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Formal Methods for the Synthesis of Biomolecular Circuits (Dagstuhl Seminar 18082)

Authors: Yaakov Benenson, Neil Dalchau, Heinz Koeppl, and Oded Maler

Published in: Dagstuhl Reports, Volume 8, Issue 2 (2018)

Abstract

This report documents the program and the outcomes of Dagstuhl Seminar 18082 "Formal Methods for the Synthesis of Biomolecular Circuits". Synthetic biology aims for the rational bottom-up engineering of new biological functionalities. Recent years have witnessed an increase in the degree of "rationality" in the design of synthetic biomolecular circuits. With it, fewer design-build-test cycles were necessary to achieve a desired circuit performance. Most of these success stories reported the realization of logic circuits, typically operating via regulation of gene expression and/or direct manipulation of DNA sequences with recombinases, executing combinatorial and sometimes sequential logic. This was often achieved with the help of two ingredients, a library of previously well-characterized parts and some computational modeling. Hence, although circuits in synthetic biology are still by far less understood and characterized than electronic circuits, the opportunity for the formal synthesis of circuit designs with respect to a behavioral specification starts to emerge in synthetic biology.

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Yaakov Benenson, Neil Dalchau, Heinz Koeppl, and Oded Maler. Formal Methods for the Synthesis of Biomolecular Circuits (Dagstuhl Seminar 18082). In Dagstuhl Reports, Volume 8, Issue 2, pp. 88-100, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2018)

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@Article{benenson_et_al:DagRep.8.2.88,
  author =	{Benenson, Yaakov and Dalchau, Neil and Koeppl, Heinz and Maler, Oded},
  title =	{{Formal Methods for the Synthesis of Biomolecular Circuits (Dagstuhl Seminar 18082)}},
  pages =	{88--100},
  journal =	{Dagstuhl Reports},
  ISSN =	{2192-5283},
  year =	{2018},
  volume =	{8},
  number =	{2},
  editor =	{Benenson, Yaakov and Dalchau, Neil and Koeppl, Heinz and Maler, Oded},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/DagRep.8.2.88},
  URN =		{urn:nbn:de:0030-drops-92912},
  doi =		{10.4230/DagRep.8.2.88},
  annote =	{Keywords: Synthetic biology, Electronic design automation, Program synthesis and verification}
}

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DOI: 10.4230/DagRep.5.9.125

Self-assembly and Self-organization in Computer Science and Biology (Dagstuhl Seminar 15402)

Authors: Vincent Danos and Heinz Koeppl

Published in: Dagstuhl Reports, Volume 5, Issue 9 (2016)

Abstract

This report documents the program and the outcomes of Dagstuhl Seminar 15402 "Self-assembly and Self-organization in Computer Science and Biology". With the trend of technological systems to become more distributed they tend to resemble closer biological systems. Biological systems on all scale are distributed and most often operate without central coordination. Taking the morphogenesis as an example, it is clear that the complexity and precision of distributed mechanisms in biology supersedes our current design attempts to distributed systems. The seminar assembled together researchers from computer science, engineering, physics and molecular biology working on the problem of decentralized coordination of distributed systems. Within every domain different terms have been coined, different analysis methods have been developed and applied and the seminar aims to foster the exchange of methods and the instantiation and alignment of important problem statements that can span across the disciplines. A representative example for a problem that is studied across domains through different methods is self-assembly. For example, computer scientists consider abstract self-assembly models such as Wang tiles to bound shape complexities while polymer physicists and biologists use molecular dynamics simulations to characterize self-assembly by means of energy and entropy. Because of its well-definedness, we deliberately placed emphasis on self-assembly that is otherwise entailed in the more general term self-organization. Within the domain of self-organization various research threads were represented at the seminar and a certain convergence of underlying concepts was possible. The seminar helped to exchange techniques from different domains and to agree on certain problem statements for future collaborations.

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Vincent Danos and Heinz Koeppl. Self-assembly and Self-organization in Computer Science and Biology (Dagstuhl Seminar 15402). In Dagstuhl Reports, Volume 5, Issue 9, pp. 125-138, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2016)

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@Article{danos_et_al:DagRep.5.9.125,
  author =	{Danos, Vincent and Koeppl, Heinz},
  title =	{{Self-assembly and Self-organization in Computer Science and Biology (Dagstuhl Seminar 15402)}},
  pages =	{125--138},
  journal =	{Dagstuhl Reports},
  ISSN =	{2192-5283},
  year =	{2016},
  volume =	{5},
  number =	{9},
  editor =	{Danos, Vincent and Koeppl, Heinz},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/DagRep.5.9.125},
  URN =		{urn:nbn:de:0030-drops-56887},
  doi =		{10.4230/DagRep.5.9.125},
  annote =	{Keywords: Self-assembly, molecular modeling, molecular dynamics, graph-rewriting grammars, self-organization, self-* systems, concurrency}
}

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Documents authored by Koeppl, Heinz

Formal Methods for the Synthesis of Biomolecular Circuits (Dagstuhl Seminar 18082)

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Self-assembly and Self-organization in Computer Science and Biology (Dagstuhl Seminar 15402)

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