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The engineering of cells for the production of fuels and chemicals involves simultaneous optimization of multiple objectives, such as specific productivity, extended substrate range and improved tolerance – all under a great degree of uncertainty. The achievement of these objectives under physiological and process constraints will be impossible without the use of mathematical modeling. However, the limited information and the uncertainty in the available information require new methods for modeling and simulation that will characterize the uncertainty and will quantify, in a statistical sense, the expectations of success of alternative metabolic engineering strategies. We discuss these considerations around the development of a framework for the Optimization and Risk Analysis of Complex Living Entities (ORACLE).