Components of biological networks, their biochemical properties and function along with the technology used for obtaining component lists will be emphasized. Top-down and bottom-up approach to modeling and reconstruction of chemical reaction networks along with biochemical networks, such as metabolic networks, regulatory networks, and signaling networks from data will be presented. Mathematical models of reconstructed reaction networks, and simulation of their emergent properties will be studied. The course will also cover classical kinetic theory, network simulation methods and constraints-based models of biochemical networks. Multi-scale modeling methods that integrate multiple cellular processes at different time and length scales will be emphasized. Existing biological models will be described and computations performed. Iterative methods for discovering novel biological function through comparison of model predictions and experimental data will be discussed in the context of Systems Biology and Bioengineering.