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Course on Modeling of Genetic and Metabolic Networks

INSA 5BIM (2014-2015)


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

-  September 17 : Introduction to regulatory systems (Hans Geiselmann), slides, articles

-  September 24 : Reminders on enzymology and kinetic modeling (Daniel Kahn), slides

Part 2. Metabolic network modeling (courses and practical 13 h)

-  October 1 and 8 : Metabolic control theory (Daniel Kahn), slides, articles,

-  November 5, 12, 26 : Practical on the modeling of a metabolic system using COPASI (Daniel Kahn), handout, manual, model

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

-  November 19 : Introduction to gene regulatory networks and recent techniques for measuring gene expression (Hidde de Jong), slides

-  December 3, 10, and 17 : Kinetic models of gene expression and dynamics of gene regulatory networks (Hidde de Jong), slides, slides, articles, slides, articles, slides, articles

-  January 14 : Structural and parametric identification of gene network models (Eugenio Cinquemani), slides, articles

-  December 10 and 17 : Practical on the qualitative modeling of bacterial regulatory networks, using GNA (Hidde de Jong), handout, model

Part 4. Concluding presentation (presentation 2 h)

-  January 21 2015 : SeMoVi seminar (Dominique de Vienne, Myriam Ferro, GaŽl Yvert), slides, articles


Homework exercises and synthesis of articles, hand-out


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