Difference between revisions of "MBV-INFX410 2013"

From projects/clsi
Jump to: navigation, search
(Bioinformatics for Molecular Biology - 2013)
 
(2 intermediate revisions by the same user not shown)
Line 1: Line 1:
 
== [https://wiki.uio.no/projects/clsi/index.php/MBV-INFX410 Bioinformatics for Molecular Biology] - 2013  ==
 
== [https://wiki.uio.no/projects/clsi/index.php/MBV-INFX410 Bioinformatics for Molecular Biology] - 2013  ==
  
'''##############'''
+
'''''THIS IS THE WIKI FOR 2013. INFORMATION FOR 2015 IS FOUND [https://wiki.uio.no/projects/clsi/index.php/MBV-INFX410_2015 HERE]!
 
 
'''''Typos in the exam: See below in the [https://wiki.uio.no/projects/clsi/index.php/MBV-INFX410_2013#Exam Exam section]'''''
 
 
 
'''##############'''
 
  
 
'''''Please bookmark this page. All future changes or announcements for the 2013 course will be posted on this page.'''''  
 
'''''Please bookmark this page. All future changes or announcements for the 2013 course will be posted on this page.'''''  

Latest revision as of 12:34, 6 August 2015

Bioinformatics for Molecular Biology - 2013

THIS IS THE WIKI FOR 2013. INFORMATION FOR 2015 IS FOUND HERE!

Please bookmark this page. All future changes or announcements for the 2013 course will be posted on this page.

All students must be present at the start of the course, at 09:00, on November 11. 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 (See contact details below).

This is the wiki for the courses MBV-INF4410, MBV-INF9410, and MBV-INF9410A offered by the Department of Biosciences and Department of Informatics at the University of Oslo (UiO).

The course consists of five weeks of lectures, exercises, a take-home exam (one week), and a take-home exam/assignment (roughly 20 pages). 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. 

Ph.D. level students may opt to take the course without the take-home partial exam/assignment for only 8 study points (MBV-INF9410A). Both MBV-INF4410 (M.Sc. level) and MBV-INF9410 (Ph.D. level) are 10 study point courses.

Course description

This intensive course will introduce students to bioinformatics resources and tools for molecular biology research. All the lecturers are among the top researchers working within the fields of bioinformatics and computational biology in the Oslo region. Students must bring their own laptop for in-course demonstrations as well as for practical lab exercises. The course is mainly intended for biology students, but also for computer science students or students from other fields of science with an interest for and some experience with molecular biology. No prior background in bioinformatics or computer science is required. All students should have a basic understanding of molecular biology, at least roughly corresponding to 5-10 university study points in molecular biology, biochemistry, or similar. If you are uncertain if your biology background is strong enough, please contact Jon (See contact details below) before you sign up for the course.

Course responsible is Dr. Jon K. Lærdahl (jonkl@medisin.uio.no) from the Department of Microbiology, Oslo University Hospital (OUH) - Rikshospitalet. Lærdahl is also employed by the CLS initiative at UiO and the Bioinformatics Core Facility (CF) at OUH and UiO.

Links to the web pages for the years 2009-2011 is found here and for 2012 here

Notes on the course format: The course has previously been given as an intensive course over two weeks with a take-home exam in the 3rd to 4th week. A take-home assignment was also a compulsory part of the 10 study points versions of the course. The compact format was ideal for students coming from outside Oslo, but it was also exhausting for students and lecturers. It gave little time to digest and dive more deeply into the various topics presented in the course. In 2013, the course will be given in weeks 46-51. However, it will only be necessary to be physically present in Oslo for parts of the coursei.e. the lectures/exercises. The schedule is presented below, but there might be small adjustments to this schedule.

TentaiveTeachingPlan-3.jpg

Time and place

The course will be offered in weeks 46 to 50, autumn 2013, i.e. starting on Monday November 11 (See schedule below). The take-home exam must be handed in in week 51, on Wednesday December 18. Each day of lectures/exercises will consist of three time slots for lectures and/or exercises/practical labs between 09:00 and 16:00. Lunch will usually be between 12:45 and 13:30. You will have to bring your own lunch or buy lunch in the local kantine. 

Lecture room: All lectures/exercises in weeks 46 and 47 (Monday to Thursday) will be given in lecture room Python in Ole-Johan Dahls hus (IFI2). A map showing the location of the building is found here. The building is located next to the Forskningsparken metro and tram stations. The room Python is on the 1st floor (2. etasje) in the northern end of the building, the end closest to the tram line. The easiest access to Python is through the entrance in the tunnel going through the building.

Lectures/exercises in week 48 (Tuesday to Friday) will be given in the lecture room Store Auditorium in Kristen Nygaards hus (IFI1), found here.

The combined lecture/CLS seminar at 11:15 on Wednesday, November 20, will take place in lecture room C in Ole-Johan Dahls hus (one floor up from lecture room Python, in the middle of the building).  

Contacts

Jon K. Lærdahl (Course coordinator) - e-mail: jonkl@medisin.uio.no, phone: +47 99 507 335

Torill Rørtveit (Course administrator, registration) - e-mail: torill.rortveit@ibv.uio.no

Computers/laptops, internet access, and UiO user account

All students must bring a laptop with either a Windows (Windows XP or more recent), Unix/Linux, or OS X (i.e. an Apple computer) operating system.

  • The computer should not be more than 2-3 years old
  • 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
  • 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
  • If you are unsure if you have a UiO user account and a valid password, you should try to log in using kiosk.uio.no or win.uio.no as described here. If you are unable to log in, try the hints you find here.
  • Instructions (in Norwegian) about how to find your user name and get a new password can be found here.

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 above) as soon as possible, and at least one week before the start of the course.

To get a UiO username/password at the UiO helpdesk you need valid ID.

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.

Programme

The schedule below is tentative, and may be changed prior to, and possibly even during, the course. Requests and suggestions are welcome.

Week 46: Monday, November 11 - Friday, November 15
Session 1 Session 2 Session 3
09:00 - 10:45 11:00 - 12:45 13:30 - 16:00
Monday 11th

Course Introduction 

Biological databases on the web

- lectures

Basic Unix tutorial with practicals

A tiny taste of simple scripting

- lectures/exercises

Jon K Lærdahl Jon K Lærdahl Jon K Lærdahl
Tuesday 12th

Practical Unix - exercise

Brief introduction to Ensembl

Brief introduction to Jalview

Applied sequence bioinformatics

- exercise

Applied sequence bioinformatics 

- exercise 

Jon K Lærdahl Jon K Lærdahl Jon K Lærdahl
Wednesday 13th

Basic Python programming

Python workshop

Python workshop

Karin Lagesen Karin Lagesen Karin Lagesen
Thursday 14th

More Python programming

Python workshop

Python workshop

Karin Lagesen Karin Lagesen Karin Lagesen
Friday 15th

Study day/Start on obligatory take-home assignment

Week 47: Monday, November 18 - Friday, November 22
Session 1 Session 2 Session 3
09:00 - 10:45 11:00 - 12:45 13:30 - 16:00
Monday 18th

Sequence searching, alignments, and multiple alignments

- lectures

Sequence searching and multiple sequence alignments

- exercise

Torbjørn Rognes Jon K Lærdahl
Tuesday 19th

Structural Biology Review -

brief lecture

Applied and structural bioinformatics

Applied and structural bioinformatics

Applied and structural bioinformatics

Jon K Lærdahl Jon K Lærdahl Jon K Lærdahl
Wednesday 20th

Homology Modeling

- exercises

Chromatin 3D
structure (See
below)

13:00 - 16:00

Docking and drug discovery

- lectures/exercises

Jon K Lærdahl Jonas Paulsen Bjørn Dalhus
Thursday 21st

UCSC Genome browser

-lectures/exercises

Galaxy computational biology platform

- lectures/exercises

13:00 - 16:00

Reproducibility/HyperBrowser

- lectures

Jon K Lærdahl Jon K Lærdahl

Geir Kjetil Sandve

Friday 22nd

Study day/Work on obligatory take-home assignment

Week 48: Monday, November 25 - Friday, November 29
Session 1 Session 2 Session 3
09:00 - 10:45 11:00 - 12:45 13:30 - 16:00
Monday 25th

Study day/Work on obligatory take-home assignment

Tuesday 26th

Introduction to statistical inference and multiple hypothesis testing

- lectures/exercises

Basic R programming and exploring your data

- lectures/exercises

Basic statistical testing in R

- lectures/exercises

Anja Bråthen Kristoffersen Anja Bråthen Kristoffersen Anja Bråthen Kristoffersen
Wednesday 27th

Analysis of gene expression data using R

- lectures/exercises

Analysis of gene expression data using R

- lectures/exercises

Analysis of gene expression data using R

- lectures/exercises

Ståle Nygård (Anja) Ståle Nygård (Anja) Ståle Nygård (Anja)
Thursday 28th

Next generation sequencing (NGS)

- lectures

NGS & variant calling lab

- lectures/exercises

NGS & variant calling lab

- lectures/exercises

Robert Lyle Tim Hughes & Robert Lyle Tim Hughes & Robert Lyle
Friday 29th

The bioinformatics of sequencing and assembling genomes - with a focus on the Atlantic cod genome project

- lectures

Gene lists & over-representation analysis (ORA)

- lectures/practicals

End of course summary

- lecture/discussion

Lex Nederbragt Ståle Nygård Jon K Lærdahl

Merete Molton Worren and Daniel Vodák from the Bioinformatics Core Facility will help dusing the laptop setup session on Monday, November 11.

Associate Professor Anja Bråthen Kristoffersen will be present during the exercises/lectures on November 13, 14, and 27.

On Wednesday November 20, between 11:15 and 12:00, there will be a combined course lecture and CLS seminar by Jonas Paulsen from Oslo University Hospital. This will be on the study of chromatin 3D structure. This lecture will take place in lecture room C in Ole-Johan Dahls hus (one floor up from lecture room Python, in the middle of the building).

Required reading material/curriculum

The curriculum comprises all lectures, lecture handouts, exercises and the reviews/articles/written material listed on this page.

Exam

##########################################

Typos in the exam (Sorry about this!):

  • In Exercise question 1e the protein PCSK9 is mentioned twice. This is a typo. It should be FTO both places.

The exam for the course was sent, by e-mail, to all students on December 11. If you did not receive the exam, please contact Jon immediately!

##########################################

The exam for this course will be a one week, take-home exam.

The exam will be sent to all participants at 3 pm, Wednesday December 11, by e-mail.

Your completed exam must be returned, at the latest, at 3 pm, Wednesday December 18. It should be sent by e-mail to the course administrator Torill Rørtveit (e-mail address: torill.rortveit@ibv.uio.no). Please put the course code and your candidate number (for this course) in the subject field (e.g. "Exam MBV-INF4410 Candidate:15").

The exam must be handed in 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-INF4410-15.pdf). Do not place your name in the document.

Written assignment

The students enrolled in MBV-INF4410 or MBV-INF9410, but not MBV-INF9410A, must complete a written assignment as part of the course requirements.

The assignment is due by 3 pm, Friday December 6. It should be of the order of 4000 words for Ph.D. level students and 2500 words for M.Sc. students. The assignment should be sent to Jon K. Lærdahl (e-mail: jonkl@medisin.uio.no) as an e-mail attachment, as a single file. Start the assignment with a brief introduction and state the total number of pages and words (e.g. calculated with Microsoft Word "Word Count").

Choose one of the following topics (one, only):

  1. Choose at least 3 biological databases from the latest NAR database issue. Write a description of the databases that for each of them includes at least the following:
    1. What is the main focus of the database?
    2. A description of some searches and their results (screen-shots might improve your description)
    3. Instructions on how to use the database
    4. Advice for first time-users. How did you overcome problems, if you had any?
    5. 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?
    6. Information on how often the database appears to be updated. Is it actively developed and maintained? Look for last release date, mailing lists, and user documentation
    7. A test of the database (or parts of it) to make certain that it is reliable. You could, for example, try doing similar searches in another database and compare the results
    8. A discussion on how useful you think the database is
    9. References to articles and other information on the database (e.g. PubMed and/or web-links)
  2. Choose at least 3 bioinformatics tools or applications, for example from the latest NAR web server issue. Learn how to use the tools. Download and install, if necessary. Write a description of the applications/programs/tools that for each of them includes at least the following:
    1. What are the problems/tasks this application is used for?
    2. What are the input and output of the tool? Screen-shots might improve your description
    3. Instructions on how to use the resource
    4. Advice for first time-users. How did you overcome problems, if you had any?
    5. A brief description of the method that the tool uses. A good place to look for this information is in the corresponding paper
    6. A brief description of how this method is related or different from other methods that solve the same or similar problems
    7. Information on how often the application appears to be updated. Is it actively developed and maintained? Look for last release date, mailing lists, and user documentation
    8. A test of the application to make certain that it is reliable. You could, for example, try using another tool that performs a similar analysis and compare the results. Alternatively, you can pose a trivial problem to the tool that you know the answer to
    9. A discussion on how useful you think the application is
    10. References to articles and other information on the application (e.g. PubMed and/or web-links)
  3. Describe how you would use 2 or more of the methods covered in the course in your own research. Your proposal is likely to be better if you include figures and/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 jonkl@medisin.uio.no or talk to Jon, before November 30, to have this approved first.

Bioinformatics mailing list for the Oslo region

The mailing list for computational biology and bioinformatics in the Oslo region is cbo-all@usit.uio.no. The list has approximately 370 members. The list is used to distribute news about seminars, positions, courses, meetings and other topics that might be of interest to students and researchers with an interest in computational life science in south-eastern Norway. If you want to receive e-mails that are sent to the list, sign up here

https://sympa.uio.no/usit.uio.no/info/cbo-all

by following the link termed "Subscribe".

Useful links

Trond Hasle Amundsen's Local guide to Linux and Unix

EMBnet Quick guide Unix

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

Norwegian EMBnet node public Galaxy server instance

The Genomic HyperBrowser

Links Directory from bioinformatics.ca