Objectives
The objective of the course is to learn mathematical modelling as applied to metabolic and gene regulatory 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 regulatory networks.
Course program
Part 1. Systems biology and kinetic modeling (courses)
September 16, 2020: Introduction to the course, slides, article
September 16, 2020: Kinetic modeling of biochemical reaction networks, slides, article
Part 2. Metabolic network modeling (courses and practical)
September 23, 2020: Metabolic control theory, slides, article
September 30, 2020: Flux balance analysis, slides, article
October 14, 2020: Practical on the modeling of metabolic networks using COBRA, handout, corrected hand-out, code, models
Part 3. Gene regulatory network modeling (courses and practical)
November 4, 2020: Quantitative modeling of gene regulatory networks, slides, article
November 11 and 18, 2020: Qualitative modeling of gene regulatory networks, slides, article
November 18, 2020: Stochastic modeling of gene regulatory networks, slides, articles
November 25 and December 2, 2020: Practical on the modeling of bacterial regulatory networks using MATLAB (Hidde de Jong), handout, models
Part 4. Models and data (courses)
December 9, 2020: Model calibration and validation, slides, article
December 9, 2020: Model-based data integration, slides, article
Evaluation
December 16, 2020: Feedback on mini-projects, list of mini-projects, presentation
Contact
Hidde de Jong (Hidde.de-Jong@inria.fr)
