582469 Computational Systems Biology (6 cr)

The course discusses functioning of cells from the systems perspective: metabolic networks and gene regulation. Guest lecturers introduce the biological background, after which analysis and modeling methods are discussed. The course is organized as collaboration of the departments of computer science and biosciences.

News

Please give feedback on the course!
No lectures or exercises during Easter holidays 13-19 April.
Hannu Maaheimo (VTT) will give a guest lecture on Thursday 6.4. at 14-16 (D122).
No lecture on Wednesday 22.3.
Matej Oresic (QBIX/VTT) will give a guest lecture on Thursday 30.3. at 14-16 (D122).
Lecture notes can be found in course material room C127.
Course grading guidelines are now available.
An info session will be held on the Master's Degree Programme in Bioinformatics on Tuesday 14.3. at 13-16 in CK122. The talks will be in Finnish.
First lecture on Wednesday 15.2. at 12-14 in D122.

Exercises

Exercise 1 (23.2.)
Exercise 2 (2.3.)
Exercise 3 (23.3.)
Exercise 4 (30.3.)
Exercise 5 (6.4.)
Exercise 6 (20.4.)
Exercise 7 (27.4.)

Lecture notes

23.2. (Teemu Teeri: Flower development)
15.3. (Metabolism, enzyme kinetics)
16.3. (Steady state analysis)
22.3. (Flux estimation)
29.3. (Flux estimation from incomplete isotopomer data)
30.3. (Matej Oresic: Metabolic profiling)
6.4. (Hannu Maaheimo: Determination of metabolic flux by NMR and mass spectroscopy)
12.4. (Metabolic control analysis)
19.4. (MCA continued)
20.4. (Biodatabases and data integration)
26.4. (SRS)

Schedule

Week	Topics
1-2 (15.2-23.2)	Biological background, regulation of gene expression
3 (15.3-16.3)	Metabolic network basics, metabolic profiling
4 (22.3-23-3)	Flux analysis, flux balance analysis, convex analysis
5 (29.3-30.3)	Isotopic tracing and flux estimation
6 (5.4-6.4)	Metabolic control analysis
7-8 (19.4-27.4)	Biodatabases, data integration, ontologies

Staff

Lecturers

Guest lecturers

Doc. Matej Oresic, Quantitative Biology and Bioinformatics, VTT
Doc. Hannu Maaheimo, VTT
Prof. Teemu Teeri, Department of Applied Biology, Faculty of Agriculture and Forestry, University of Helsinki

Course assistant

Esa Pitkänen, Department of Computer Science

Date and place

The course is held in the Exactum building, Kumpula Campus.

Lectures: 15-23.2., 15.3.-27.4. Wednesdays at 12-14 in D122, Thursdays at 14-16 in D122
Exercises: 23.2.-2.3., 23.3.-4.5. Thursdays 12-14 in C220

Grading

Exercises: max. 10 points
Course exam: max. 50 points
You need 30 points in total to pass the course (grade 1/5)
At least 50 points are required to get the grade 5/5

Exam

Course exam: Friday 5.5. at 16.00-19.00 in A111
List of course exam dates and places

Course material

E. Klipp et al.: Systems Biology in Practice. Concepts, Implementation and Application. Wiley-VCH, Weinheim, 2005.
You can get the lecture notes from the course material room C127.

Previous update: 05.05.2006 15:55 - Esa Pitkänen

Department of Computer Science

Department information