Algorithms for Bioinformatics
Koe
Vuosi | Lukukausi | Päivämäärä | Periodi | Kieli | Vastuuhenkilö |
---|---|---|---|---|---|
2011 | syksy | 05.09-12.10. | 1-1 | Englanti | Veli Mäkinen |
Luennot
Aika | Huone | Luennoija | Päivämäärä |
---|---|---|---|
Ma 12-14 | B222 | Veli Mäkinen | 05.09.2011-12.10.2011 |
Ke 10-12 | B222 | Veli Mäkinen | 05.09.2011-12.10.2011 |
Harjoitusryhmät
Aika | Huone | Ohjaaja | Päivämäärä | Huomioitavaa |
---|---|---|---|---|
To 10-12 | BK107 | Niko Välimäki | 12.09.2011—14.10.2011 |
Yleistä
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.
Kurssin suorittaminen
The course consists of lectures, study groups, and exercices, as follows:
- Mon 12-14 there will be (mandatory) study group meeting aiming at an in-depth coverage of the week's topics.
- Wed 10-12 there will be an introductory lecture to the next week's topics. (cycle starts here)
- Thu 10-12 there will be an exercice session on the week's topics.
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 Monday, 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 Monday'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.
Kirjallisuus ja materiaali
Course book
Neil C. Jones & Pavel A. Pevzner: An Introduction to Bioinformatics Algorithms (MIT Press, 2004).
Course content
- Mon 5.9. No lecture: University opening seremony
- Wed 7.9. 10-12. Introduction to Chapters 1-3: Primer to algorithms and to molecular biology (Niko Välimäki)
- Mon 12.9. 12-14. Study group on Chapter 1-3: assignments on slides 32-33
- Wed 14.9. 10-12. Introduction to Chapter 4: Exhaustive search and motif finding
- Thu 15.9. 10-12. Exercises on Chapters 1-3: exercise sheet, example solutions
- Mon 19.9. 12-14. Study group on Chapter 4: assignments on slides 85-88
- Wed 21.9. 10-12. Introduction to Chapter 5: Greedy algorithms and genome rearrangements
- Thu 22.9. 10-12. Exercises on Chapter 4: exercise sheet, example solutions
- Mon 26.9. 12-14. Study group on Chapter 5: assignments on slides 52-54
- Wed 28.9. 10-12. Introduction to Chapter 6: Dynamic programming and sequence alignment
- Thu 29.9. 10-12 Exercises on Chapter 5: exercise sheet, example solutions
- Mon 3.10. 12-14 Study group on Chapter 6: assignment on slides 28-30
- Wed 5.10. 10-12. Introduction to Chapter 8: Graph algorithms and DNA sequencing
- Thu 6.10. 10-12 Exercises on Chapter 6: exercise sheet , example solutions
- Mon 10.10. 12-14. Introduction to Chapter 10: Distance-based clustering and phylogeny (+interval graphs from previous slide set)
- Wed 12.10. 10-12. Study group on Chapters 8 and 10: exercise sheet , example solutions
- Thu 13.10. 10-12. Exercises on Chapters 8 and 10: exercise sheet, example solutions
- Course exam: Wednesday 19.10 at 9.00 (sharp!, don't be late) B123
- Course graded, see 2. floor notice board
- Grounds for grading
- Feedback session 31.10. at 11-12, room A219; also anonymous feedback is welcome, especially ideas to improve the course
- Check later exam dates here