Abstraction Layers for Scalable Microfluidic Biocomputers (Extended Version)
Author(s)
Thies, William
Urbanski, John Paul
Thorsen, Todd
Amarasinghe, Saman
Advisor(s)
Saman Amarasinghe
Date Issued
May 5, 2006
Series/Report no.
Massachusetts Institute of Technology Computer Science and Artificial Intelligence Laboratory
Abstract
Microfluidic devices are emerging as an attractive technology for automatically orchestrating the reactions needed in a biological computer. Thousands of microfluidic primitives have already been integrated on a single chip, and recent trends indicate that the hardware complexity is increasing at rates comparable to Moore's Law. As in the case of silicon, it will be critical to develop abstraction layers--such as programming languages and Instruction Set Architectures (ISAs)--that decouple software development from changes in the underlying device technology.Towards this end, this paper presents BioStream, a portable language for describing biology protocols, and the Fluidic ISA, a stable interface for microfluidic chip designers. A novel algorithm translates microfluidic mixing operations from the BioStream layer to the Fluidic ISA. To demonstrate the benefits of these abstraction layers, we build two microfluidic chips that can both execute BioStream code despite significant differences at the device level. We consider this to be an important step towards building scalable biocomputers.
Subjects
biological computing
DNA computing
microfluidics
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