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A compiler for cyber-physical digital microfluidic biochips

Authors:

Christopher Curtis,

Daniel Grissom, and

Philip BriskAuthors Info & Claims

CGO 2018: Proceedings of the 2018 International Symposium on Code Generation and Optimization

February 2018

Pages 365 - 377

https://doi.org/10.1145/3168826

Published: 24 February 2018 Publication History

Abstract

Programmable microfluidic laboratories-on-a-chip (LoCs) offer the benefits of automation and miniaturization to the life sciences. This paper presents an updated version of the BioCoder language and a fully static (offline) compiler that can target an emerging class of LoCs called Digital Microfluidic Biochips (DMFBs), which manipulate discrete droplets of liquid on a 2D electrode grid. The BioCoder language and runtime execution engine leverage advances in sensor integration to enable specification, compilation, and execution of assays (bio-chemical 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 DMFB, 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 a DMFB.

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Published In

cover image ACM Conferences

CGO 2018: Proceedings of the 2018 International Symposium on Code Generation and Optimization

February 2018

377 pages

ISBN:9781450356176

DOI:10.1145/3179541

General Chairs:
Jens Knoop
Vienna University of Technology, Austria
,
Markus Schordan
Lawrence Livermore National Laboratory, USA
,
Program Chairs:
Teresa Johnson
Google, USA
,
Michael O'Boyle
University of Edinburgh, UK

Copyright © 2018 ACM.

Permission to make digital or hard copies of all or part of this work for personal or classroom use is granted without fee provided that copies are not made or distributed for profit or commercial advantage and that copies bear this notice and the full citation on the first page. Copyrights for components of this work owned by others than ACM must be honored. Abstracting with credit is permitted. To copy otherwise, or republish, to post on servers or to redistribute to lists, requires prior specific permission and/or a fee. Request permissions from [email protected]

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SIGPLAN: ACM Special Interest Group on Programming Languages
SIGMICRO: ACM Special Interest Group on Microarchitectural Research and Processing
IEEE-CS: Computer Society

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Association for Computing Machinery

New York, NY, United States

Publication History

Published: 24 February 2018

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National Science Foundation

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CGO '18

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CGO '18: 16th Annual IEEE/ACM International Symposium on Code Generation and Optimization

February 24 - 28, 2018

Vienna, Austria

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Overall Acceptance Rate 312 of 1,061 submissions, 29%

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Albin DBuecherl LKochavi ENiehaus ENovack SUragoda SMyers CAlistar M(2024)PhageBox: An Open Source Digital Microfluidic Extension With Applications for Phage DiscoveryIEEE Transactions on Biomedical Engineering10.1109/TBME.2023.329541871:1(217-226)Online publication date: Jan-2024
https://doi.org/10.1109/TBME.2023.3295418
Loveless TBrisk PDubach CBruening DHardekopf B(2023)Compiling Functions onto Digital MicrofluidicsProceedings of the 21st ACM/IEEE International Symposium on Code Generation and Optimization10.1145/3579990.3580023(136-148)Online publication date: 17-Feb-2023
https://dl.acm.org/doi/10.1145/3579990.3580023
Shi KChen ZLi XXiao ZSun WHu W(2023)Inferring Activity Patterns from Sparse Step Counts Data with Recurrent Neural NetworksACM Transactions on Computing for Healthcare10.1145/35604684:1(1-20)Online publication date: 27-Feb-2023
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Ma FRen MOuyang LChen YZhu JChen TZheng YDai XJiang YSun J(2023)Pied-Piper: Revealing the Backdoor Threats in Ethereum ERC Token ContractsACM Transactions on Software Engineering and Methodology10.1145/356026432:3(1-24)Online publication date: 26-Apr-2023
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He XZhang YFeng FSong CYi LLing GZhang Y(2023)Addressing Confounding Feature Issue for Causal RecommendationACM Transactions on Information Systems10.1145/355975741:3(1-23)Online publication date: 7-Feb-2023
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Swain JPyne S(2023)A Flooding-Based Droplet Routing Protocol for Digital Microfluidic BiochipJournal of Circuits, Systems and Computers10.1142/S021812662350302432:17Online publication date: 30-May-2023
https://doi.org/10.1142/S0218126623503024
Swain JPyne S(2023)A bidirectional droplet routing in digital microfluidics biochipMicroprocessors & Microsystems10.1016/j.micpro.2023.10477498:COnline publication date: 1-Apr-2023
https://dl.acm.org/doi/10.1016/j.micpro.2023.104774
Grohe MKaminski BKatoen JLindner P(2022)Generative Datalog with Continuous DistributionsJournal of the ACM10.1145/355910269:6(1-52)Online publication date: 30-Aug-2022
https://dl.acm.org/doi/10.1145/3559102
Zheng JLi ZQiu YLin HXiao HLi YLiu Y(2022)WebAssembly-based Delta Sync for Cloud Storage ServicesACM Transactions on Storage10.1145/350284718:3(1-31)Online publication date: 21-Sep-2022
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Lembke JRoman PEugster P(2022)DEFUSE: An Interface for Fast and Correct User Space File System AccessACM Transactions on Storage10.1145/349455618:3(1-29)Online publication date: 26-Sep-2022
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