Synthesis of biochemical applications on digital microfluidic biochips with operation variability

Mirela Alistar, Elena Maftei, Paul Pop, Jan Madsen

    Research output: Chapter in Book/Report/Conference proceedingArticle in proceedingsResearchpeer-review

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    Abstract

    Microfluidic-based biochips are replacing the conventional biochemical analyzers, and are able to integrate on-chip all the necessary functions for biochemical analysis using microfluidics. The digital microfluidic biochips are based on the manipulation of liquids not as a continuous flow, but as discrete droplets. Researchers have presented approaches for the synthesis of digital microfluidic biochips, which, starting from a biochemical application and a given biochip architecture, determine the allocation, resource binding, scheduling and placement of the operations in the application. Existing approaches consider that on-chip operations, such as splitting a droplet of liquid, are perfect. However, these operations have variability margins, which can impact the correctness of the biochemical application.We consider that a split operation, which goes beyond specified variability bounds, is faulty. The fault is detected using on-chip volume sensors. We have proposed an abstract model for a biochemical application, consisting of a sequencing graph, which can capture all the fault scenarios in the application. Starting from this model, we have proposed a synthesis approach that, for a given chip area and number of sensors, can derive a fault-tolerant implementation. Two fault-tolerant scheduling techniques have been proposed and compared. We show that, by taking into account fault-occurrence information, we can derive better quality implementations, which leads to shorter application completion times, even in the case of faults. The proposed synthesis approach under operation variability has been evaluated using several benchmarks.
    Original languageEnglish
    Title of host publication2010 Symposium on Design Test Integration and Packaging of MEMS/MOEMS
    PublisherIEEE
    Publication date2010
    Pages350-357
    ISBN (Print)978-1-4244-6636-8
    Publication statusPublished - 2010
    Event2010 Symposium on Design Test Integration and Packaging of MEMS/MOEMS - Seville, Spain
    Duration: 5 May 20107 May 2010
    http://www.ieee.org/conferences_events/conferences/conferencedetails/index.html?Conf_ID=16860

    Conference

    Conference2010 Symposium on Design Test Integration and Packaging of MEMS/MOEMS
    CountrySpain
    CitySeville
    Period05/05/201007/05/2010
    Internet address

    Bibliographical note

    Copyright 2010 IEEE. Personal use of this material is permitted. However, permission to reprint/republish this material for advertising or promotional purposes or for creating new collective works for resale or redistribution to servers or lists, or to reuse any copyrighted component of this work in other works must be obtained from the IEEE.

    Cite this

    Alistar, M., Maftei, E., Pop, P., & Madsen, J. (2010). Synthesis of biochemical applications on digital microfluidic biochips with operation variability. In 2010 Symposium on Design Test Integration and Packaging of MEMS/MOEMS (pp. 350-357). IEEE.
    Alistar, Mirela ; Maftei, Elena ; Pop, Paul ; Madsen, Jan. / Synthesis of biochemical applications on digital microfluidic biochips with operation variability. 2010 Symposium on Design Test Integration and Packaging of MEMS/MOEMS. IEEE, 2010. pp. 350-357
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    author = "Mirela Alistar and Elena Maftei and Paul Pop and Jan Madsen",
    note = "Copyright 2010 IEEE. Personal use of this material is permitted. However, permission to reprint/republish this material for advertising or promotional purposes or for creating new collective works for resale or redistribution to servers or lists, or to reuse any copyrighted component of this work in other works must be obtained from the IEEE.",
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    Alistar, M, Maftei, E, Pop, P & Madsen, J 2010, Synthesis of biochemical applications on digital microfluidic biochips with operation variability. in 2010 Symposium on Design Test Integration and Packaging of MEMS/MOEMS. IEEE, pp. 350-357, 2010 Symposium on Design Test Integration and Packaging of MEMS/MOEMS, Seville, Spain, 05/05/2010.

    Synthesis of biochemical applications on digital microfluidic biochips with operation variability. / Alistar, Mirela; Maftei, Elena; Pop, Paul; Madsen, Jan.

    2010 Symposium on Design Test Integration and Packaging of MEMS/MOEMS. IEEE, 2010. p. 350-357.

    Research output: Chapter in Book/Report/Conference proceedingArticle in proceedingsResearchpeer-review

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    AU - Pop, Paul

    AU - Madsen, Jan

    N1 - Copyright 2010 IEEE. Personal use of this material is permitted. However, permission to reprint/republish this material for advertising or promotional purposes or for creating new collective works for resale or redistribution to servers or lists, or to reuse any copyrighted component of this work in other works must be obtained from the IEEE.

    PY - 2010

    Y1 - 2010

    N2 - Microfluidic-based biochips are replacing the conventional biochemical analyzers, and are able to integrate on-chip all the necessary functions for biochemical analysis using microfluidics. The digital microfluidic biochips are based on the manipulation of liquids not as a continuous flow, but as discrete droplets. Researchers have presented approaches for the synthesis of digital microfluidic biochips, which, starting from a biochemical application and a given biochip architecture, determine the allocation, resource binding, scheduling and placement of the operations in the application. Existing approaches consider that on-chip operations, such as splitting a droplet of liquid, are perfect. However, these operations have variability margins, which can impact the correctness of the biochemical application.We consider that a split operation, which goes beyond specified variability bounds, is faulty. The fault is detected using on-chip volume sensors. We have proposed an abstract model for a biochemical application, consisting of a sequencing graph, which can capture all the fault scenarios in the application. Starting from this model, we have proposed a synthesis approach that, for a given chip area and number of sensors, can derive a fault-tolerant implementation. Two fault-tolerant scheduling techniques have been proposed and compared. We show that, by taking into account fault-occurrence information, we can derive better quality implementations, which leads to shorter application completion times, even in the case of faults. The proposed synthesis approach under operation variability has been evaluated using several benchmarks.

    AB - Microfluidic-based biochips are replacing the conventional biochemical analyzers, and are able to integrate on-chip all the necessary functions for biochemical analysis using microfluidics. The digital microfluidic biochips are based on the manipulation of liquids not as a continuous flow, but as discrete droplets. Researchers have presented approaches for the synthesis of digital microfluidic biochips, which, starting from a biochemical application and a given biochip architecture, determine the allocation, resource binding, scheduling and placement of the operations in the application. Existing approaches consider that on-chip operations, such as splitting a droplet of liquid, are perfect. However, these operations have variability margins, which can impact the correctness of the biochemical application.We consider that a split operation, which goes beyond specified variability bounds, is faulty. The fault is detected using on-chip volume sensors. We have proposed an abstract model for a biochemical application, consisting of a sequencing graph, which can capture all the fault scenarios in the application. Starting from this model, we have proposed a synthesis approach that, for a given chip area and number of sensors, can derive a fault-tolerant implementation. Two fault-tolerant scheduling techniques have been proposed and compared. We show that, by taking into account fault-occurrence information, we can derive better quality implementations, which leads to shorter application completion times, even in the case of faults. The proposed synthesis approach under operation variability has been evaluated using several benchmarks.

    M3 - Article in proceedings

    SN - 978-1-4244-6636-8

    SP - 350

    EP - 357

    BT - 2010 Symposium on Design Test Integration and Packaging of MEMS/MOEMS

    PB - IEEE

    ER -

    Alistar M, Maftei E, Pop P, Madsen J. Synthesis of biochemical applications on digital microfluidic biochips with operation variability. In 2010 Symposium on Design Test Integration and Packaging of MEMS/MOEMS. IEEE. 2010. p. 350-357