Natural Computing

, Volume 7, Issue 2, pp 255–275

Abstraction layers for scalable microfluidic biocomputing

  • William Thies
  • John Paul Urbanski
  • Todd Thorsen
  • Saman Amarasinghe
Article

DOI: 10.1007/s11047-006-9032-6

Cite this article as:
Thies, W., Urbanski, J.P., Thorsen, T. et al. Nat Comput (2008) 7: 255. doi:10.1007/s11047-006-9032-6
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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 biological computers.

Keywords

MicrofluidicsLaboratory automationDNA computingBiological computationSelf-assemblyProgramming languages

Copyright information

© Springer Science+Business Media, Inc. 2007

Authors and Affiliations

  • William Thies
    • 1
  • John Paul Urbanski
    • 2
  • Todd Thorsen
    • 2
  • Saman Amarasinghe
    • 1
  1. 1.Computer Science and Artificial Intelligence LaboratoryMassachusetts Institute of TechnologyCambridgeUSA
  2. 2.Hatsopoulos Microfluids LaboratoryMassachusetts Institute of TechnologyCambridgeUSA