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International Conference on Theory and Practice of Natural Computing

TPNC 2019: Theory and Practice of Natural Computing pp 82–94Cite as

Boolean Recombinase-Based Devices

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Part of the book series: Lecture Notes in Computer Science ((LNTCS,volume 11934))

Abstract

This paper relates to a central problem in synthetic biology, which is that of designing Recombinase-based biological devices by matching a functional specification expressed as a Boolean function. This task is challenging as exploring the space of possibilities is typically unfeasible, and therefore many non-trivial design alternatives remain unexplored. Also, the issue has been so far regarded mainly from a practical perspective and is still lacking of formal foundations on which the definition of algorithms for assisting the biologists in their design tasks can be based. In this work, we present the first formal study of the problem, and give a formal semantics for a family of Recombinase-based biological devices. We then exhibit a set of semantic properties leading to the definition of representative devices, a notion that allows one to express infinitely large classes of design possibilities in a finite way. Building on this, we then provide a terminating algorithm for generating representative devices for n-input Boolean functions. An open online database of 18M design solutions for 4-inputs devices generated with our method has been released at http://recombinator.lirmm.fr.

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Notes

  1. 1.

    \(\varphi \) also denotes the Boolean function associated with the logic formula built with the inputs. For instance, \(\varphi _{(\lnot i_1 \wedge i_2)} = \{ 00\mapsto 0, 01\mapsto 1, 10\mapsto 0, 11\mapsto 0\}\).

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Author information

Authors and Affiliations

  1. LIRMM, CNRS UMR 5506, University of Montpellier, Montpellier, France

    Guillaume Pérution-Kihli, Federico Ulliana & Michel Leclère

  2. CBS, INSERM U154, CNRS UMR 5048, University of Montpellier, Montpellier, France

    Sarah Guiziou & Jérôme Bonnet

  3. Department of Biology, University of Washington, Seattle, WA, 98195, USA

    Sarah Guiziou

Authors
  1. Guillaume Pérution-Kihli
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  2. Sarah Guiziou
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  3. Federico Ulliana
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  4. Michel Leclère
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  5. Jérôme Bonnet
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Corresponding author

Correspondence to Michel Leclère .

Editor information

Editors and Affiliations

  1. Rovira i Virgili University, Tarragona, Spain

    Carlos Martín-Vide

  2. Royal Military College of Canada, Kingston, ON, Canada

    Geoffrey Pond

  3. University of Extremadura, Cáceres, Spain

    Miguel A. Vega-Rodríguez

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Cite this paper

Pérution-Kihli, G., Guiziou, S., Ulliana, F., Leclère, M., Bonnet, J. (2019). Boolean Recombinase-Based Devices. In: Martín-Vide, C., Pond, G., Vega-Rodríguez, M. (eds) Theory and Practice of Natural Computing. TPNC 2019. Lecture Notes in Computer Science(), vol 11934. Springer, Cham. https://doi.org/10.1007/978-3-030-34500-6_5

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  • DOI: https://doi.org/10.1007/978-3-030-34500-6_5

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  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-030-34499-3

  • Online ISBN: 978-3-030-34500-6

  • eBook Packages: Computer ScienceComputer Science (R0)

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