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Course on Modeling of Genetic and Metabolic networks

INSA 5BIM (2011-2012)


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 21 : Introduction to the course (Hidde de Jong), slides, articles

-  October 5 : Reminders on dynamical systems (Hidde de Jong), slides, articles

-  October 19 : Introduction to regulatory systems (Hans Geiselmann), slides

-  October 19, November 2 : Reminders on enzymology and kinetic modeling, introduction to metabolomics (Daniel Kahn), slides

Part 2. Gene regulatory network modeling (courses 12 h, and practicals 6 h)

-  November 2 : Introduction to recent techniques for measuring gene expression (Hidde de Jong), slides, article

-  November 9 and 16 : Kinetic models of gene expression and dynamics of gene regulatory networks (Hidde de Jong), slides, slides, articles

-  January 18 : Structural and parametric identification of gene network models (Eugenio Cinquemani), slides, articles

-  November 9 and 16 : Practical on the qualitative modeling of E. coli regulatory networks, using GNA (Hidde de Jong), handout, model

Part 3. Metabolic network modeling (courses 8 h, and practicals 9 h)

-  November 23, 30, December 7 and 14 : Metabolic control theory (Daniel Kahn), slides, article slides, slides, articles, slides, slides, articles

-  November 23, December 7 and 14 : Practical on the modeling of a metabolic system using COPASI (Daniel Kahn), handout

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

-  January 25 : 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)