Difference between revisions of "MBV-INFX410 2018"

Latest revision as of 16:24, 7 December 2018

Bioinformatics for Molecular Biology - 2018

Messages

• December 7: Everyone should have gotten the exam by email. If you haven't received it, please send me a mail ASAP.
• You can find the home assignment here and a useful python script here.
• November 21: We will be in room 4613 all day.
• November 22 will be a short summary of the Unix and Python material we have learned so far, including a short exercise showing what you are expected to accomplish. The material is made available so you can take a look and if it is very easy it is not so important to attend that day.
• Notice that some days we will use a different room than 4424. See the Detailed program

• You need to install the following software on your laptops:
  • PyMOL (https://www.pymol.org/). PyMOL is free for students but you have to register for a license. Go to "New users" and "Buy license" and click on Student/Teacher (or click here)
  • R (https://www.r-project.org/)
  • RStudio (https://www.rstudio.com/)
  • Windows users only: PuTTY (http://www.putty.org/). Optional: In addition to PuTTY, windows users can also install Cygwin if you want to have a Unix-style environment also locally on your computer. Git Bash can be a nice alternative to Cygwin.
  • 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.

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 (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 username/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 4424 on the 4th floor of Biology Buiding (Kristine Bonnevies Hus, KB).But check the program because changes will happen..

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.

Recommended reading material / curriculum

The curriculum comprises all lectures, lecture handouts and exercises. The articles listed below are only recommended but not mandatory:

• 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

Learn R, using R (swirl)

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

Nice introductory eBook about statistics for biology and introduction to R (including downloadable R scripts)