Course information¶
👩🏫 Instructor: An-Chi Wei @ MD 521
🦜 Teaching assistant: Wen-Wei Tseng @ MD 705
📝 Announcements & homeworks: NTU Cool
📗 Textbook: Mathematical Modeling in Systems Biology(2013), by Brian P. Ingalls (pdf, MATLAB code)
📚 Additional materials
An Introduction to Stochastic Processes with Applications to Biology (Google the pdf file)
Course content¶
Chapter 1-4 describes mathematical modelling in molecular systems biology.
Basic notions of mathematical modelling.
Dynamic mathematical models of chemical reaction networks. (ODE models)
Biochemical kinetics of enzyme-catalyzed reactions and cooperative binding.
Model reductions.
Analyzing differential equation models: phase plane, stability, bifurcations, sensitivity analysis.
Chapter 5 and beyond are applications in specific biological domain(s).
Stoichiometric modelling for large-scale metabolic networks. e.g. COBRA
Signal transduction pathways.
Gene regulatory networks.
Electrophysiology and action potentials in excitable cells.
Other topics:
Agent-based modeling (ABM)
(Metabolic) flux balance analysis