Multiscale Design of Cell Factories

Developing commercially viable cell factories for production of chemicals and proteins requires design at multiple levels from DNA, to proteins, pathways, organisms, processes, and industries. At each level computational tools can be used to guide and constrain design choices. The metabolic engineering community is most familiar with organism level design to identify genetic manipulation targets, but it is equally important to make correct design choices at other levels. Unfortunately, different sets of tools and methodologies are used at each level making it difficult to perform multiscale design. We are developing a comprehensive software and conceptual framework for designing pathways, organisms, processes and industries simultaneously. This framework can be used to assess biological, technical, economic and ecological performance of possible target molecules for metabolic engineering. The framework will be demonstrated with case studies focusing on commodity chemical production in microbial host organisms.