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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)
Mechanical design tools would be considerably more useful if we could interact with them in the way that human designers communicate design ideas to one another, i.e., using crude sketches and informal speech. Those crude sketches frequently contain pen strokes of two different sorts, one type portraying device structure, the other denoting gestures, such(More)
Today’s business processes are more connected than ever before, driven by the ability to share the right information with the right partners at the right time. While this interconnectedness and situational awareness is crucial to success, it also opens the possibility for misuse of the same capabilities by sophisticated adversaries to spread attacks and(More)
We present a workflow for the design and production of biological networks from high-level program specifications. The workflow is based on a sequence of intermediate models that incrementally translate high-level specifications into DNA samples that implement them. We identify algorithms for translating between adjacent models and implement them as a set(More)
While sketches are commonly and effectively used in the early stages of design, some information is far more easily conveyed verbally than by sketching. In response, we have combined sketching with speech, enabling a more natural form of communication. We studied the behavior of people sketching and speaking, and from this derived a set of rules for(More)
Synthetic Biology Open Language (SBOL) Visual is a graphical standard for genetic engineering. It consists of symbols representing DNA subsequences, including regulatory elements and DNA assembly features. These symbols can be used to draw illustrations for communication and instruction, and as image assets for computer-aided design. SBOL Visual is a(More)
Engineering biological systems with predictable behavior is a foundational goal of synthetic biology. To accomplish this, it is important to accurately characterize the behavior of biological devices. Prior characterization efforts, however, have generally not yielded enough high-quality information to enable compositional design. In the TASBE (A Tool-Chain(More)