Metabolic Modelling, Spring 09 (4 cr, 2 cu)
Computational methods in the analysis of metabolic networks are studied, including the reconstruction and regulation of metabolism, analysis of metabolic fluxes, and structural analysis of metabolic networks. Prerequisities: Introduction to bioinformatics and basic linear algebra skills.
Lectures: Juho Rousu
Exercises: Markus Heinonen
The course will be lectured in english. The exam questions may be answered in finnish or in english.
News
Excercises are completed at home and are then presented at the excercise session by the students.
The next normal exercises will be at tuesday 21.4 (no exercise in 14.4). Also an extra writing assignment has the deadline friday 24.4
Course exam
- Wednesday 29.4.2009 9am-12pm, in A111
- Examined contents: Lecture slides and excercises. The lecture of Hannu Maaheimo and the scientific articles are not part of the examined contents.
Time and place
- Lectures: 10.03.-24.04. Tuesday, Friday: 14-16 B119
- Exercises: 16.03.-24.04. Tuesday 16-18 C221
Lecture Schedule
- 10.3: Introduction, Metabolic reconstruction
- 13.3: BioCyc Webinars
- 17.3: Representation of metabolic models: graphs
- 20.3: Structural analysis of metabolic networks, stoichiometry
- 24.3: Stoichiometric analysis of metabolic networks
- 27.3: FBA, Gapless reconstruction (Esa Pitkänen)
- 31.3: Null space, SVD, Elementary Flux Modes
- 3.4: Metabolic flux estimation
- 7.4: Isotopomers
- 10.4: Easter holiday, no lectures
- 14.4: Easter holiday, no lectures
- 17.4: Kinetics, MCA
- 21.4: Lecture by Hannu Maaheimo
- 24.4:
Exercises
- 17.3: Excercise 1: Write a summary about the paper describing PathoLogic tool.
- 24.3: Excercise 2 [ Solutions
]: Computer practicals using MATLAB in the class in BK107. - 30.3: Excercise 3 [ Solutions ]
- 7.4: Excercise 4 [ Solutions ]
- 21.4: Excercise 5 [ Solutions ]. Note that an extra summary writing exercise is due at 24.4.
Course Materials
- Lecture slides
- BioCyc Webinars:
- Part 1: Building the Database (56:42) [WMV
] [Quicktime 
] - Part 2A: General Editing Strategies (8:00) [WMV ] [Quicktime ]
- Part 2B: Creating and Editing Reactions and Compounds (17:32) [WMV ] [Quicktime ]
- Part 2C: Working With Proteins, Citations, GO Terms, and Enzymatic Reactions (26:10) [WMV ] [Quicktime ]
- Part 2D: Making and Editing Pathways (9:42) [WMV ] [Quicktime ]
- Part 1: Building the Database (56:42) [WMV
Background literature
- E. Klipp, R. Herlig, A. Kowald, C. Wierling, H. Lehrach: Systems Biology in Practice. Wiley-VCH, 2005.
- B. Palsson: Systems Biology: Properties of Reconstructed Networks. Cambridge University Press, 2006.