Algorithms for Bioinformatics
Luennot
Aika | Huone | Luennoija | Päivämäärä |
---|---|---|---|
Ma 12-14 | B222 | Veli Mäkinen | 06.09.2010-13.10.2010 |
Ke 10-12 | B222 | Veli Mäkinen | 06.09.2010-13.10.2010 |
To 10-12 | BK107 | Veli Mäkinen | 07.10.2010-07.10.2010 |
Harjoitusryhmät
Aika | Huone | Ohjaaja | Päivämäärä | Huomioitavaa |
---|---|---|---|---|
Ma 10-12 | C222 | Niko Välimäki | 13.09.2010—15.10.2010 |
The lecture on Wed 6th of Oct has been moved to Thu 7th of Oct at 10-12 in room BK107.
Information for international students
Course will be given in English.
Yleistä
News: Exam graded. See 2. floor notice board for results and here for solutions and grounds for grading. Feedback session is on 1st November at 14:15-15:00 B218.
Course introduces basic algorithmic concepts through motivation by selected computational molecular biology problems. It is targeted especially to students from biological sciences who want to obtain a foundational level understanding of computer science behind bioinformatics tools. Also suitable for first year students in Master"s Degree Programme in Bioinformatics. Prerequisites: programming skills.
Kurssin suorittaminen
The course consists of lectures, study groups, and exercices, as follows:
- Mon 12-14 there will be an introductory lecture to the week's topics.
- Wed 10-12 there will be (mandatory) study group meeting aiming at an in-depth coverage of the week's topics.
- Mon 10-12 there will be an exercice session on the previous 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 Wednesday, with the fellow student 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 Wednesday'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 60 points at the maximum. Active participation to exercises gives maximum 6 extra points (25%->1p,37.5%->2p,50%->3p,62.5%->4p,75%->5p,87.5%->6p). The grading is then based on the total points achieved.
Kirjallisuus ja materiaali
Course book
Neil C. Jones & Pavel A. Pevzner: An Introduction to Bioinformatics Algorithms (MIT Press, 2004).
Course content
- Mon 6.9. No lecture: University opening seremony
- Wed 8.9. 10-12. Introduction to Chapters 1-3: Primer to algorithms and to molecular biology
- Mon 13.9. 10-12. Exercises on Chapters 1-3: exercise sheet, ex1_3.py, ex1_5.py, solutions
- Mon 13.9. 12-14. Introduction to Chapter 4: Exhaustive search and motif finding
- Wed 15.9. 10-12. Study group on Chapter 4
- Mon 20.9. 10-12. Exercises on Chapter 4: exercise sheet, solutions
- Mon 20.9. 12-14. Introduction to Chapter 5: Greedy algorithms and genome rearrangements (page 27 updated after the exam; see here for the reason.)
- Wed 22.9. 10-12. Study group on Chapter 5: presentations material for group 3
- Mon 27.9. 10-12. Exercises on Chapter 5: exercise sheet, solutions
- Mon 27.9. 12-14. Introduction to Chapter 6: Dynamic programming and sequence alignment
- Wed 29.9. 10-12 Study group on Chapter 6: presentations
- Mon 4.10. 10-12 Exercises on Chapter 6: exercise sheet, solutions
- Mon 4.10. 12-14. Introduction to Chapter 8: Graph algorithms and DNA sequencing
- Thu 7.10. 10-12 room BK107 Study group on Chapter 8
- Mon 11.10. 10-12. Exercises on Chapter 8: exercise sheet, solutions
- Mon 11.10. 12-14. Sequencing by hybridization & Chapter 12: Randomized algorithms and motif finding
- Wed 13.10. 10-12. Study group / exercises on Monday's lecture: exercise sheet, solutions
- Wed 20.10. 9-12 A111 COURSE EXAM: solutions / grounds for grading
- Check renewal/separate exam dates here