Automatic Synthesis of Microfluidic Large Scale Integration Chips from a Domain-Specific Language

Automatic Synthesis of Microfluidic Large Scale Integration Chips from a

Domain-Specific Language

Jeffrey McDaniel, Christopher Curtis, Philip Brisk

University of California, Riverside

Biomedical Circuits and Systems ConferenceRotterdam, Netherlands, November 1, 2013

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The Future Of Chemistry

Microfluidics

Miniaturization + AutomationLaboratory-on-Chip (LoC)

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Applications

Biochemical assays and immunoassaysClinical pathology

Drug discovery and testingRapid assay prototypingTesting new drugs (via lung-on-a-chip)

Biochemical terror and hazard detectionDNA extraction & sequencing

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Design of Continuous Fluid-flow LoCs

AutoCADDraw each layer of the chip manuallyAkin to transistor-level design of ICs with manual wire routing

Limited AutomationMulti-layer soft lithography

[Amin et al., ICCD 2009][Minhass et al. CASES 2011 & 2012][McDaniel et al. ASPDAC 2013]

Capillary dielectrophoresis[Pfeiffer et al. TCAD 2006][Hsieh and Ho, VLSI Design 2011]

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Current input specification[Minhass et al. CASES 2012]

Sequencing Graphs

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Sequencing Graphs

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BioCoder CompilerHigh-Level Language for assay specification

Our Contributions

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BioCoderRestricted BioCoder language

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Example: Influenza Detection

The thermocycling protocol applied to the device consists of 92 degrees C for 30s, and then 35 cycles of the following: 92 degrees C for 5s, 55 degrees C for 10s, and 72 degrees C for 20s, and finally 72 degrees C for 60s, for a total cycling time of 22 minutes. A portion of the PCR product (~60nl) is subsequently subjected to a restriction endonuclease digestion within the same device. The restriction digest reaction is performed at 37 degrees C for 10 min.

[Pal et al., Lab-on-a-Chip 2005]

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Example: Influenza Detection

[Pal et al., Lab-on-a-Chip 2005]

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Example: Influenza Detection

[Pal et al., Lab-on-a-Chip 2005]

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Example: Influenza DetectionInfluenza Detection

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Example: Influenza Detection

[Pal et al., Lab-on-a-Chip 2005]

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Example: Influenza Detection

[Pal et al., Lab-on-a-Chip 2005]

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Example: Influenza Detection

[Pal et al., Lab-on-a-Chip 2005]

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Conclusion and Future WorkBioCoder Compiler

High-level language for assay specificationRestricted BioCoder specific to LoC’s

Interface to existing tool-chainsProvides intuitive interface for biochemists

Future WorkComplete design automation toolsExtend the restricted BioCoder