One-Pass Design

  • Oliver Keszocze
  • Robert Wille
  • Rolf Drechsler
Chapter

Abstract

So far, this book dealt with the routing of droplets and the multitude of different problems and use cases that arise from it. The goal for DMFBs is not simply showing that these droplet movements are possible but automating laboratory procedures in biochemistry and molecular biology. Moving droplets correctly is only a part of successfully conducting an experiment on a DMFB, many other aspects, such as choosing the right hardware devices and placing them on the biochip, need to be taken into account. The process of determining a biochip configuration that is capable of performing a given experiment is known as design or synthesis. The whole procedure is usually conducted by solving the different design steps independently. This means that there are specialized solutions for the scheduling, binding, placement, routing, and pin assignment steps (see Chap.  1 for an overview of the design flow of DMFBs). This can lead to problems when trying to generate an overall solution from the partial solutions. This chapter deals with this issue by presenting one-pass design approaches that overcome the design gaps between the individual steps by synthesizing an experiment in a holistic fashion. While all examples in this chapter use rectangular geometries to illustrate the methodologies, they are, by no means, restricted to them. The choice is purely made to keep the explanation simple. Synthesis problems on DMFBs with non-rectangular geometries as shown in the third figure of Chap.  4 can be solved as well. After an example of a design gap in Sect. 6.1, motivating the need for a one-pass approach, two one-pass solutions, one heuristic approach and one exact approach, for the design problem are presented in Sects. 6.2.1 and 6.2.2, respectively. Afterwards, the experimental results are discussed in Sect. 6.3.

References

  1. [BST10]
    Barrett C, Stump A, Tinelli C (2010)The SMT-LIB standard: version 2.0. In: Gupta A, Kroening D (eds) International workshop on satisfiability modulo theories, EdinburghGoogle Scholar
  2. [DB08]
    De Moura L, Bjørner N (2008) Z3: an efficient SMT solver. In: Tools and algorithms for the construction and analysis of systems. Springer, Berlin, pp 337–340. Z3 is available at https://github.com/Z3Prover/z3
  3. [Gri+12]
    Grissom D et al (2012) A digital microfluidic biochip synthesis framework. In: VLSI of System-on-Chip, pp 177–182Google Scholar
  4. [Kes+14]
    Keszocze O et al (2014) Exact one-pass synthesis of digital microfluidic biochips. In: Design automation conference. DAC, pp 142:1–142:6Google Scholar
  5. [Rie+14]
    Riener H et al (2014) A logic for cardinality constraints. In: Methoden und Beschreibungssprachen zur Modellierung und Verifikation von Schaltungen und SystemenGoogle Scholar
  6. [Rie+16]
    Riener H et al (2016) metaSMT: focus on your application and not on solver integration. Int J Softw Tools Technol Transfer, 1–17. metaSMT is available at https://github.com/agra-uni-bremen/metaSMT
  7. [SC08]
    Su F, Chakrabarty K (2008) High-level synthesis of digital microfluidic biochips. ACM J Emerg Technol Comput Syst 3(4):1:1–1:32CrossRefGoogle Scholar
  8. [Wil+15]
    Wille R et al (2015) Scalable one-pass synthesis for digital microfluidic biochips. Des Test 32(6):41–50Google Scholar

Copyright information

© Springer International Publishing AG, part of Springer Nature 2019

Authors and Affiliations

  • Oliver Keszocze
    • 1
  • Robert Wille
    • 2
  • Rolf Drechsler
    • 1
  1. 1.University of Bremen and DFKI GmbHBremenGermany
  2. 2.Johannes Kepler University LinzLinzAustria

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