INTRO COMPUTATIONAL SYSTEMS BIOLOGY: MODELING & DESIGN PRINCIPLES OF BIOCHEM NETWORKS

Credit Hours: 3 · Graduate

The course summarizes techniques for quantitative analysis and simulations of basic circuits in genetic regulation, signal transduction, and metabolism. The class is based on MATLAB, with a brief refresher provided at the beginning. We discuss engineering approaches adapted to computational systems biology and aim to formulate evolutionary design principles explaining the organization of networks in terms of their physiological demands. Topics include end-product inhibition in biosynthesis, optimality and robustness of the signaling networks, and kinetic proofreading. The topics covered include modeling of enzyme kinetics, biochemical reaction networks, gene regulation, stochasticity of gene expression, and evolutionary and epidemiological population dynamics. The final project focuses on modeling synthetic biology circuits. Cross-list: BIOE 552 . Recommended Prerequisite(s): Basic knowledge of biochemistry, cell biology, linear algebra, and ordinary differential equations is expected. Experience with MATLAB or Python programming is highly recommended.