Automated requirements analysis for a molecular watchdog timer

Ellis, Samuel J.; Henderson, Eric; Klinge, Titus H.; Lathrop, James I.; Lutz, Jack H.; Lutz, Robyn R.; Mathur, Divita; Miner, Andrew S.

doi:10.1145/2642937.2643007

Cited by 12 publications

(8 citation statements)

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“…The new failure frame technique that we describe arose from our recent work in a relatively new field of computation, that of molecular programming [6], [7]. Molecular programming is programming in the literal sense, in that DNA can be programmed to implement computational algorithms, and DNA tile self-assembly is Turing universal [8].…”

Section: Introductionmentioning

confidence: 99%

The Role of Environmental Assumptions in Failures of DNA Nanosystems

Tun¹,

Lutz²,

Nakayama³

et al. 2015

2015 IEEE/ACM 1st International Workshop on Complex Faults and Failures in Large Software Systems (COUFLESS)

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Many failures arise from complex and imperfectly understood interactions of a computational system with aspects of the environment in which it operates. By environment we mean the computational system's broader context, also called the problem world. In this work, we propose a new analysis technique called failure frames, a variation of Jackson's problem frames, to identify and model classes of environmental assumptions whose violation is known from experience to have prevented the requirements from being satisfied. We use instances of failure frames, called failure diagrams, to make explicit in the requirements model the environmental assumptions that contributed to past failures. Developers want to reuse such knowledge of past failures to prevent failures in similar, new systems. We show that failure frames and failure diagrams can capture environmental assumptions that developers need to check in order to prevent recurrence of certain failures in similar application areas. The new failure frame approach that we describe arose from our work in molecular programming of DNA nanosystems. Inaccurate assumptions about the environment are a source of many failures in DNA nanosystems and can be extremely challenging to resolve. We describe the structure of a failure catalog for DNA nanosystems that we have prototyped for use by molecular programmers. We hypothesize that the failure frame approach and catalog can be broadly useful for reducing failure recurrence in other large, distributed applications with autonomous or nondeterministic behavior that must operate in uncertain environments.

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Section: Introductionmentioning

confidence: 99%

The Role of Environmental Assumptions in Failures of DNA Nanosystems

Tun¹,

Lutz²,

Nakayama³

et al. 2015

2015 IEEE/ACM 1st International Workshop on Complex Faults and Failures in Large Software Systems (COUFLESS)

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“…These shapes can be imbued with information and function including algorithmic calculations [147,148,149], single-molecule analyses [64,150], therapeutics [83,77,74], mechanical actuation [132,138], and a host of other capabilities [84,110,151,152].…”

Section: Introductionmentioning

confidence: 99%

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confidence: 99%

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confidence: 99%

“…In the requirements analysis of an existing DNA device family[126,127] (the DNA "nanopliers[133]"), careful retrospective study identified a failure mode embedded in the current architecture that leads to a false negative output (binding of different Streptavidin molecules to the two arms of the nanoplier). Moreover, the formal definition of the goal diagram corresponding to the nanopliers can be instrumental in mitigating similar failures in the designing of future nanosystems.Preliminary work on the design and optimization of the Molecular WatchdogTimer (MWT)[147] has paved the way towards effcient experimental implementationof programmable molecular circuits by providing crucial information about toehold lengths and associated reaction times. The study on the role of environmental assumptions in failures of DNA nanosystems resulted in a useful open-access repository of key definitions and known environmental assumptions, a useful guide for future scientific endeavours in DNA nanotechnology.…”

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Dynamic self-assembling DNA nanosystems: design and engineering

Mathur

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Words fail me in thanking my family, the Saraf, Mathur and Sangar clans, who let me choose a course of life for myself, and always provided me with unwavering support and love. I am especially grateful to the women in my life-my grandmother, mother, aunts and sisters-who were the best role models I could have asked for. I do not know of a stronger group of people. In some ways, this thesis is also dedicated to my father, who has been a constant support, in spirit, and in his favorite words on strength, courage and integrity. And finally, I would like to express my heartfelt gratitude to Nikhil Panicker, for his emotional support through every kind of obscenity the past six years of our lives have thrown at us, through the good times too, and for letting me learn ever so much from him. For bringing out the best in me. xii

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