582653 Computational methods of systems biology (4 cr)
The course is an advanced introduction to computational methods for analysing genomic and gene expression data to find different functional units (such as genes) and regulatory structures and relations (such as gene enhancers).
News
- The extra exercises are now available.
- More background material (appendixes of Alon's book) has been distributed in the lectures. If you do not have a copy yet, you can get it from Leena Salmela (Room B226).
- Esa Pitkänen gives the lecture on Dec 1st. See background material for the lecture.
- Checklist (in intranet) of exercise points is available.
- Two sets of background material have been distributed in the lectures. If you do not have a copy yet, you can get it from Leena Salmela (Room B226).
Course Prerequisites
- Data structures, Basic skills in probability or statistics
Lectures
- Prof. Esko Ukkonen | 03.11.-10.12. | Tuesday 10-12, Thursday 10-12 | B222
Lecture Material
- Lecture 0 (Nov. 3rd)
- Lecture 1 (Nov. 10th)
- Lecture 2 (Nov. 12th)
- Lecture 3 (Nov. 17th)
- Lecture 4 (Nov. 19th)
- Lecture 5 (Nov. 24th)
- Lecture 6 (Nov. 26th)
- Lecture 7 by Esa Pitkänen (Dec. 1st)
- Lecture 8 (Dec. 3rd)
- Lecture 9 (Dec. 8th)
- Lecture 10 (Dec. 10th)
Background material
- M. Durot, P.-Y. Bourguignon, and V. Schachter: Genome-scale models of bacterial metabolism: reconstruction and applications. FEMS Microbiol Rev. 33:164-190, 2009. (Sections Introduction, Foundations of genome-scale metabolic modeling, and Building the models)
Exercise sessions
- Group 1: D.Sc.(Tech) Leena Salmela | 12.11.-10.12. | Thursday 14-16 | B119
- Group 2: D.Sc.(Tech) Leena Salmela | 12.11.-10.12. | Thursday 16-18 | B119
- If you cannot participate exercise session, you may return your exercise solutions electronically or on paper to Leena Salmela (Room B226) by Thursday at 14.00
- To be eligible to take the exam you have to solve at least 50 percent of the total number of exercise problems. If you solve more than that you'll get 0..10 points such that solving 80 percent or more gives full 10 points
- Checklist (in intranet) of exercise points
Exercises
- Exercise 1 (Nov. 12th)
- Exercise 2 (Nov. 19th)
- Exercise 3 (Nov. 26th)
- Exercise 4 (Dec. 3rd)
- Exercise 5 (Dec. 10th)
- Exercise 6 (Extra exercises)
Grading
- 60 points maximum
- exercise activity 10 points
- exam 50 points
Exam
- Thursday 17th of December from 16.00 to 19.00 in A111, Exactum.
Leena Salmela Last modified: Dec 15 13:06:00 EEST 2009