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.
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References
Braich, R.S., Chelyapov, N., Johnson, C., Rothemund, P.W.K., Adleman, L.: Solution of a 20-variable 3-SAT problem on a DNA computer. Science 296 (2002)
Farfel, J., Stefanovic, D.: Towards practical biomolecular computers using microfluidic deoxyribozyme logic gate networks. In: DNA 11 (2005)
Gehani, A., Reif, J.: Micro flow bio-molecular computation. Biosystems 52 (1999)
Grover, W.H., Mathies, R.A.: An integrated microfluidic processor for single nucleotide polymorphism-based DNA computing. Lab on a Chip 5 (2005)
Livstone, M.S., Weiss, R., Landweber, L.F.: Automated design and programming of a microfluidic DNA computer. Natural Computing (2006)
McCaskill, J.S.: Optically programming DNA computing in microflow reactors. BioSystems 59 (2001)
Somei, K., Kaneda, S., Fujii, T., Murata, S.: A microfluidic device for DNA tile self-assembly. In: DNA 11 (2005)
van Noort, D.: A programmable molecular computer in microreactors. In: DNA 11 (2005)
van Noort, D., Gast, F.U., McCaskill, J.S.: DNA computing in microreactors. In: DNA 8 (2002)
van Noort, D., Zhang, B.T.: PDMS valves in DNA computers. In: SPIE International Symposium on Smart Materials, Nano, and Micro-Smart Systems (2004)
Breslauer, D.N., Lee, P.J., Lee, L.P.: Microfluidics-based systems biology. Molecular BioSystems 2 (2006)
Erickson, D., Li, D.: Integrated microfluidic devices. Anal. Chim. Acta 507 (2004)
Sia, S.K., Whitesides, G.M.: Microfluidic devices fabricated in poly(dimethylsiloxane) for biological studies. Electrophoresis 24 (2003)
Thorsen, T., Maerkl, S., Quake, S.: Microfluidic large scale integration. Science 298 (2002)
Hong, J.W., Quake, S.R.: Integrated nanoliter systems. Nature BioTechnology 21(10) (2003)
Allan, L., Morrice, N., Brady, S., Magee, G., Pathak, S., Clarke, P.: Inhibition of caspase-9 through phosphorylation at Thr 125 by ERK MAPK. Nature Cell Biology 5 (2003)
Urbanski, J.P., Thies, W., Rhodes, C., Amarasinghe, S., Thorsen, T.: Digital microfluidics using soft lithography. Lab on a Chip 6 (2006)
Chou, H., Unger, M., Quake, S.: A microfabricated rotary pump. Biomedical Microdevices 3 (2001)
Faulhammer, D., Cukras, A.R., Lipton, R.J., Landweber, L.F.: Molecular computation: RNA solutions to chess problems. PNAS 97(4) (2000)
Ouyang, Q., Kaplan, P.D., Liu, S., Libchaber, A.: DNA solution of the maximal clique problem. Science 278 (1997)
Yamamoto, M., Matsuura, N., Shiba, T., Kawazoe, Y., Ohuchi, A.: Solutions of shortest path problems by concentration control. In: DNA 7 (2002)
Paik, P., Pamula, V., Fair, R.: Rapid droplet mixers for digitial microfluidic systems. Lab on a Chip 3 (2003)
Thies, W., Urbanski, J.P., Thorsen, T., Amarasinghe, S.: Abstraction layers for scalable microfluidic biocomputers (Extended version). Technical Report MIT-CSAIL-TR-2006-034, MIT (2006), http://hdl.handle.net/1721.1/32543
Gascoyne, P.R.C., Vykoukal, J.V., Schwartz, J.A., Anderson, T.J., Vykoukal, D.M., Current, K.W., McConaghy, C., Becker, F.F., Andrews, C.: Dielectrophoresis-based programmable fluidic processors. Lab on a Chip 4 (2004)
Su, F., Chakrabarty, K.: Architectural-level synthesis of digital microfluidics-based biochips. In: ICCAD (2004)
Su, F., Chakrabarty, K.: Unified high-level synthesis and module placement for defect-tolerant microfluidic biochips. In: DAC (2005)
King, R.D., Whelan, K.E., Jones, F.M., Reiser, P.G.K., Bryant, C.H., Muggleton, S.H., Kell, D.B., Oliver, S.G.: Functional genomic hypothesis generation and experimentation by a robot scientist. Nature 427 (2004)
Gu, W., Zhu, X., Futai, N., Cho, B.S., Takayama, S.: Computerized microfluidic cell culture using elastomeric channels and Braille displays. PNAS 101(45) (2004)
Johnson, C.: Automating the DNA Computer to Solve n-Variable 3-SAT Problems. In: DNA 12 (2006)
Dertinger, S.K.W., Chiu, D.T., Jeon, N.L., Whitesides, G.M.: Generation of gradients having complex shapes using microfluidic networks. Anal. Chem. 73 (2001)
Neils, C., Tyree, Z., Finlayson, B., Folch, A.: Combinatorial mixing of microfluidic streams. Lab on a Chip 4 (2004)
Lin, F., Saadi, W., Rhee, S.W., Wang, S.J., Mittalb, S., Jeon, N.L.: Generation of dynamic temporal and spatial concentration gradients using microfluidic devices. Lab on a Chip 4 (2004)
Pollack, M., Fair, R., Shenderov, A.: Electrowetting-based actuation of liquid droplets for microfluidic applications. Applied Physics Letters 77(11) (2000)
Ren, H., Srinivasan, V., Fair, R.: Design and testing of an interpolating mixing architecture for electrowetting-based droplet-on-chip chemical dilution. Transducers (2003)
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Thies, W., Urbanski, J.P., Thorsen, T., Amarasinghe, S. (2006). Abstraction Layers for Scalable Microfluidic Biocomputers. In: Mao, C., Yokomori, T. (eds) DNA Computing. DNA 2006. Lecture Notes in Computer Science, vol 4287. Springer, Berlin, Heidelberg. https://doi.org/10.1007/11925903_24
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DOI: https://doi.org/10.1007/11925903_24
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-540-49024-1
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