Fusun Yaman

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Raising the level of abstraction for synthetic biology design requires solving several challenging problems, including mapping abstract designs to DNA sequences. In this paper we present the first formalism and algorithms to address this problem. The key steps of this transformation are feature matching, signal matching, and part matching. Feature matching(More)
A long-standing goal of synthetic biology is to rapidly engineer new regulatory circuits from simpler devices. As circuit complexity grows, it becomes increasingly important to guide design with quantitative models, but previous efforts have been hindered by lack of predictive accuracy. To address this, we developed Empirical Quantitative Incremental(More)
There is a pressing need for design automation tools for synthetic biology systems. Compared to electronic circuits, cellular information processing has more complex elementary components and a greater complexity of interactions among components. Moreover, chemical computation within a cell is strongly a↵ected both by other computations simultaneously(More)
W e designed the Simple Hierarchical Ordered Planner (SHOP) and its successor , SHOP2, with two goals in mind: to investigate research issues in automated planning and to provide some simple, practical planning tools. SHOP and SHOP2 are based on a planning formalism called hierarchical task network planning, which is described in more detail in the sidebar,(More)
There are a wide range of applications in which it would be useful to have a small synthetic biology circuit that could reliably classify cell state. For example, in [5], the authors propose cancer therapy based on a circuit that uses miRNA markers to test whether a cell belongs to a particular type of cancer and then kills only those cells. The authors(More)
Long-lived complex electromechanical systems, such as vehicles or industrial machinery, often need to be adapted for new uses or new environments. Adapting the design for such a system is frequently complicated by the fact that they are often tightly integrated, such that any change will have consequences throughout the design, and must take many different(More)
The engineering of biological systems can be greatly aided by better models, derived from high-quality characterization data, and by better means for designing and debug-ging new genetic circuits. Web-based tools and repositories have proven a successful approach to distributing such techniques , particularly because the centralization of infrastructure(More)