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Course on Modeling of Genetic and Metabolic Networks

INSA 5BIM (2010-2011)


Objectives

The objective of the course is to learn kinetic modelling as applied to genetic and metabolic networks. This will concern both theoretical foundations and concrete applications to diverse systems of biological regulation. Applications will rely on the practical use of computer tools for the modelling, analysis and simulation of biological networks.

Course program

Part 1. Systems biology and kinetic modeling (courses 12 h)

-  September 22 : Introduction to the course (Hidde de Jong), slides, articles

-  September 29 : Introduction to regulatory systems (Hans Geiselmann), slides, articles

-  October 6 : Reminders on dynamical systems (Hidde de Jong), slides, articles

-  October 15 : Reminders on enzymology and kinetic modeling (Daniel Kahn), slides, articles

Part 2. Metabolic network modeling (courses 12 h, and practicals 9 h)

-  November 3 : Introduction to metabolomics (Michel Lagarde), slides, articles

-  October 20, November 10, 17 and 24 : Metabolic control theory (Daniel Kahn), slides, slides, slides, slides, articles, articles

-  November 10, 17 and 24 : Practical on the modeling of a metabolic system using general purpose (MATLAB) or specialised tools (COPASI) (Daniel Kahn), handout, model, data

Part 3. Gene regulatory network modeling (courses 12 h, and practicals 8 h)

-  October 13 : Introduction to recent techniques for measuring gene expression (Hans Geiselmann), slides

-  December 1, 8, and 15 : Kinetic models of gene expression and dynamics of gene regulatory networks (Hidde de Jong), slides, slides, articles

-  January 12 and 19 : Structural and parametric identification of gene network models (Eugenio Cinquemani), slides, articles

-  December 8 and 15 : Practical on the qualitative modeling of E. coli regulatory networks, using GNA (Hidde de Jong), handout, model

Part 4. Towards integrated models of regulatory networks (courses 2 h)

-  January 26 : MetaGenoReg project (Daniel Kahn and Hidde de Jong), slides

Evaluation

Homework exercises and synthesis of articles (hand-out, article).

Contact

Daniel Kahn (kahn@biomserv.univ-lyon1.fr) and Hidde de Jong (Hidde.de-Jong@inria.fr)