Analysis and design of biological circuits and systems

Systems and synthetic biology are two emerging disciplines that hold promise to revolutionize our understanding of biological systems and to herald a new era of programmable hardware, respectively. Mathematical abstraction and today's abundance of quantitative biological data enables the up-scaling of analysis and design methodologies. In this tutorial paper we provide an engineering-centered introduction to those disciplines. Biological key concepts such as the central dogma of molecular biology are discussed, descriptions of bio-molecular reaction networks in terms of continuous-time Markov processes and ordinary differential equations are reviewed. Topological analysis of networks is introduced and the methods of metabolic flux balance analysis and elementary flux modes or extreme pathways are discussed.