Computational bioalchemy: Optimal search algorithms for the analysis and synthesis of metabolic systems

This dissertation will focus on the application of novel metabolic pathway search technology to the emerging disciplines of systems biology and synthetic biology. Systems biology can be thought of as the reverse engineering of biological systems - it is the application of engineering methods to the analysis of biological systems. Synthetic biology can be thought of as the forward engineering of biological systems --- it is the application of engineering methods to the synthesis of biological systems. As metabolism is one of the primary functions of biological systems, it is a large focus of these new biological approaches. Where systems biology looks to model and simulation metabolic pathways and networks, synthetic biology looks to create them to produce useful metabolic products. Metabolic pathway search has an important role to play in not only understanding natural systems but also as a tool for generating novel systems. The metabolic network is computationally quite complex and finding pathways to secondary metabolites can be almost computationally intractable without the use of the informed search algorithms like those developed in this work. Through several examples from both systems biology and synthetic biology we demonstrate how metabolic pathway search can be used as tool for solving complex biological problems.