Automatic Synthesis of Microfluidic Large Scale Integration Chips from a Domain-Specific Language
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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
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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. - PowerPoint PPT Presentation
Transcript of 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
