Campus Units

Genetics, Development and Cell Biology, Computer Science

Document Type

Conference Proceeding

Conference

29th ACM/IEEE international conference on Automated software engineering

Publication Version

Accepted Manuscript

Publication Date

2014

Journal or Book Title

Proceedings of the 29th ACM/IEEE international conference on Automated software engineering

First Page

767

Last Page

778

DOI

10.1145/2642937.2643007

Conference Title

29th ACM/IEEE international conference on Automated software engineering

Conference Date

September 15-19, 2014

City

Vasteras, Sweden

Abstract

Dynamic systems in DNA nanotechnology are often programmed using a chemical reaction network (CRN) model as an intermediate level of abstraction. In this paper, we design and analyze a CRN model of a watchdog timer, a device commonly used to monitor the health of a safety critical system. Our process uses incremental design practices with goal-oriented requirements engineering, software verification tools, and custom software to help automate the software engineering process. The watchdog timer is comprised of three components: an absence detector, a threshold filter, and a signal amplifier. These components are separately designed and verified, and only then composed to create the molecular watchdog timer. During the requirements-design iterations, simulation, model checking, and analysis are used to verify the system. Using this methodology several incomplete requirements and design flaws were found, and the final verified model helped determine specific parameters for biological experiments.

Comments

© ACM, 2014. This is the author's version of the work. It is posted here by permission of ACM for your personal use. Not for redistribution. The definitive version was published in Proceedings of the 29th ACM/IEEE international conference on Automated software engineering, (2014) http://doi.acm.org/10.1145/2642937.2643007.

Copyright Owner

ACM

Language

en

File Format

application/pdf

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