Title of Document: a Systems Engineering Framework for Metabolic Engineering Experiments a Systems Engineering Framework for Metabolic Engineering Experiments Dedication Acknowledgements

Title of Document: A SYSTEMS ENGINEERING FRAMEWORK FOR METABOLIC ENGINEERING EXPERIMENTS Joseph Johnnie, Master of Science in Systems Engineering, 2011 Directed By: Dr. Mark Austin, Department of Civil and Environmental Engineering, and the Institute for Systems Research, University of Maryland at College Park Cells of living organisms simultaneously operate hundreds or thousands of interconnected chemical reactions. Metabolic networks include these chemical reactions and compounds participating in them. Metabolic engineering is a science centered on the analysis and purposeful modification of an organism's metabolic network toward a beneficial purpose, such as production of fuel or medicinal compounds in microorganisms. Unfortunately, there are problems with the design and visualization of modified metabolic networks due to lack of standardized and fully developed visual modeling languages. The purposes of this paper are to propose a multilevel framework for the synthesis, analysis and design of metabolic systems, and then explore the extent to which abstractions from systems engineering (e.g., SysML) can complement and add value to the abstractions currently under development within the greater biological community (e.g., SBGN). The computational test-bed that accompanies this work is production of the anti-malarial drug artemisinin in genetically engineered Saccaharomyces cerevisiae (yeast). A SYSTEMS ENGINEERING FRAMEWORK FOR METABOLIC ENGINEERING EXPERIMENTS