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From Specification to Implementation: Assume-Guarantee Contracts for Synthetic Biology

Pandey, Ayush and Incer, Inigo and Sangiovanni-Vincentelli, Alberto and Murray, Richard M. (2022) From Specification to Implementation: Assume-Guarantee Contracts for Synthetic Biology. . (Unpublished) https://resolver.caltech.edu/CaltechAUTHORS:20220412-265499000

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Abstract

We provide a new perspective on using formal methods to model specifications and synthesize implementations for the design of biological circuits. In synthetic biology, design objectives are rarely described formally. We present an assume-guarantee contract framework to describe biological circuit design objectives as formal specifications. In our approach, these formal specifications are implemented by circuits modeled by ordinary differential equations, yielding a design framework that can be used to design complex synthetic biological circuits at scale. We describe our approach using the design of a biological AND gate as a motivating, running example.


Item Type:Report or Paper (Discussion Paper)
Related URLs:
URLURL TypeDescription
https://doi.org/10.1101/2022.04.08.487709DOIDiscussion Paper
https://colab.research.google.com/drive/1Hznt1QWCpxeU6wGiv-ozG6tn5869eq5C?usp=sharingRelated ItemCode
ORCID:
AuthorORCID
Pandey, Ayush0000-0003-3590-4459
Sangiovanni-Vincentelli, Alberto0000-0003-1298-8389
Murray, Richard M.0000-0002-5785-7481
Additional Information:The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license. The authors have declared no competing interest.
DOI:10.1101/2022.04.08.487709
Record Number:CaltechAUTHORS:20220412-265499000
Persistent URL:https://resolver.caltech.edu/CaltechAUTHORS:20220412-265499000
Official Citation:From Specification to Implementation: Assume-Guarantee Contracts for Synthetic Biology Ayush Pandey, Inigo Incer, Alberto Sangiovanni-Vincentelli, Richard M Murray bioRxiv 2022.04.08.487709; doi: https://doi.org/10.1101/2022.04.08.487709
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:114241
Collection:CaltechAUTHORS
Deposited By: George Porter
Deposited On:12 Apr 2022 19:47
Last Modified:12 Apr 2022 19:47

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