MBV-INFX410 2016
Contents
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.
Mon | Tue | Wed | Thu | Fri | |
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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 here and there and try to have a lunch break between 12:00 - 13:00.
Week | Monday | Tuesday | Wednesday | Thursday | Friday |
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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) |
09:15 - 12:00
Docking and drug discovery 13:15 - 16:00 Practical Unix/Python exercise |
09:15 - 16:00
Statistical epigenomics (& reproducibility). Lectures / exercises | |
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 |
09:15 - 16:00
Introduction to statistical inference and R. Basic R. |
09:15 - 16:00
Analysing transcriptome data using R |
09:15 - 16:00
Next Generation Sequencing & variant calling |
Last course day
09:15 - 11:00 What does it mean to do bioinformatics? |
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:
- 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)
- 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
Trond Hasle Amundsen's Local guide to Linux and Unix
EMBnet Quick guide Unix
Useful command line one-liners by Stephen Turner
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