Algorithms for Bioinformatics
Exam
Year | Semester | Date | Period | Language | In charge |
---|---|---|---|---|---|
2013 | autumn | 03.09-10.10. | 1-1 | English | Alexandru Tomescu |
Lectures
Time | Room | Lecturer | Date |
---|---|---|---|
Tue 12-14 | C222 | Alexandru Tomescu | 03.09.2013-10.10.2013 |
Thu 12-14 | B222 | Alexandru Tomescu | 03.09.2013-10.10.2013 |
Exercise groups
Time | Room | Instructor | Date | Observe |
---|---|---|---|---|
Tue 10-12 | B119 | Anna Kuosmanen | 09.09.2013—11.10.2013 |
General
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.
Topics covered: Exhaustive search and motif finding, Greedy algorithms and genomic rearrangements, Dynamic programming and sequence alignment, Graph algorithms and DNA sequencing, Distance-based clustering and phylogeny
Prerequisites: programming skills.
Completing the course
The course consists of lectures, study groups, and exercises, as follows:
First week
- Tue 12-14 - First lecture (introductory)
- Thu 12-14 - Second lecture
Other weeks
- Tue 10-12 - Exercise session on the previous week's topics
- Tue 12.30-14 - 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 12.30-14 - Lecture
Lectures end with a list of topics and their assignments to the students. 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. 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:
- The course exam is on 16.10.2013, at 16.00 in Room A111, and lasts for 2.5 hours http://www.cs.helsinki.fi/kokeet/kkokeets13.html
- To take this exam, you must have attended all study group meetings (or have contacted the lecturer that you cannot attend), and gotten at least 1 point from the exercise sessions
- There is no separate registration required for the course exam
- Gounds for grading the exam here.
Separate exam:
- The first separate exam is on 26.11.2013, at 16.00 in Room B123, and lasts for 3.5 hours http://www.cs.helsinki.fi/kokeet/ekokeets13.html
- You don't need study group attendance or the extra points from the exercise sessions
- However, if you have points from the exercise sessions, this is the only separate exam at which you can use them
- You must register for the separate exam in ilmo.cs.helsinki.fi by Monday of the previous week (that is, 18.11.)
- Gounds for grading the exam here.
Course feedback
- Your feedback in imporving the course is greatly appreciated. Please use this anonymous feedback form.
Literature and material
Course material & schedule
Lectures and study groups start at 12.30 and end at 14.00.
If you have questions about the lectures, you can make an appointment by e-mail at tomescu@cs.helsinki.fi (propose a time between 10 - 12 and 13 - 16.30).
Week 1:
- Molecular biology primer (Tue 3.09.2013)
- Introductory lecture (Tue 3.09.2013, 12-14 pm)
- Some videos: The inner life of a cell, DNA Sequencing's Promise for Personalized Medicine, Illumina sequencing, Google's Larry Page on healthcare, Google's Larry Page on DNA sequencing
- Lecture 2: Exhaustive search and motif finding (Thu 5.09.2013, 12-14 pm)
Week 2:
- Exercise session (Tue 10.09.2013, 10-12 am) - Exercise 1 problems
- Study group meeting (Tue 10.09.2013, 12.30-14 pm) - assignments given on slides 29-30 of Introductory lecture and in slides 85-87 of Lecture 2
- Lecture 3: Greedy Algorithms and Genomic Rearrangements (Thu 12.09.2013 - 12.30 - 14 pm)
Week 3:
- Exercise session (Tue 17.09.2013, 10-12 am) - Exercise 2 problems
- Study group meeting (Tue 17.09.2013, 12.30-14 pm) - assignments given on slides 49-51 of Lecture 3
- Lecture 4: Dynamic Programming and Sequence Alignment (Thu 19.09.2013, 12.30 - 14) -- slide 27 corrected
Week 4:
- Exercise session (Tue 24.09.2013, 10-12 am) - Exercise 3 problems
- Study group meeting (Tue 24.09.2013, 12.30-14 pm) - assignments given on slides 33-35 of Lecture 4
- Lecture 5: Graph Algorithms and DNA Sequencing (Thu 26.09.2013, 12.30 - 14)
Week 5:
- Exercise session (Tue 1.10.2013, 10-12 am) - Exercise 4 problems
- Study group meeting (Tue 01.10.2013, 12.30-14) - assignments given on slides 30-32 of Lecture 5
- Lecture 6: Distance based clustering and phylogeny (Thu 03.10.2013, 12.30-14)
Week 6:
- Exercise session (Tue 08.10.2013, 10-12) - Exercise 5 problems
- Study group meeting (Tue 08.10.2013, 12.30-14) - assignments given on slides 35-37 of Lecture 6.
Course book
Neil C. Jones & Pavel A. Pevzner: An Introduction to Bioinformatics Algorithms (MIT Press, 2004). It is not necessary to purchase the book, but the course will follow a similar structure.
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.