Mathematical Modeling in Systems Biology

Mathematical Modeling in Systems Biology#

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

Contents