Cours on modeling of metabolic and genetic networks, INSA de Lyon (2018-2019)

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)

- September 26, 2018: Introduction to the course (Hidde de Jong), slides, article

- September 26, 2018: Introduction to regulatory systems (Hans Geiselmann), slides

- October 10, 2018: Reminders on enzymology and kinetic modeling (Daniel Kahn), slides, slides, article

Part 2. Metabolic network modeling (courses and practical)

- October 10, 17, and 24, 2018: Metabolic control theory (Daniel Kahn), slides, slides, slides, hand-out, hand-out, article, article, article

- November 7, 2018: Flux balance analysis (Daniel Kahn), slides, article

- October 17, 2018: Practical on the modeling of metabolic networks using Copasi (Daniel Kahn), manual, model

- November 7, 2018: Practical on the modeling of metabolic networks using Cobra (Daniel Kahn), material

Part 3. Gene regulatory network modeling (courses)

- October 3, 2018: Introduction to gene regulatory networks and recent techniques for measuring gene expression (Hidde de Jong), slides, article

- October 3, November 14, 21, and 28, 2018: Modeling and identification of gene regulatory networks using deterministic models (Hidde de Jong), slides, articles, slides, article, slides, articles, slides, articles

- December 5 and 12, 2018: Modeling and identification of gene regulatory networks using stochastic models (Eugenio Cinquemani), slides, articles, additional material

Part 4. Integrated network modeling (courses and practical)

- November 28, 2018: Modeling of integrated networks of metabolism and gene expression (Hidde de Jong), slides

- November 14, 21, and 28, 2018: Practical on the modeling of bacterial regulatory networks using MATLAB (Hidde de Jong), handout, models

 

Evaluation

- January 9, 2018: Written exam

Contact

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

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