Highly complex and networked systems are being introduced into all levels of our global infrastructure. They provide the basis for many application domains including automated transportation networks, distributed power generation, and formation-flying satellites. The study of these systems, however, has yet to be formalized as a proper engineering discipline. A fundamental goal of work done within the Cooperative Networks and Controls Lab, therefore, is to contribute to the development of the network sciences and engineering as a formal engineering science. Towards this goal, our research focuses on the complimentary problems of analysis and design of networked and multi-agent systems. Our scientific approach is to explore how the mathematical field of graph theory can interface with dynamic systems and control theory in the study of these systems. We are currently focused on three core projects: i) analysis and design of networked systems, ii) formation control and multi-robot coordination, and iii) distributed power generation and the smart-grid. We focus on fundamental theory while also exploring implementation challenges on a multi-robot testbed as a demonstrator.