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Fault-Tolerant Digital Microfluidic Biochips

Compilation and Synthesis

  • Book
  • © 2016

Overview

Authors:
  1. Paul Pop

    1. Department of Applied Mathematics and Computer Science, Technical University of Denmark, Kongens Lyngby, Denmark

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  2. Mirela Alistar

    1. Department of Applied Mathematics and Computer Science, Technical University of Denmark, Kongens Lyngby, Denmark

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  3. Elena Stuart

    1. Netcompany A/S, Copenhagen, Denmark

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  4. Jan Madsen

    1. Department of Applied Mathematics and Computer Science, Technical University of Denmark, Kongens Lyngby, Denmark

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  • Presents the current models used for the research on compilation and synthesis techniques of digital microfluidic biochips (DMBs) in a tutorial fashion
  • Includes a set of "benchmarks", which are presented in great detail and includes the source code of all the techniques presented, including solutions to the basic compilation and synthesis problems
  • Discusses several new research problems in detail, using numerous examples

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Table of contents (14 chapters)

  1. Front Matter

    Pages i-xii
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  2. Introduction

    • Paul Pop, Mirela Alistar, Elena Stuart, Jan Madsen
    Pages 1-10

  3. Preliminaries

    1. Front Matter

      Pages 11-11
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    2. Design Methodology for Digital Microfluidic Biochips

      • Paul Pop, Mirela Alistar, Elena Stuart, Jan Madsen
      Pages 13-28

    3. Biochip Architecture Model

      • Paul Pop, Mirela Alistar, Elena Stuart, Jan Madsen
      Pages 29-50

    4. Biochemical Application Model

      • Paul Pop, Mirela Alistar, Elena Stuart, Jan Madsen
      Pages 51-66

  4. Compilation

    1. Front Matter

      Pages 67-67
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    2. The Compilation Problem

      • Paul Pop, Mirela Alistar, Elena Stuart, Jan Madsen
      Pages 69-76

    3. Module-Based Compilation

      • Paul Pop, Mirela Alistar, Elena Stuart, Jan Madsen
      Pages 77-90

    4. Module-Based Compilation with Reconfigurable Operation Execution

      • Paul Pop, Mirela Alistar, Elena Stuart, Jan Madsen
      Pages 91-103

    5. Module-Based Compilation with Droplet-Aware Operation Execution

      • Paul Pop, Mirela Alistar, Elena Stuart, Jan Madsen
      Pages 105-114

    6. Routing-Based Compilation

      • Paul Pop, Mirela Alistar, Elena Stuart, Jan Madsen
      Pages 115-133

  5. Compilation for Error Recovery and Uncertainty

    1. Front Matter

      Pages 135-135
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    2. Fault-Tolerant Module-Based Compilation

      • Paul Pop, Mirela Alistar, Elena Stuart, Jan Madsen
      Pages 137-143

    3. Compilation for Error Recovery

      • Paul Pop, Mirela Alistar, Elena Stuart, Jan Madsen
      Pages 145-174

    4. Compilation for Operation Execution Time Variability

      • Paul Pop, Mirela Alistar, Elena Stuart, Jan Madsen
      Pages 175-193

  6. Architecture Synthesis

    1. Front Matter

      Pages 195-195
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    2. Synthesis of Fault-Tolerant Biochips

      • Paul Pop, Mirela Alistar, Elena Stuart, Jan Madsen
      Pages 197-207

    3. Synthesis of Application-Specific Architectures

      • Paul Pop, Mirela Alistar, Elena Stuart, Jan Madsen
      Pages 209-234
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Keywords

About this book

This book describes for researchers in the fields of compiler technology, design and test, and electronic design automation the new area of digital microfluidic biochips (DMBs), and thus offers a new application area for their methods.  The authors present a routing-based model of operation execution, along with several associated compilation approaches, which progressively relax the assumption that operations execute inside fixed rectangular modules.  Since operations can experience transient faults during the execution of a bioassay, the authors show how to use both offline (design time) and online (runtime) recovery strategies. The book also presents methods for the synthesis of fault-tolerant application-specific DMB architectures.

·         Presents the current models used for the research on compilation and synthesis techniques of DMBs in a tutorial fashion;

·         Includes a set of “benchmarks”, which are presented in great detail and includes the source code of most of the techniques presented, including solutions to the basic compilation and synthesis problems;

·         Discusses several new research problems in detail, using numerous examples.

Authors and Affiliations

  • Department of Applied Mathematics and Computer Science, Technical University of Denmark, Kongens Lyngby, Denmark

    Paul Pop, Mirela Alistar, Jan Madsen

  • Netcompany A/S, Copenhagen, Denmark

    Elena Stuart

About the authors

Paul Pop is has joined DTU Compute as an associate professor in May 2006. Previously, he was an assistant professor at Linköping University, Sweden, where he has received his Ph.D. in Computer Systems in 2003. Paul’s research is about methods for systems engineering: modeling, analysis, simulation and optimization. Systems engineering is the treatment of engineering design as a decision making-process. He has applied systems engineering methods in the design of embedded systems, which are special-purpose computer systems dedicated to perform a specific function.

Bibliographic Information

  • Book Title: Fault-Tolerant Digital Microfluidic Biochips

  • Book Subtitle: Compilation and Synthesis

  • Authors: Paul Pop, Mirela Alistar, Elena Stuart, Jan Madsen

  • DOI: https://doi.org/10.1007/978-3-319-23072-6

  • Publisher: Springer Cham

  • eBook Packages: Engineering, Engineering (R0)

  • Copyright Information: Springer International Publishing Switzerland 2016

  • Hardcover ISBN: 978-3-319-23071-9Published: 15 September 2015

  • Softcover ISBN: 978-3-319-37333-1Published: 01 November 2016

  • eBook ISBN: 978-3-319-23072-6Published: 07 September 2015

  • Edition Number: 1

  • Number of Pages: XII, 234

  • Number of Illustrations: 27 b/w illustrations, 82 illustrations in colour

  • Topics: Circuits and Systems, Biomedical Engineering and Bioengineering, Electronic Circuits and Devices

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