Language and Compiler Design for Laboratories-on-a-Chip

Speaker

Prof. Philip Brisk, University of California, Riverside, USA-- 12-12-2017

Abstract

Microfluidics is a multidisciplinary field at the intersection of engineering, physics, chemistry, biochemistry, nanotechnology, and biotechnology. It has practical applications to the design of integrated systems that process sub-microliter-scale volumes of fluid. Microfluidics has enabled the emergence of a Laboratories-on-a-Chip (LoCs), which integrate multiple laboratory functions into devices whose physical size ranges from square millimeters to square centimeters. Compared to traditional benchtop chemistry methods, LoCs offer the benefits of automation and miniaturization; software-programmable LoCs offer an important additional benefit: programmability.

This talk will introduce BioScript, a domain-specific language for programmable LoCs, and its compiler. Extensibility is particularly important for language design, as each LoC target features a unique set of capabilities, and there is no universal functionality among LoCs akin to Turing completeness. The BioScript compiler presently targets a specific class of semiconductor-based LoCs which manipulate discrete liquid droplets on a 2D electrode grid. The language, compiler, and runtime leverage advances in sensor integration to execute biochemical procedures that feature online decision-making based on sensory data acquired during assay execution. The compiler features a novel hybrid intermediate representation (IR) that interleaves fluidic operations with computations performed on sensor data. The IR extends the traditional notions of liveness and interference to fluidic variables and operations, as needed to target the LoC, which itself can be viewed as a spatially reconfigurable array. The code generator converts the IR into the following: (1) a set of electrode activation sequences for each basic block in the control flow graph (CFG); (2) a set of computations performed on sensor data, which dynamically determine the result of each control flow operation; and (3) a set of electrode activation sequences for each control flow transfer operation (CFG edge). The compiler is validated using a software simulator which produces animated videos of realistic bioassay execution on the device. 

Bio

Philip Brisk received, the BS, MS, and PhD Degrees, all in Computer Science, from UCLA in 2002, 2003, an 2006 respectively. From 2006-2009 he was a Postdoctoral Scholar at EPFL in Switzerland. He has been with UC Riverside since 2009. His research interests include programmable microfluidics and lab-on-a-chip technology, FPGAs and reconfigurable computing, and other forward-looking applications of computer engineering principles. 

Slides

 

 

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