http://www.dagstuhl.de/18082

18. – 23. Februar 2018, Dagstuhl Seminar 18082

Formal Methods for the Synthesis of Biomolecular Circuits

Organisatoren

Yaakov Benenson (ETH Zürich – Basel, CH)
Neil Dalchau (Microsoft Research UK – Cambridge, GB)
Heinz Koeppl (TU Darmstadt, DE)
Oded Maler (VERIMAG – Grenoble, FR)

Auskunft zu diesem Dagstuhl Seminar erteilen

Simone Schilke zu administrativen Fragen

Andreas Dolzmann zu wissenschaftlichen Fragen

Dokumente

Programm des Dagstuhl Seminars (Hochladen)

(Zum Einloggen bitte Seminarnummer und Zugangscode verwenden)

Motivation

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 are now required 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 achieved with the help of two types of resources: libraries of previously well-characterized genetic components and mechanistic or machine learning-based predictive 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.

This Dagstuhl Seminar will bring together experts in formal methods for the verification and synthesis of hardware and software with wet-lab and dry-lab synthetic biologists to (1) achieve a common understanding of the current state of design methodology in synthetic biology; (2) to identify the limitations of current approaches; and (3) to investigate dedicated solutions to the synthesis problem in synthetic biology. Some of these methods will be based on leveraging experience and methods from cyber-physical systems design, electronic design automation and from program synthesis and verification. In addition, ideas for entirely new methodologies specifically tailored for synthetic biology are likely to emerge. For example, features that are less pronounced in electronic circuits such as heterogeneity and variability between cells and between the circuits embedded in different cells, will be addressed.

License
  Creative Commons BY 3.0 DE
  Yaakov Benenson, Neil Dalchau, Heinz Koeppl, and Oded Maler

Classification

  • Bioinformatics
  • Modelling / Simulation
  • Semantics / Formal Methods

Keywords

  • Synthetic biology
  • Electronic design automation
  • Program synthesis and verification

Buchausstellung

Bücher der Teilnehmer 

Buchausstellung im Erdgeschoss der Bibliothek

(nur in der Veranstaltungswoche).

Dokumentation

In der Reihe Dagstuhl Reports werden alle Dagstuhl-Seminare und Dagstuhl-Perspektiven-Workshops dokumentiert. Die Organisatoren stellen zusammen mit dem Collector des Seminars einen Bericht zusammen, der die Beiträge der Autoren zusammenfasst und um eine Zusammenfassung ergänzt.

 

Download Übersichtsflyer (PDF).

Publikationen

Es besteht weiterhin die Möglichkeit, eine umfassende Kollektion begutachteter Arbeiten in der Reihe Dagstuhl Follow-Ups zu publizieren.

Dagstuhl's Impact

Bitte informieren Sie uns, wenn eine Veröffentlichung ausgehend von
Ihrem Seminar entsteht. Derartige Veröffentlichungen werden von uns in der Rubrik Dagstuhl's Impact separat aufgelistet  und im Erdgeschoss der Bibliothek präsentiert.