Difference between revisions of "MBV-INFX410 2017"
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== [https://wiki.uio.no/projects/clsi/index.php/MBV-INFX410 Bioinformatics for Molecular Biology] - 2017 == | == [https://wiki.uio.no/projects/clsi/index.php/MBV-INFX410 Bioinformatics for Molecular Biology] - 2017 == | ||
=== Messages === | === Messages === | ||
− | * '''20 nov: NB! In order to get everybody at an acceptable level in | + | * 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.''' | * '''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 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).''''' | ||
Line 229: | Line 232: | ||
09:15 - 12:00 | 09:15 - 12:00 | ||
− | Docking and drug discovery | + | [[Docking and drug discovery]] |
13:15 - 14:00 | 13:15 - 14:00 | ||
− | Practical Unix/Python | + | [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''' | | style="background: #cefdce; vertical-align: top;" |'''Room 2203a''' | ||
Line 257: | Line 260: | ||
| 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;" | | + | | style="background: #87CEFA; vertical-align: top;" |Obligatory home assignment |
|- | |- | ||
|<b>49</b> | |<b>49</b> | ||
Line 268: | Line 271: | ||
| | | | ||
| style="background: #cefdce; vertical-align: top;" |'''Room 4613''' | | style="background: #cefdce; vertical-align: top;" |'''Room 4613''' | ||
− | 09:15 - 16:00 | + | 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''' | | style="background: #cefdce; vertical-align: top;" |'''Room 4613''' | ||
− | 09:15 - | + | 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''' | | style="background: #cefdce; vertical-align: top;" |'''Room 4613''' | ||
− | 09:15 - | + | 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''' | | style="background: #cefdce; vertical-align: top;" |'''Room 4613''' | ||
− | 09:15 - | + | 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 | + | 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''' | | style="background: #cefdce; vertical-align: top;" |'''Room 4613''' | ||
09:15 - 16:00 | 09:15 - 16:00 | ||
− | Statistical epigenomics | + | [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> | <span style="color:red">Hand out exam</span> | ||
Line 329: | Line 352: | ||
*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)] | *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)] | *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)] | *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)] | *N. Nagarajan & M. Pop, "Sequence assembly demystified", [http://dx.doi.org/10.1038/nrg3367 Nat. Rev. Genet. <b>14</b>, 157 (2013)] |
Latest revision as of 16:54, 8 December 2017
Contents
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):
- 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)
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.
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.
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
11:15 - 12:00
Lunch
Setting up laptops
Basic Unix (exercises) |
Room 3213
09:15 - 11:00 Genome browsers (lecture / exercises) and Jalview (lecture)
Working with sequences and databases (lecture)
Lunch
Applied sequence bioinformatics (exercises) |
Room 4613
09:15 - 12:00 UiO LifePortal (lecture)
Lunch
More Unix (lecture) |
Room 4424
09:15 - 16:00 |
NB! Notice room change: Seminarrom U30 Helga Enghs Hus (see Messages)
09:15 - 16:00 | |
47 | Nov 20 | Nov 21 | Nov 22 | Nov 23 | Nov 24 |
Room 4613
09:15 - 16:00 |
Room 4613
09:15 - 16:00 |
Room 4613
09:15 - 16:00 |
Room 4424
09:15 - 12:00
|
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 |
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 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:
- J. R. A. Hutchins, "Genomic Database Searching", in Bioinformatics pp 225-269. Springer (2017).
- R.F. Service, "Biology's dry future", Science 342, 186 (2013)
- EMBnet, A Quick Guide to UNIX
- NCBI Resource Coordinators, "Database resources of the National Center for Biotechnology Information", Nucleic Acids Res. 43, D6 (2015)
- The UniProt Consortium, "UniProt: a hub for protein information", Nucleic Acids Res. 43, D204 (2015)
- P. Flicek et al., "Ensembl 2015", Nucleic Acids Res. 43, D662 (2015)
- P.W. Rose et al., "The RCSB Protein Data Bank: new resources for research and education", Nucleic Acids Res. 41, D475 (2013)
- P.J.A. Cock et al., "Biopython: freely available Python tools for computational molecular biology and bioinformatics", Bioinformatics 25, 1422 (2009)
- A.M. Waterhouse et al., "Jalview Version 2--a multiple sequence alignment editor and analysis workbench", Bioinformatics 25, 1189 (2009)
- G.M. Boratyn et al., "BLAST: a more efficient report with usability improvements", Nucleic Acids Res. 41, 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", Nat. Protoc. 6, 1669 (2011)
- L. Bordoli et al., "Protein structure homology modeling using SWISS-MODEL workspace", Nat. Protoc. 4, 1 (2009)
- J. Carlsson et al., "Ligand discovery from a dopamine D3 receptor homology model and crystal structure", Nat. Chem. Biol. 7, 769 (2011)
- R.M. Kuhn et al., "The UCSC genome browser and associated tools", Brief. Bioinform. 14, 144 (2013)
- J. Goecks et al., "Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences", Genome Biol. 11, R86 (2010)
- G.K. Sandve et al., "Ten Simple Rules for reproducible computational Research", PLoS Comput. Biol. 9, e1003285 (2013)
- G.K. Sandve et al., "The Genomic HyperBrowser: an analysis web server for genome-scale data", Nucleic Acids Res. 41, W133 (2013)
- M.L. Mertzker, "Sequencing technologies - the next generation", Nat. Rev. Genet. 11, 31 (2010)
- Nielsen, R. et al., "Genotype and SNP calling from next-generation sequencing data", Nat Rev Genet. (2011).
- A. Altmann et al., "A beginners guide to SNP calling from high-throughput DNA-sequencing data", Hum. Genet. 131, 1541 (2012)
- N. Nagarajan & M. Pop, "Sequence assembly demystified", Nat. Rev. Genet. 14, 157 (2013)
- D.W. Huang et al., "Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources", Nat. Protoc. 4, 44 (2009)
Other good articles (not curriculum)
- Z. Yang & B. Rannala, "Molecular phylogenetics: principles and practice", Nat. Rev. Genet. 13, 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
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
Tons of free programming books, about anything really.
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