/hb HyperBrowser]
 +
 
 +
[http://bioinformatics.ca/links_directory Links Directory] from bioinformatics.ca
 +
 
 +
The 2017 Nucleic Acids Research [https://academic.oup.com/nar/issue/45/D1 Database 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]

Revision as of 10:39, 29 August 2018

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