Optimization and Biological Networks

Catalog description

Mathematical optimization, formulation and solution techniques for linear, nonlinear, and mixed-integer problems; optimization-based tools for reconstruction, analysis, and redesign of biological networks. CH E 512 Optimization and Biological Networks (3) This course focuses on the principles and applications of mathematical optimization in biological systems. The first part of the course addresses optimization theory, solution algorithms, and implementation software. Topics include nonlinear optimization, linear programming, mixed-integer linear and nonlinear optimization, and bi-level optimization. Emphasis will be placed on understanding the logic of the methodology, underlying key assumptions, comparative merits and shortcomings, and applications for solving engineering problems. Valuable hands-on experience will be provided on coding optimization models using GAMS (General Algebraic Modeling System) and specialized optimization solvers. The latter part of the course concentrates on applying the tools necessary to address the challenges arising in biological networks. Specifically, the use of optimization in reconstructing and analyzing genome-scale models of metabolism, protein library design strategies, regulatory network elucidation, and synthetic circuits design as well as optimal modifications in metabolic networks for various bioengineering tasks will be studied.