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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 Conference Rotterdam, Netherlands, Novemb er 1, 2013.

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

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  1. 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 Conference Rotterdam, Netherlands, November 1, 2013

  2. The Future Of Chemistry Microfluidics Miniaturization + Automation Laboratory-on-Chip (LoC)

  3. Applications • Biochemical assays and immunoassays • Clinical pathology • Drug discovery and testing • Rapid assay prototyping • Testing new drugs (via lung-on-a-chip) • Biochemical terror and hazard detection • DNA extraction & sequencing

  4. Design of Continuous Fluid-flow LoCs • AutoCAD • Draw each layer of the chip manually • Akin to transistor-level design of ICs with manual wire routing • Limited Automation • Multi-layer soft lithography • [Amin et al., ICCD 2009] • [Minhasset al. CASES 2011 & 2012] • [McDaniel et al. ASPDAC 2013] • Capillary dielectrophoresis • [Pfeiffer et al. TCAD 2006] • [Hsieh and Ho, VLSI Design 2011]

  5. Sequencing Graphs • Current input specification • [Minhass et al. CASES 2012]

  6. Sequencing Graphs

  7. Our Contributions • BioCoder Compiler • High-Level Language for assay specification

  8. BioCoder • Restricted BioCoder language

  9. Example: Influenza Detection [Pal et al., Lab-on-a-Chip 2005] 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.

  10. Example: Influenza Detection [Pal et al., Lab-on-a-Chip 2005]

  11. Example: Influenza Detection [Pal et al., Lab-on-a-Chip 2005]

  12. Example: Influenza Detection Influenza Detection

  13. Example: Influenza Detection [Pal et al., Lab-on-a-Chip 2005]

  14. Example: Influenza Detection [Pal et al., Lab-on-a-Chip 2005]

  15. Example: Influenza Detection [Pal et al., Lab-on-a-Chip 2005]

  16. Conclusion and Future Work • BioCoder Compiler • High-level language for assay specification • Restricted BioCoder specific to LoC’s • Interface to existing tool-chains • Provides intuitive interface for biochemists • Future Work • Complete design automation tools • Extend the restricted BioCoder

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