Spatial Coordination of Pervasive Services through Chemical-Inspired Tuple Spaces
ACM Transactions on Autonomous and Adaptive Systems (TAAS)
Core operational semantics of Proto
Proceedings of the 2011 ACM Symposium on Applied Computing
Bridging biology and engineering together with spatial computing
CMC'11 Proceedings of the 12th international conference on Membrane Computing
Operational semantics of proto
Science of Computer Programming
Synthetic Biology and Microdevices: A Powerful Combination
ACM Journal on Emerging Technologies in Computing Systems (JETC) - Special Issue on Bioinformatics
Functional synthesis of genetic regulatory networks
Proceedings of the 1st annual workshop on Functional programming concepts in domain-specific languages
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High level languages greatly increase the power of a programmer at the cost of programs that consume more resources than those written at a lower level of abstraction. This inefficiency is a major concern for the programming of biological systems: although advances in synthetic biology are beginning to allow bacteria to be programmed at an "assembly language'' level, metabolic and chemical constraints currently place tight limits on the computational resources available. We find, however, that the semantics of the Proto spatial computing language appear to be a good match for engineered genetic regulatory networks, and particularly for describing the spatial differentiation necessary to construct tissues or organs. In this paper, we propose a mapping between Proto programs and standardized biological parts. We then demonstrate the plausibility of this mapping by applying it to a band detection program, finding that standard code optimization techniques can transform the inefficient program produced by the initial mapping into an efficient design equivalent to the Weiss laboratory's hand-designed band detector.