Algorithms for Bioinformatics
4
Bioinformatics
Intermediate studies
Course introduces some basic algorithmic concepts and techniques through motivation by selected computational molecular biology problems. The goal is to obtain a solid basis for advanced studies in bioinformatics. Prerequisites: programming skills. Course book: Neil C. Jones and Pavel A. Pevzner: An Introduction to Bioinformatics Algorithms, MIT Press, 2000.
Exam
17.10.2012
09.00
B123
| Year | Semester | Date | Period | Language | In charge |
|---|---|---|---|---|---|
| 2012 | autumn | 04.09-11.10. | 1-1 | English | Leena Salmela |
Lectures
| Time | Room | Lecturer | Date |
|---|---|---|---|
| Tue 12-14 | B120 | Leena Salmela | 04.09.2012-11.10.2012 |
| Thu 12-14 | B120 | Leena Salmela | 04.09.2012-11.10.2012 |
Exercise groups
| Time | Room | Instructor | Date | Observe |
|---|---|---|---|---|
| Thu 10-12 | B119 | Niko Välimäki | 06.09.2012—12.10.2012 |
General
Course introduces some basic algorithmic concepts and techniques through motivation by selected computational molecular biology problems. The goal is to obtain a solid basis for advanced studies in bioinformatics. Prerequisites: programming skills.
Completing the course
The course consists of lectures, study groups, and exercices, as follows:
- Tue 12-14 there will be (mandatory) study group meeting aiming at an in-depth coverage of the week's topics.
- Thu 10-12 there will be an exercise session on the week's topics
- Thu 12-14 there will be an introductory lecture to the next week's topics. (cycle starts here)
Introductory lecture ends with a list of topics and their assignments to the students. The topic is to be studied carefully before gathering to the study group meeting on Tuesday, with the fellow students studying the same topic, to form a common understanding of the assigned topic. Then the groups will be mixed so that each group has an expert from each topic, and the rest of the Tuesday's study group is devoted to teaching each others the material adopted. Exercise session tests the understanding of all topics.
There will be an exam giving 48 points at the maximum. Active participation to exercises gives at the maximum 12 points (30%->1p,85%->12p, linear scale). The grading is then based on the total points (maximum 60) achieved.
Literature and material
Course book
Neil C. Jones & Pavel A. Pevzner: An Introduction to Bioinformatics Algorithms (MIT Press, 2004).
Schedule
- Tue 4.9. 12-14 Introduction to Chapters 1-3: Primer to algorithms and molecular biology, Molecular biology primer
- Thu 6.9. 10-12 Study groups on Chapters 1-3, assignments on slides 30-31
- Thu 6.9. 12-14 Introduction to Chapter 4: Exhaustive search and motif finding
- Tue 11.9. 12-14 Study groups on Chapter 4, assignments on slides 85-87
- Thu 13.9. 10-12 Exercises on Chapters 1-4, exercise sheet, model solutions
- Thu 13.9. 12-14 Introdiction to Chapter 5: Greedy algorithms and genomic rearrangements
- Tue 18.9. 12-14 Study groups on Chapter 5, assignments on slides 54-56
- Thu 20.9. 10-12 Exercises on Chapter 5, exercise sheet, model solutions
- Thu 20.9. 12-14 Introduction to Chapter 6: Dynamic programming and sequence alignment
- Tue 25.9. 12-14 Study groups on Chapter 6, assignments on slides 33-35
- Thu 27.9. 10-12 Exercises on Chapter 6, exercise sheet, model solutions
- Thu 27.9. 12-14 Introduction to Chapter 8: Graph algorithms and DNA sequencing
- Tue 2.10. 12-14 Study groups on Chapter 8, assignments on slides 31-33
- Thu 4.10. 10-12 Exercises on Chapter 8, exercise sheet, model solutions
- Thu 4.10. 12-14 Introduction to Chapter 10: Distance based clustering and phylogeny (Errors in presenting neighbor joining fixed!)
- Tue 9.10. 12-14 Study groups on Chapter 10, assignments on slides 36-38
- Thu 11.10. 10-12 Exercises on Chapter 10, exercise sheet, model solutions
- Thu 11.10. 12-14 No lecture!
Exams
-
Course exam: Wednesday Oct 17th at 9:00 sharp (don't be late)
- Course graded, see 2nd floor notice board
- Grounds for grading
- Feedback session 1.11. at 14-15, room A219; also anonymous feedback is welcome, especially ideas to improve the course
- Check later exam dates here