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Course on Modeling of Genetic and Metabolic Networks

INSA 5BIM (2012-2013)


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 7 h)

-  September 26 : Introduction to the course (Hidde de Jong), slides, articles

-  September 26 : Introduction to regulatory systems (Hans Geiselmann), slides, articles

-  October 3 : Reminders on dynamical systems (Hidde de Jong), slides, articles

-  October 10 : Reminders on enzymology and kinetic modeling (Daniel Kahn), slides, articles

Part 2. Metabolic network modeling (courses 6 h and practicals 9 h)

-  October 17 and 24, December 5 : Metabolic control theory (Daniel Kahn), slides, slides, slides, articles, slides, articles

-  November 14 and 28, December 5 : Practical on the modeling of a metabolic system using COPASI (Daniel Kahn), handout, manual

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

-  November 21 : Introduction to gene regulatory networks and recent techniques for measuring gene expression (Hidde de Jong), slides

-  November 21, December 12 and 19 : Kinetic models of gene expression and dynamics of gene regulatory networks (Hidde de Jong), slides, slides, articles, slides, articles, slides, articles

-  January 23 : Structural and parametric identification of gene network models (Eugenio Cinquemani), slides, articles, slides Khammash

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

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, article, SI article

Contact

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