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Course on Modeling of Genetic and Metabolic Networks

INSA 5BIM (2013-2014)


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 8 h)

-  September 25 : Introduction to the course (Hidde de Jong), slides, articles

-  September 25 : Reminders on dynamical systems (Hidde de Jong), slides, articles

-  October 2 : Reminders on enzymology and kinetic modeling (Daniel Kahn), slides, articles

-  October 23 : Introduction to regulatory systems (Hans Geiselmann), slides, articles

Part 2. Metabolic network modeling (courses and practical 18 h)

-  October 9 and 16 : Metabolic control theory (Daniel Kahn), slides, slides, slides, articles, slides, article

-  November 6, 13, 20 and 27 : Practical on the modeling of a metabolic system using COPASI (Daniel Kahn), handout, handout,manual, model, data

Part 3. Gene regulatory network modeling (courses 14 h, and practicals 6 h)

-  December 4 : Introduction to gene regulatory networks and recent techniques for measuring gene expression (Hidde de Jong), slides

-  December 4, 11, and 18 : Kinetic models of gene expression and dynamics of gene regulatory networks (Hidde de Jong), slides, articles, slides, slides, articles, slides, articles

-  January 15 : Structural and parametric identification of gene network models (Eugenio Cinquemani), slides, articles

-  December 11 and 18 : Practical on the qualitative modeling of bacterial regulatory networks, using GNA (Hidde de Jong), handout, model

Part 4. Concluding presentation (presentation 2 h)

-  January 28 : SeMoVi seminar (Uwe Sauer), slides, articles

Evaluation

Homework exercises and synthesis of articles, hand-out

Contact

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