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Course on Modeling of Biological Networks

INSA 5BIM (2009-2010)


The objective of the course is to master 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 24 : Introduction to the course (Hidde de Jong), slides

-  October 1 : Reminders on dynamical systems (Sandrine Charles), slides

-  October 8 and 15 : Introduction to regulatory systems (Hans Geiselmann), slides

-  October 9 : Reminders on enzymology (Michel Lagarde), slides

-  October 22 : Reminders on kinetic modeling (Daniel Kahn), slides

Part 2. Metabolic network modeling (courses 10 h, and practicals 8 h)

-  October 16 and 23 : Introduction to metabolome (Michel Lagarde), slides

-  November 5, 12 and 26 : Metabolic control theory (Daniel Kahn), slides, articles

-  November 6 and 27 : 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 10 h, and practicals 8 h)

-  December 10 and 17, January 14 : Kinetic models of gene expression and dynamics of gene regulatory networks (Hidde de Jong), slides, slides

-  January 21 and 28 : Identification and inference of gene network models (Lilia Brinza and Eugenio Cinquemani), slides, slides

-  January 20 and 27 : 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)

-  February 4 : MetaGenoReg project (Daniel Kahn and Hidde de Jong), slides


Homework exercises (hand-out) and article synthesis (articles)


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