Bioinformatics for molecular biology 2011
This is an archive page for a past course. For the latest version of this course please see http://bioinformatics.uio.no/wiki/Bioinformatics_course
Contents
Bioinformatics for molecular biology - Fall 2011
November 21st to December 2nd
Description
The aim of the course is to introduce students to bioinformatics resources and tools for molecular biology research by having some of the best researchers in Norway to talk about their field in general and then present their own work. Students are encouraged to bring a lap-top; we will be set up for in-course demonstrations as well as practical lab exercises. The course is intended for biology students or computer science/math students. No prior background in bioinformatics or computer science is required.
The course is jointly delivered by the Biotechnology Centre of Oslo, the Department of Molecular Biosciences (IMBV), the Department of Informatics (IFI) and the Norwegian University of Life Sciences. This course is one of the Ph.D. School courses offered by the Biotechnology Centre of Oslo (http://www.biotek.uio.no/ny-web/events/). The UiO page for this course is http://www.uio.no/studier/emner/matnat/molbio/MBV-INF4410/.
Registration is open now (June of 2011).
MBV-INF 4410 (M.Sc. level course code)10.0 study points
MBV-INF 9410 (Ph.D. level course code) 10.0 study points
MBV-INF 9410A (Ph.D. level course code) 8.0 study points
The course consists of two weeks of lectures, a final take-home exam (one week) and an essay (10 to 20 pages) to be completed by the middle of December.
Ph.D. level students may opt to take the course without the essay for only 8 study points.
Please bookmark this page. All future changes or announcements for the 2011 course will be posted to this page.
Information:
ragni.indahl@biotek.uio.no (about course administration)
ian.donaldson@biotek.uio.no (about course content)
Registration:
torill.rortveit@imbv.uio.no
Dates and times
The course will occur November 21st to December 2nd.
Each day will consist of three time slots for lectures and/or practical labs between 9 AM and 4 PM.
New Place!
Mondays and Tuesdays:
Prolog Seminar room, Ole Johan Dahls Hus, IFI2
Gaustadalleen 23c
Same floor as entrance level. Use entrance nearest to Problemveien.
Wednesdays, Thursdays and Fridays:
Seminar room 510 in Veglaboratoriet Gaustadalleen 25
Fifth floor.
Map
This mapshows closest entrances to use for both buildings.
Closest T-bane
Forskningsparken.
Contacts during the course
Ian Donaldson (course coordinator) ian.donaldson@biotek.uio.no +47 99115149
Problems with room access or audiovisual
Sigrun Lien: 22852953
Line Valbø: 22852415
Programme
Note: The schedule displayed below is tentative. Ongoing changes will be made to this page as we organize speakers before and during the course. Requests and suggestions are welcome. For examples of material presented last year, see Bioinformatics for molecular biology 2010).
| Week 1: Monday, November 21st - Friday, November 25th | |||
| Session 1 | Session 2 | Session 3 | |
| 09:00 – 10:45 | 11:00 – 12:45 | 14:00 – 15:45 | |
| Mon. 21st | Database lecture notes | Install Perl | |
| Ian Donaldson | Ian Donaldson, Antonio Mora, Paul Boddie | Ian Donaldson, Antonio Mora, Paul Boddie | |
| Tue. 22nd | Perl | More Perl | Perl lab |
| Antonio Mora | Antonio Mora | Antonio Mora, Paul Boddie | |
| Wed. 23rd | Introduction to R | R lab | R lab |
| Bjørn-Helge Mevik | Bjørn-Helge Mevik, Katerina Michalickova, Antonio Mora | Bjørn-Helge Mevik, Katerina Michalickova, Antonio Mora | |
| Thur. 24th | Exploratory data analysis Extra material | An introduction to statistical inference | Multiple hypothesis testing |
| Anja Bråthern Kristoffersen | TBA | Clara-Cecilie Günter | |
| Fri. 25th | Microarray data analysis | Microarray data lab | Gene lists and ORA |
| Ståle Nygård | Ståle Nygård | Donaldson | |
| Week 2: Monday, November 28th - Friday, December 2nd. | |||
| Session 1 | Session 2 | Session 3 | |
| 09:00 – 10:45 | 11:00 – 12:45 | 14:00 – 15:45 | |
| Mon 28th | Interaction data resources | Cytoscape lab | Cytoscape plugin lab |
| Donaldson | Donaldson Mora Boddie | Donaldson Mora Boddie | |
| Tue. 29th | ht sequencing 1 | ht sequence lab notes | |
| Robert Lyle | Robert Lyle | ||
| Wed 30th | TBA | Motif scanning and discovery in DNA | Sequence lab |
| TBA | Geir Sandve | Geir Sandve | |
| Thur 1st | Structural biology review | Structural biology tools, predictors and 3D modelling | PyMOL and structural biology tutorial |
| Jon K. Laerdahl | Jon K. Laerdahl | Jon K. Laerdahl | |
| Fri 2nd | Modeling guide | Modeling excercises | Homology modeling excercise |
| Jon K. Laerdahl | Jon K. Laerdahl | Jon K. Laerdahl | |
Written assignment
Students enrolled in MBV-INF4410 or 9410 must complete a written assignment as part of the course requirements.
The assignment is due by Monday, December 19th.
It should be emailed to ian.donaldson at biotek.uio.no preferably as a PDF document (Microsoft Word or OpenOffice is also acceptable).
The assignment is to be at least 1000 words for M.Sc. level students and at least 1500 words for Ph.D. students.
Topics 1 and 2 below are new topics.
Choose ONE of the following topics:
1) choose three bioinformatics applications. They may be Cytoscape plugins for example. Download, install (if necessary) and learn how to use it. Write a description of the application that includes at least
a) what problem the application is used for. b) what the input and output of the tool are (screen-shots can be used) c) a pointer to instructions on how to use the resource (a web-link is fine if one exists). d) any advice for first time-users;i.e. did you have any problems using the tool and how did you overcome them. e) a brief description of the method that the tool uses (hint - look for the corresponding paper). If possible, include a brief description of how this method is related or different from other methods that solve the same problem. f) does the application appear to be actively developed and maintained - hint: look for last release date, mailing lists, user documentation. g) if you have time, try to test the tool (or parts of it) to make certain that it is reliable and doing what it should be doing - hint: you can pose a trivial problem to the tool that you know the answer to or you could use another tool that performs a similar analysis and compare the results. h) references (PubMed and or web-links).
2) choose three bioinformatics databases. Try browsing http://bioinformatics.ca/links_directory/index.php
Learn how to use it. Write a description of the database that includes at least
a) what is the focus of the database. b) describe and explain some sample searches and their results (screen-shots can be used) c) a pointer to instructions on how to use the database(a web-link is fine if one exists). d) any advice for first time-users;i.e. did you have any problems using the database and how did you overcome them. e) Include a brief description of how this database is related to other databases (what does it link out to and what does it provide that other databases do not provide). f) does the database appear to be actively developed and maintained - hint: look for last release date, mailing lists, user documentation. g) if you have time, try to test the database(or parts of it) to make certain that it is reliable - hint: you could try doing similar searches in another database and compare the results. h) references (PubMed and or web-links).
3) describe how you would use two or more of the methods covered in the course in your own research. Your proposal may include figures or tables. Give a short introduction to your problem area, clearly state your hypothesis and how you think it might be addressed by each of the methods. Provide justifications for your proposal as well as expected outcome. Describe potential risks (say, the method provides no meaningful results) and what you would do to mitigate this risk. List any resources you use.
4) you may define your own alternative topic. Please send an email to ian.donaldson at biotek.uio.no to have your topic approved first.
Exam
Please note: The exam for this course will be a one week take home exam. The exam will be emailed to candidates on Monday, December 5th before 5PM. The exam must be emailed back by Monday, December 12th at 5 PM to Torill Rortveit (torill.rortveit@imbv.uio.no) as a single PDF document (Microsoft Word or an Open Office Document is also acceptable). The document should be named with the course code and your candidate number only (e.g. MBV-INF 4410-1.pdf). Do not place your name in the document.
Bioinformatics links relevant to the course
| Name | URL | Description | |
|---|---|---|---|
| Statistics | |||
| StatSoft textbook | http://statsoft.com/textbook/stathome.html | Good overview of methods and concepts | |
| SAS manuals | http://support.sas.com/onlinedoc/913/ | Thorough overview of analysis procedures found in SAS | |
| GraphPad | http://graphpad.com/help/prism5/prism5help.html?usingstatistical_analyses_step_by_s.htm | See the GraphPad statistical guide for easy introductions to many concepts in statistics | |
| R | http://cran.r-project.org/ | The Comprehensive R Archive Network | |
|
Introduction to R Exploratory data analysis Hypothesis testing |
http://bioinformatics.ca/workshops/2009/course-content | See the CBW course on "Exploratory Data Analysis Essential Statistics using R" at the bottom of this page. Slides and lecture recordings from Modules 1-3 cover much of the same material covered in the first two days of this course. | |
| Learning R | http://www.ploscompbiol.org/article/info:doi%2F10.1371%2Fjournal.pcbi.1000482 | A Quick Guide to Teaching R Programming to Computational Biology Students | |
| R reference card | http://cran.r-project.org/doc/contrib/Short-refcard.pdf | A reference card for R syntax | |
| UCLA tutorials | http://www.ats.ucla.edu/stat/r/ | Useful example code while learning R | |
| R vs. other languages | http://www.johndcook.com/R_language_for_programmers.html | A brief description of how R differs from other programming languages. Useful if you already know a programming language. | |
| Which test do I use | http://www.practicalstats.com/which/index.html | An interactive guide to choosing which statistical test to use. | |
| EMBNet Microarray course | http://vit-embnet.unil.ch/CoursEMBnet/Arrays06/Material.html | An online course with R/Bioconductor example tutorials | |
| EMBNet tutorials | http://www.ch.embnet.org/pages/courses2.html | Other helpful tutorials with R examples related to biostatistics | |
| SIB tutorials | http://edu.isb-sib.ch/ | Portal to the SIB bioinformatics tutorials - includes R, Unix, Perl, statisitics and lots more. | |
| CBW tutorials | http://bioinformatics.ca | Portal to the Canadian Bioinformatics Workshop material. Includes R, statistics and lots more. | |
| Microarrays | |||
| NMC | http://www.mikromatrise.no/ | Norwegian Microarray Consrtium | |
| MACF | http://core.rr-research.no/ | UiO MicroArray Facility | |
| Bioinformatics core facility | http://core.rr-research.no/index.php?section=3 | The Bioinformatics Core Facility established at Rikshospitalet-Radiumhospitalet (RR) will provide its users at RR and the University of Oslo with a range of services within bioinformatics, including analysis of DNA and protein sequences, analysis of microarray data, protein structure analysis and access to useful databases and web services | |
| Sequence | |||
| RSAT | RSAT | A collection of several motif-related tools | |
| ConTra | ConTra | A more user-friendly tool for matching a collection of Position Weighted Matrices against promoter sequences across species | |
| Structure | |||
| Networks | |||
| Required files | [Sample network[1]] [Node atributes[2]] | Please download these and uncompress before using | |
| Cytoscape | http://www.cytoscape.org/ | Cytoscape home page | |
| Cytoscape | http://cytoscape.org/cgi-bin/moin.cgi/Presentations | Tutorial on Cytoscape | |
| Cytoscape | http://cytoscape.wodaklab.org/wiki/How_to_increase_memory_for_Cytoscape | Solution to common problem with working with large networks in Cytoscape. | |
| Alternative source for the RUAL.sif data | http://chianti.ucsd.edu/cytoscape-data/ | ||
| Alternative source for the node attribute data | http://chianti.ucsd.edu/svn/cyto_web/branches/initial/tut/filters.editor/ | ||
| iRefIndex Cytoscape plugin | http://irefindex.uio.no/wiki/iRefScape | iRefIndex installation | |
| iRefIndex | http://irefindex.uio.no/ | iRefIndex wiki | |
| iRefIndex publication | http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=18823568 | Full details of iRefIndex | |
| DAVID | http://www.nature.com/nprot/journal/v4/n1/pdf/nprot.2008.211.pdf | Nature Protocols paper | |
| GSEA | http://www.broadinstitute.org/gsea/doc/subramanian_tamayo_gsea_pnas.pdf | PNAS paper | |
| GSEA | http://www.broadinstitute.org/gsea | Gene Set Enrichment Analysis application | |
Bioinformatics Mailing Lists
If you are interested in being informed of future courses, talks and new related to bioinformatics in the Oslo region, then consider signing up for the cbo mailing list.
https://sympa.uio.no/usit.uio.no/info/cbo-all
You might also consider the Norwegian-wide bioinformatics email list. You can sign up at
http://mailman.uib.no/listinfo/bioinfo.users.
Both lists are run by members of the Norwegian Bioinformatics Platform.
Archived courses
http://donaldson.uio.no/wiki/Bioinformatics_for_molecular_biology_2010
http://donaldson.uio.no/wiki/Bioinformatics_for_molecular_biology_2009
