article

Abstraction layers for scalable microfluidic biocomputing

Authors:

John Paul Urbanski,

Saman AmarasingheAuthors Info & Claims

Natural Computing: an international journal, Volume 7, Issue 2

Pages 255 - 275

https://doi.org/10.1007/s11047-006-9032-6

Published: 01 June 2008 Publication History

Abstract

Microfluidic devices are emerging as an attractive technology for automatically orchestrating the reactions needed in a biological computer. Thousands of microfluidic primitives have already been integrated on a single chip, and recent trends indicate that the hardware complexity is increasing at rates comparable to Moore's Law. As in the case of silicon, it will be critical to develop abstraction layers--such as programming languages and Instruction Set Architectures (ISAs)--that decouple software development from changes in the underlying device technology. Towards this end, this paper presents BioStream, a portable language for describing biology protocols, and the Fluidic ISA, a stable interface for microfluidic chip designers. A novel algorithm translates microfluidic mixing operations from the BioStream layer to the Fluidic ISA. To demonstrate the benefits of these abstraction layers, we build two microfluidic chips that can both execute BioStream code despite significant differences at the device level. We consider this to be an important step towards building scalable biological computers.

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Cited By

Zhou YOliveira SSanka RMcIntyre DDensmore D(2025)Vespa: Logic-Level Constraint-Based Validation for Continuous-Flow Microfluidic DevicesIEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems10.1109/TCAD.2024.343570644:2(483-496)Online publication date: 1-Feb-2025
https://dl.acm.org/doi/10.1109/TCAD.2024.3435706
Dong CChen XChen Z(2024)Reactant and Waste Minimization during Sample Preparation on Micro-Electrode-Dot-Array Digital Microfluidic Biochips using Splitting TreesJournal of Electronic Testing: Theory and Applications10.1007/s10836-024-06103-z40:1(87-99)Online publication date: 1-Feb-2024
https://dl.acm.org/doi/10.1007/s10836-024-06103-z
Kundu DRoy S(2023)Multi-target Fluid Mixing in MEDA Biochips: Theory and an Attempt toward Waste MinimizationACM Transactions on Design Automation of Electronic Systems10.1145/362278528:6(1-26)Online publication date: 16-Oct-2023
https://dl.acm.org/doi/10.1145/3622785
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Abstraction layers for scalable microfluidic biocomputing

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Published In

cover image Natural Computing: an international journal

Natural Computing: an international journal Volume 7, Issue 2

June 2008

149 pages

ISSN:1567-7818

Issue’s Table of Contents

Copyright © Copyright © 2008 Springer Science+Business Media B.V.

Publisher

Kluwer Academic Publishers

United States

Publication History

Published: 01 June 2008

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Cited By

Zhou YOliveira SSanka RMcIntyre DDensmore D(2025)Vespa: Logic-Level Constraint-Based Validation for Continuous-Flow Microfluidic DevicesIEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems10.1109/TCAD.2024.343570644:2(483-496)Online publication date: 1-Feb-2025
https://dl.acm.org/doi/10.1109/TCAD.2024.3435706
Dong CChen XChen Z(2024)Reactant and Waste Minimization during Sample Preparation on Micro-Electrode-Dot-Array Digital Microfluidic Biochips using Splitting TreesJournal of Electronic Testing: Theory and Applications10.1007/s10836-024-06103-z40:1(87-99)Online publication date: 1-Feb-2024
https://dl.acm.org/doi/10.1007/s10836-024-06103-z
Kundu DRoy S(2023)Multi-target Fluid Mixing in MEDA Biochips: Theory and an Attempt toward Waste MinimizationACM Transactions on Design Automation of Electronic Systems10.1145/362278528:6(1-26)Online publication date: 16-Oct-2023
https://dl.acm.org/doi/10.1145/3622785
Winston CWillsey MCeze L(2023)Virtualizing Existing Fluidic ProgramsACM Journal on Emerging Technologies in Computing Systems10.1145/355855019:3(1-14)Online publication date: 21-Jun-2023
https://dl.acm.org/doi/10.1145/3558550
Poddar SFink GHaselmayr WWille R(2022)A Generic Sample Preparation Approach for Different Microfluidic Labs-on-ChipsIEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems10.1109/TCAD.2021.313532341:11(4612-4625)Online publication date: 1-Nov-2022
https://dl.acm.org/doi/10.1109/TCAD.2021.3135323
Ibrahim MZhong ZBhattacharya BChakrabarty K(2022)Efficient Regulation of Synthetic Biocircuits Using Droplet-Aliquot Operations on MEDA BiochipsIEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems10.1109/TCAD.2021.310890941:8(2490-2503)Online publication date: 1-Aug-2022
https://dl.acm.org/doi/10.1109/TCAD.2021.3108909
Poddar SBhattacharjee SFang SHo TBhattacharya B(2021)Demand-Driven Multi-Target Sample Preparation on Resource-Constrained Digital Microfluidic BiochipsACM Transactions on Design Automation of Electronic Systems10.1145/347439227:1(1-21)Online publication date: 13-Sep-2021
https://dl.acm.org/doi/10.1145/3474392
Bera NMajumder SDas SMukherjee SAryani NBhattacharya B(2021)SIMOP: A SIMulation-Guided OPtimization Mechanism for Sample Preparation with Digital Microfluidic BiochipSN Computer Science10.1007/s42979-021-00506-x2:2Online publication date: 10-Feb-2021
https://dl.acm.org/doi/10.1007/s42979-021-00506-x
Roy PBanerjee ABhattacharya B(2021)A framework for end-to-end verification for digital microfluidicsInnovations in Systems and Software Engineering10.1007/s11334-021-00398-317:3(231-245)Online publication date: 1-Sep-2021
https://dl.acm.org/doi/10.1007/s11334-021-00398-3
Choudhary GPal SKundu DBhattacharjee SYamashita SLi BSchlichtmann URoy SDi Natale GFummi F(2020)Transport-free module binding for sample preparation using microfluidic fully programmable valve arraysProceedings of the 23rd Conference on Design, Automation and Test in Europe10.5555/3408352.3408657(1335-1344)Online publication date: 9-Mar-2020
https://dl.acm.org/doi/10.5555/3408352.3408657
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