# 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 ]

## 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.