Fluigi: a computer aided design framework for combining microfluidics and synthetic biology

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Haiyao Huang, Swapnil Bhatia, Ahmad Khalil, Douglas Densmore

United States

The integration of microfluidics and synthetic biology has the potential to produce rapid prototyping platforms for characterization of genetic devices, testing of drug candidates, and development of biosensors. Microfluidics and synthetic biology may be combined to increase the complexity of genetic circuits. Due to the size and complexity of some genetic circuits, a Compuer Aided Design (CAD) framework will be needed to map the circuits to a microfluidic chip. We describe here the CAD framework Fluigi for optimizing the layout of genetic circuits on a microfluidic chip, generating the control sequence of the valves on the microfluidic chip, and simulating the behavior of the chip and the circuits it contains. Fluigi will provide the following features: logic minimization, technology mapping, place and route, valve control plan generation, and chip-level simulation. The user will input a series of boolean logic expressions, where each expression has some number of inputs and generates one output from those inputs, which will be then be converted to a minimal form to eliminate redundant logic. The minimal expressions will be converted to a tree of logic gates, where each gate is an available genetic circuit defined by the user, and will then be mapped to the chambers on the microfluidic chip within a given set of constraints. The sequence of valve controls will be generated from this mapping. Finally, Fluigi will run the sequence of valve controls and simulate the behavior of the chip. Fluigi and the functions it provides represent an important step towards the integration of synthetic biology and microfluidic platforms.