Algorithms for Bioinformatics
4
Bioinformatiikka
Aineopinnot
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.
Koe
20.10.2015
09.00
A111
| Vuosi | Lukukausi | Päivämäärä | Periodi | Kieli | Vastuuhenkilö |
|---|---|---|---|---|---|
| 2015 | syksy | 01.09-15.10. | 1-1 | Englanti | Juha Kärkkäinen |
Luennot
| Aika | Huone | Luennoija | Päivämäärä |
|---|---|---|---|
| Ti 12-14 | B222 | Juha Kärkkäinen | 01.09.2015-15.10.2015 |
| To 12-14 | B222 | Juha Kärkkäinen | 01.09.2015-15.10.2015 |
Harjoitusryhmät
| Aika | Huone | Ohjaaja | Päivämäärä | Huomioitavaa |
|---|---|---|---|---|
| Ti 10-12 | B222 | Daniel Valenzuela | 07.09.2015—16.10.2015 |
Yleistä
The course exam has been graded. See results at TIKLI and grounds for grading. You can see your exam paper and get feedback on Wed 4.11. at 14:00-14:30 in room B214 (or contact the lecturer for another time).
The 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 exercises, as follows:
First week
- Tue 12-14 - First lecture
- Thu 12-14 - Second lecture
Other weeks
- Tue 10-12 - Exercise session on the previous week's topics
- Tue 12-14 - Study group meeting, aiming at an in-depth coverage of the previous week's topics. This is mandatory; in case you cannot attend for contact me personally.
- Thu 12-14 - Lecture
The study group assignments are provided on the lectures. The assigned 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. The 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). You need at least 1p from the exercise seesion to enter the exam.
- With 35 exercise problems in total, 10 solved problems is needed for 1 extra point and 29 solved problems gives the maximum 12 points.
The grading is then based on the total points (maximum 60) achieved (~30 points -> 1 and ~50 points -> 5, depending on the difficulty of the exam).
COURSE EXAM
- Tue 20.10. at 9:00 (not 9:15) in A111. The exam lasts 2.5 hours.
- Look at the exams from the previous years' courses to see examples of exam questions. (But note that the content of the course has changed.)
- To participate in the exam, you need at least 10 solved exercises and all 5 study group attendances (projects in TIKLI). You can check your status in TIKLI. Please check that the number of exercises have been correctly registered. Please contact the lecturer if you find errors or are not sure about your eligibility.
- Grounds for grading. You can see your exam paper and get feedback on Wed 4.11. at 14:00-14:30 in room B214 (or contact the lecturer for another time).
RENEWAL/SEPARATE EXAM
- Tue 01.12.2015 at 16:00 in B123 (Please check time and place later). The exam lasts 3.5 hours.
- May be taken as a renewal exam (which replaces the course exam) or as a separate exam (which does not require exercises or study groups).
Kirjallisuus ja materiaali
Lecture notes, exercise problems and other material will added here during the course.
WEEK 1
Tue 1.9.
- 12-13: Introductory lecture
- 13-14: Lecture 1: Algorithmic warm-up (part 1)
Thu 3.9.
- 12-13: Lecture 1: Algorithmic warm-up (part 2)
- 13-14: Python crash course
WEEK 2
Tue 8.9.
-
10-12: Exercises 1: Problems
- ROSALIND
- To get started, this program reads and prints the input for ROSALIND problem BA1B
- 12-14: Study group
Thu 10.9.
WEEK 3
Tue 15.9.
- 10-12: Exercises 2: Problems
- 12-14: Study groups 2: Assignments
Thu 17.9.
WEEK 4
Tue 22.9.
-
10-12: Exercises 3: Problems
- Example input and output for Rosalind problem NEWBA3C: input_newba3c_1.txt, output_newba3c_1.txt (corrected 17.9. at 16:15)
- Example input and output for Rosalind problem NEWBA3D: input_newba3d_1.txt, output_newba3d_1.tx
- 12-14: Study groups 3: Assignments
Thu 24.9.
WEEK 5
Tue 29.9.
- 10-12: Exercises 4: Problems
-
12-14: Study groups 4: Assignments
- If you were not present at the lecture, please contact the lecturer about your assignment.
Thu 1.10.
- 12-14: Lecture 5: Combinatorial algorithms and genome rearrangements
WEEK 6
Tue 6.10.
- 10-12: Exercises 5: Problems
- 12-14: Study groups 5: Assignments
Thu 8.10.
- 12-14: Lecture 6: Combinatorial pattern matching
WEEK 7
Tue 13.10.
- 10-12: Exercises 6: Problems
- No study group
Thu 15.10.
- No lecture
Course book
Philip Compeau & Pavel Pevzner: Bioinformatics Algorithms: An Active Learning Approach (Active Learning Publishers, 2014). It is not necessary to purchase the book, but the course will follow a similar structure.
The previous course book covers a lot of the same topics: Neil C. Jones & Pavel A. Pevzner: An Introduction to Bioinformatics Algorithms (MIT Press, 2004). The book seems to be freely available here: http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.218.3258 (click on the PDF icon on the right) or directly here. A local copy is here.