582606 Introduction to bioinformatics (4 cr, Autumn 2008)

This course gives an introduction to the central topics in bioinformatics, and gives a foundation for further courses in the Master's Degree Programme in Bioinformatics (MBI). You do not need to be in MBI, however, to take the course! The course was previously given in Autumn 2007, and will follow roughly the same structure.

News

20.4.2009	Results from the separate exam 31.3.2009 are available in CS intranet. Please see this page for exam dates in summer 2009.
28.1.2009	Results from the separate exam 16.1.2009 are available in CS intranet. Next separate exam will be on Tuesday 31 March at 16.00-20.00 in Exactum A111. Check the date and place before exam.
9.12.2008	Results from the separate exam 8.11.2008 are available in CS intranet. Contact Esa if you want to discuss your grading. Next separate exam will be on Friday 16 January at 16.00-20.00 in Exactum A111.
4.11.2008	You can come and discuss your results with Esa and Lauri on Thursday 6 Nov at 14.00-15.00 in Exactum A217, or ask us by email.
2.11.2008	Results from the course exam are available in CS intranet. You should be able to access the results with your CS account username/password. Note that only passed grades are reported in results. The results will be posted on the 2nd floor CS bulletin board during Monday 3 Nov. There will be a session where you can discuss your exam results with Esa and Lauri, and examine your answer papers. Session time and place to be announced. The first separate exam is held on Tuesday 18 Nov at 16.00 in Exactum A111.
9.10.2008	Please give anonymous feedback on the course! (Scroll down the list to find Introduction to Bioinformatics) Feedback form in Finnish.
29.9.2008	Added questions of two past separate exams in the Exams section.
18.9.2008
16.9.2008	Exercise note return policy changed: send your notes to Lauri before the exercise session where you are going to starts.
11.9.2008	Second exercise group: Wednesday 14.15-16.00 Exactum B120. You may choose to attend either group. Important note: you have to return your exercise notes by email at latest before exercise group 1 starts (Tue 16.15), regardless of the group you are going to attend to (see above). In addition, when sending exercise notes, tell Lauri Eronen which group you are going to go to.
26.8.2008	First lecture on Tuesday 2 September at 14.15 in Exactum C221! Exercises start Tuesday 9 September at 16.15 in Exactum C221.
8.8.2008	Course web page is open.

Lecture schedule & slides

Lecture material: [Pages 1-431] [Systems biology lecture]

Tue 2.9. First lecture: What is bioinformatics? Molecule biology primer. [slides] [handouts]
Fri 5.9. Molecule biology primer continued. Biological words [slides] [handouts]
Tue 9.9. Genome sequencing and assembly [slides] [handouts]
Fri 12.9. Sequence alignment / Global alignment [slides] [handouts]
Tue 16.9. Local sequence alignment. Overlap alignment. Multiple alignment (generalisation of previous algorithms, CLUSTALW). FASTA. [slides] [handouts]
Fri 19.9. BLAST [slides] [handouts]
Genome rearrangements [slides] [handouts]
Tue 23.9. Genome rearrangements continued (breakpoint removal method) [slides] [handouts]
Phylogenetic trees (preliminaries) [slides] [handouts]
Fri 26.9. Phylogenetic trees (parsimony and distance-based methods)
Note that the slides contain material that will be covered on Tuesday 7 October. [slides] [handouts]
Tue 30.9. Clustering. [slides]
Fri 3.10. Gene expression analysis [slides]
Tue 7.10. Phylogenetic trees (neighbour-joining algorithm). Systems biology. [slides] [handouts]
Fri 10.10. Wrap-up / Question & Answer session [slides] [handouts]
Wed 15.10. Course exam. Check the time and place (below).

Exercises

Problems for each exercise session will be distributed approximately one week before the session. You are expected to be prepared to present your solutions in the exercise session.

In addition, you need to send notes of the assignments you are going to mark to Lauri Eronen by email before your exercise group starts (Tuesdays 16.15 or Wednesday 14.15). In addition, you should tell Lauri Eronen about the group where you are going to go to present your solutions.

These exercise notes should contain a brief description of the steps you took to solve the assignment, as well as the results. Important: When sending email, use subject of form "ITB exercise X, Tue/Wed group" where X is the exercise session number, and Tue/Wed indicates which group you are going to go to. Send your notes in email text body. If you need to include a figure, send it as an attachment.

Time and place

Lectures: Tuesday & Friday 14.15-16.00 Exactum C221
Exercises
- Group 1: Tuesday 16.15-18.00 Exactum C221
- Group 2: Wednesday 14.15-16.00 Exactum B120

Enrolling for the course

Please use the registration system of the Department of Computer Science to enroll for the course.

This is the list of topics covered on the course.

Biological background (Deonier's book chapter 1)
Probability calculus (chapter 2)
Word distributions and occurrences (chapter 3)
Genome rearrangements (chapter 5)
Sequence alignment (chapter 6)
Rapid alignment methods: FASTA and BLAST (chapter 7)
Sequencing and sequence assembly (chapter 8)
Similarity, distance and clustering (chapter 10)
Expression data analysis (chapter 11)
Phylogenetic trees (chapter 12)

Course organizers

University Lecturer Esa Pitkänen, Department of Computer Science, University of Helsinki
Lecturing Researcher Jarkko Salojärvi, Department Information and Computer Science, Helsinki University of Technology
MSc Lauri Eronen (exercises), Department of Computer Science, University of Helsinki

Grading

To successfully pass the course, you have to get a total of 30 out of 60 points from the course exam and exercises.

Course exam: max. 48 points
Exercises: max. 12 points (0% completed assignments gives you 0 points, 80% gives 12 points)

You may also take a separate exam. In the first separate exam, you will get the maximum points of the following two options:

Maximum of 48 points from the exam, max. 12 points from exercises.
Maximum of 60 points from the exam, no points from exercises.

In the second and subsequent separate exams, only the second option will be available (exercise points are not taken into account).

Exams

The course exam will be held after the course (check the time and place from below) in which you will have to answer 4-5 questions in 2.5 hours. The three-hour time slot given below includes some extra time in case the start of exam is delayed.

In a separate exam, you have 3.5 hours to answer 5-6 questions. Questions in separate exams are in general somewhat more difficult than course exam questions.

Course exam: Wed 15 October 16.00-19.00 Exactum A111. Note: exam starts 16.00, not 15 past like lectures!

A list of separate exams in autumn 2008 and in spring 2009.

The course exam of a previous course is available here: [ps] [pdf]
Questions of two past separate exams: [exam 1] [exam 2]
Note that the course contents have changed a bit since the course was previously held.

Literature

Lectures will be based on

Richard C. Deonier, Simon Tavaré and Michael S. Waterman: Computational Genome Analysis: An Introduction, Springer, 2005.
Neil C. Jones and Pavel A. Pevzner: Introduction to Bioinformatics Algorithms, MIT Press, 2004.

Additional material

Lars Paulin's lecture on next-generation sequencing methods

Hiroaki Kitano: Systems Biology: A Brief Overview, Science 295, 2002.
Marie E. Csete, John C. Doyle: Reverse Engineering of Biological Complexity, Science 295, 2002.
Yuri Lazebnik: Can a biologist fix a radio? - Or, what I learned while studying apoptosis, Cancer Cell 2, 2002.

Molecular biology for computer scientists [pdf]
Lodish et al. (ed.) 1999: Molecular and Cell Biology, 4th ed., Freeman & Co.
Griffiths et al.: Introduction to Genetic Analysis, 9th ed., New York, Freeman & Co.
Griffiths et al. (ed.) 1999: Modern Genetic Analysis, York, Freeman & Co.
Guido van Rossum: Python tutorial
Kelly Black: R tutorial

Previous update: 09.09.2009 16:06 - Esa Pitkänen

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