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A compiler for cyber-physical digital microfluidic biochips

Authors:

Christopher Curtis,

Daniel Grissom,

Philip BriskAuthors Info & Claims

CGO '18: Proceedings of the 2018 International Symposium on Code Generation and Optimization

Pages 365 - 377

https://doi.org/10.1145/3168826

Published: 24 February 2018 Publication History

Abstract

Programmable microfluidic laboratories-on-a-chip (LoCs) offer the benefits of automation and miniaturization to the life sciences. This paper presents an updated version of the BioCoder language and a fully static (offline) compiler that can target an emerging class of LoCs called Digital Microfluidic Biochips (DMFBs), which manipulate discrete droplets of liquid on a 2D electrode grid. The BioCoder language and runtime execution engine leverage advances in sensor integration to enable specification, compilation, and execution of assays (bio-chemical procedures) that feature online decision-making based on sensory data acquired during assay execution. The compiler features a novel hybrid intermediate representation (IR) that interleaves fluidic operations with computations performed on sensor data. The IR extends the traditional notions of liveness and interference to fluidic variables and operations, as needed to target the DMFB, which itself can be viewed as a spatially reconfigurable array. The code generator converts the IR into the following: (1) a set of electrode activation sequences for each basic block in the control flow graph (CFG); (2) a set of computations performed on sensor data, which dynamically determine the result of each control flow operation; and (3) a set of electrode activation sequences for each control flow transfer operation (CFG edge). The compiler is validated using a software simulator which produces animated videos of realistic bioassay execution on a DMFB.

References

[1]

M. Pollack, A. Shenderov, and R. Fair. 2002. Electrowetting-based actuation of droplets for integrated microfluidics. Lab-on-a-Chip 2, 2 (May, 2002), 96-101.

[2]

J. P. Urbanski, W. Thies, C. Rhodes, S. Amarasinghe, and T. Thorsen. 2006. Digital microfluidics using soft lithography. Lab-on-a-Chip 6, 1, (Jan. 2006), 96-104.

[3]

A. M. Amin, M. Thottethodi, T. N. Vijaykumar, S. Wereley, and S. C. Jacobson. 2007. Aquacore: A programmable architecture for microfluidics. In Proceedings of the 34th International Symposium on Computer Architecture (ISCA'07). 254-265.

Digital Library

[4]

E. C. Jensen, B. P. Bhat, and R. A. Mathies. 2010. A digital microfluidic platform for the automation of quantitative biomolecular assays. Lab-on-a-Chip 10, 6 (Mar. 2010), 685-691.

[5]

L. M. Fidalgo and S. J. Maerkl. 2011. A software-programmable microfluidic device for automated biology. Lab-on-a-Chip 11, 9 (May, 2011), 1612-1619,

[6]

K. Leung, H. Zahn, T. Leaver, K. M. Konwar, N. W. Hanson, A. P. Page, C-C. Lo, P. S. Chain, S. J. Hallam, and C. L. Hansen. 2012. A programmable droplet-based microfluidic device applied to multiparameter analysis of single microbes and microbial communities. Proceedings of the National Academies of Sciences of the United States of America 109, 20 (May 2012). 7665- 7670.

[7]

A. M. Amin, R. Thakur, S. Madren, H. S. Chuang, M. Thottethodi, T. N. Vijaykumar, S. T. Wereley, and S. C. Jacobson. 2013. Software-programmable continuous-flow multi-purpose lab-on-a-chip. Microfluidics and Nanofluidics 15, 5 (Nov. 2013), 657-659.

[8]

G. Linshiz, E. Jensen, N. Stawski, C. Bi, N. Elsbree, H. Jiao, J. Kim, R. Mathies, J. D. Keasling, and N. J. Hillson. 2016. End-to-end automated microfluidic platform for synthetic biology: from design to functional analysis. Journal of Biological Engineering 10 (Feb. 2016), Article #3.

[9]

H. Ren, R. B. Fair, and M. G. Pollack. 2004. Automated on-chip droplet dispensing with volume control by eletrowetting actuation and capacitance metering. Sensors and Actuators B: Chemical 98, 2-3 (Mar. 2004). 319-327.

[10]

V. Srinivasan, V. K. Pamula, and R. B. Fair. Droplet-based microfluidic lab-on-a-chip for glucose detection. Analytica Chimica Acta 507, 1 (Apr. 2004) 145- 150.

[11]

J. Gong and C-J. Kim. 2008. All-electronic droplet generation on-chip with real-time feedback control for EWOD digital microfluidics. Lab-on-a-Chip 8, 6 (June 2008). 898-906.

[12]

S. C. C. Shih, R. Fobel, P. Kumar, and A. R. Wheeler. 2011. A feedback control system for high-fidelity digital microfluidics. Lab-on-a-Chip 11, 3 (Feb. 2011). 535-540.

[13]

S. Sadeghi, H. Ding, G. J. Shah, S. Chen, P. Y. Keng, C-J. Kim, and R. M. van Dam. 2012. On chip droplet characterization: a practical, high-sensitivity measurement of droplet impedance in digital microfluidics. Analytical Chemistry 84, 4 (Jan. 2012). 1915-1923.

[14]

M. J. Schertzer, R. Ben Mrad, and P. E. Sullivan. 2012. Automated detection of particle concentration and chemical reactions in EWOD devices. Sensors and Actuators B: Chemical 164, 1 (Mar. 2012). 1-6.

[15]

M. Murran and H. Najjaran. 2012. Capacitance-based droplet position estimator for digital microfluidic devices. Lab-on-a-Chip 12, 11 (Mar. 2012). 2053-2059.

[16]

L. Luan, M. W. Royal, R. Evans, R. B. Fair, and N. M. Jokerst. 2012. Chip scale optical microresonator sensors integrated with embedded thin film photodetectors on electrowetting digital microfluidics platforms. IEEE Sensors Journal 12, 6 (June 2012). 1794-1800.

[17]

T. Lederer, S. Clara, B. Jakoby, and W. Hilber. 2012. Integration of impedance spectroscopy sensors in a digital microfluidic platform. Microsystem Technologies 18, 7-8 (Aug. 2012). 1163-1180.

Digital Library

[18]

B. Bhattacharjee and H. Najjaran. 2012. Droplet sensing by measuring the capacitance between coplanar electrodes in a digital microfluidic system. Lab-on-a-Chip 12, 21 (Nov. 2012). 4416-4423.

[19]

J. Gao, X. Liu, T. Chen, P. I. Mak, Y. Du, M. I. Vai, B. Lin, and R. P. Martins. 2013. An intelligent digital microfluidic system with fuzzy-enhanced feedback for multi-droplet manipulation. Lab-on-a-Chip 13, 3 (Feb. 2013). 443- 451.

[20]

S. C. Shih, I. Barbulovic-Nad, X. Yang, R. Fobel, and A. R. Wheeler. 2013. Digital microfluidics with impedance sensing for integrated cell culture and analysis. Biosensors and Bioelectronics 42, (Apr. 2013). 314-320.

[21]

M. W. Royal, N. M. Jokerst, and R. B. Fair. 2013. Droplet-based sensing: optical microresonator sensors embedded in digital electrowetting microfluidics systems. IEEE Sensors Journal 13, 12 (Dec. 2013). 4733-4742.

[22]

Y. Li, H. Li, and R. Baker. 2014. Volume and concentration identification by using an electrowetting on dielectric device. In Proceedings of the IEEE Dallas Circuits and Systems Conference (DCAS'14). 1-4.

[23]

Y. Li, H. Li, and R. J. Baker. 2015. A low-cost and high-resolution droplet position detector for an intelligent electrowetting on dielectric device. Journal of Laboratory Automation 20, 6 (Jan. 2015). 663-669.

[24]

Y. Shin and J. Lee. 2010. Machine vision for digital microfluidics. Review of Scientific Instruments 81, 1 (Jan. 2010). 014302.

[25]

A. S. Basu. 2013. Droplet morphometry and velocimetry (dmv): a video processing software for time-resolved, label-free tracking of droplet parameters," Lab-on-a-Chip 13, 10 (May 2013). 1892-1901.

[26]

R. Fobel, C. Fobel, and A. R. Wheeler. 2013. Dropbot: An open source digital microfluidic control system with precise control of electrostatic driving force and instantaneous drop velocity measurement. Applied Physics Letters 102, 19 (May 2013). 193513.

[27]

K. Hu, B. Hsu, A. Madison, K. Chakrabarty, and R. B. Fair. 2013. Fault detection, real-time error recovery, and experimental demonstration for digital microfluidic biochips. In Proceedings of Design Automation and Test in Europe (DATE'13). 559-564.

Digital Library

[28]

P. Q. N. Vo, M. C. Husser, F. Ahmadi, H. Sinha, and S. C. C. Shih. 2017. Image-based feedback and analysis system for digital microfluidics. Lab-on-a-Chip 17, 20, (Sep. 2017), 3437-3446.

[29]

Z. Li, K. Y-T. Lai, J. McCrone, P-H. Yu, K. Chakrabarty, M. Pajic, T-Y. Ho, and C-Y. Lee. 2017. Efficient and adaptive error recovery in a micro-electrode-dot-array digital microfluidic biochip. IEEE TCAD (July 2017). Preprint.

[30]

Y. Zhao, T. Xu, and K. Chakrabarty. 2010. Integrated control-path design and error recovery in the synthesis of digital microfluidic lab-on-a-chip. ACM JETC 6, 3 (Aug. 2010). Article #11.

Digital Library

[31]

M. Alistar, P. Pop, and J. Madsen. 2012. Online synthesis for error recovery in digital microfluidic biochips with operation variability. In Proceedings on the 2012 Symposium on Design, Test, Integration and Packaging of MEMS/MOEMS (DTIP'12).

[32]

Y. Luo, K. Chakrabarty, and T-Y. Ho. 2013. Error recovery in cyberphysical digital microfluidic biochips. IEEE TCAD 32, 1 (Jan. 2013). 59-72.

Digital Library

[33]

Y. Luo, K. Chakrabarty, and T-Y. Ho. 2013. Real-time error recovery in cyberphysical digital-microfluidic biochips using a compact dictionary. IEEE TCAD 32, 12 (Dec. 2013). 1839-1852.

Digital Library

[34]

Y-L. Hsieh, T-Y. Ho, and Krishnendu Chakrabarty. 2014. Biochip synthesis and dynamic error recovery for sample preparation using digital microfluidics. IEEE TCAD 33, 2 (Feb. 2014). 183-196.

Digital Library

[35]

M. Ibrahim and K. Chakrabarty. 2015. Error recovery in digital microfluidics for personalized medicine. In Proceedings of Design Automation and Test in Europe (DATE'15). 247-252.

Digital Library

[36]

C. Jaress, P. Brisk, and D. T. Grissom. 2015. Rapid online fault recovery for cyber-physical digital microfluidic biochips. In Proceedings of the IEEE VLSI Test Symposium (VTS'15). 1-6.

[37]

M. Alistar and P. Pop. 2015. Synthesis of biochemical applications on digital microfluidic biochips with operation execution time variability. Integration: The VLSI Journal 51, (Sep. 2015) 158-168.

Digital Library

[38]

S. Poddar, S. Ghoshal, K. Chakrabarty, and B. B. Bhattacharya. 2016. Error-correcting sample preparation with cyberphysical digital microfluidic lab-on-chip. ACM TODAES 22, 1 (July 2016), Article #2.

Digital Library

[39]

M. Ibrahim, K. Chakrabarty, and K. Scott. 2017. Synthesis of cyberphysical digital-microfluidic biochips for real-time quantitative analysis. IEEE TCAD 36, 5 (May, 2017). 733-746.

Digital Library

[40]

H. Moon, S. K. Cho, R. L. Garrell, and C-J. Kim. 2002. Low voltage electrowetting-on-dielectric. Journal of Applied Physics 92, 7 (Sep. 2002).

[41]

J. Gong and C-J. Kim. 2008. Direct-referencing two-dimensional array digital microfluidics using multilayer printed circuit board. Journal of Microelectromechanical Systems 17, 2 (Apr. 2008). 257-264.

[42]

G. Wang, D. Teng, and S-K. Fan. 2011. Digital microfluidic operations on micro-electrode dot array architecture. IET Nanobiotechnology 5, 4 (Dec. 2011). 152-160.

[43]

J. H. Noh, J. Noh, E. Kreit, J. Heikenfeld, and P. D. Rack. 2012. Toward active-matrix lab-on-a-chip: programmable electrofluidic control enabled by arrayed oxide thin film transistors. Lab-on-a-Chip 2, 2 (Jan. 2012). 353-360.

[44]

B. Hadwen, G. R. Broder, D. Morganti, A. Jacobs, C. Brown, J. R. Hector, Y. Kubota, and H. Morgan. 2012. Programmable large area digital microfluidic array with integrated droplet sensing for bioassays. Lab-on-a-Chip 12, 18 (Sep. 2012). 3305-3313.

[45]

G. Wang, D. Teng, Y-T. Lai, Y-W. Lu, Y. Ho, and C-Y. Lee. 2014. Field-programmable lab-on-a-chip based on microelectrode dot array architecture. IET Nanobiotechnology 8, 3 (Sep. 2014). 163-171.

[46]

A. Banerjee, J. H. Noh, Y. Liu, P. D. Rack, and I. Papautsky. 2015. Programmable electrowetting with channels and droplets. Micromachines 6, 2 (Jan. 2015). 172-185.

[47]

S. Kalsi, M. Valiadi, M. N. Tsaloglou, L. Parry-Jones, A. Jacobs, R. Watson, C. Turner, R. Amos, B. Hadwen, J. Buse, C. Brown, M. Sutton, and H. Morgan. 2015. apid and sensitive detection of antibiotic resistance on a programmable digital microfluidic platform. Lab-on-a-Chip 5, 14 (Jul. 2015). 3065-3075.

[48]

D. Grissom, C. Curtis, and P. Brisk. 2014. Interpreting assays with control flow on digital microfluidic biochips. ACM JETC 10, 3 (Apr. 2014). Article #24.

Digital Library

[49]

C. Curtis and P. Brisk. 2015. Simulation of feedback-driven pcr assays on a 2d electrowetting array using a domain-specific high-level biological programming language. Microelectronic Engineering 148 (Dec. 2015). 110-116.

Digital Library

[50]

J. Ding, K. Chakrabarty, and R. B. Fair. 2001. Scheduling of microfluidic operations for reconfigurable two-dimensional electrowetting arrays. IEEE TCAD 20, 12 (Dec. 2001). 1463-1468.

Digital Library

[51]

R. C. Backer, J. R. Monforte, and A. Poklis. 2005. Evaluation of the DRI oxycodone immunoassay for the detection of oxycodone in urine. Journal of Analytical Toxicology 29, 7 (Oct. 2005). 675-677.

[52]

C. L. Mao, K. D. Zientek, P. T. Colahan, M. Y. Kuo, C. H. Liu, K. M. Lee, and C. C. Chou. 2006. Development of an enzyme linked immunosorbent assay for fentanyl and applications of fentanyl antibody-coated nanoparticles for sample preparation. Journal of Pharmaceutical and Biomedical Analysis 41, 4 (June 2006). 1332-1341.

[53]

Y. Jiang, X. Huang, K. Hu, W. Yu, X. Yang, and L. Lv. 2011. Production and characterization of monoclonal antibodies against small hapten-ciprofloxacin. African Journal of Biotechnology 10, 65 (2011). 14342-14347.

[54]

E. Miller, A. H. C. Ng, U. Uddayasankar, and A. Wheeler. 2011. A digital microfluidic approach to heterogeneous immunoassays. Analytical and Bioanalytical Chemistry 339, 1 (Jan. 2011). 337-345.

[55]

V. Ananthanarayanan and W. Thies. 2010. Biocoder: A programming language for standardizing and automating biology protocols. Journal of Biological Engineering 4 (Nov. 2010). Article #13.

[56]

D. Grissom, C. Curtis, S. Windh, C. Phung, N. Kumar, Z. Zimmerman, O. Kenneth, J. McDaniel, N. Liao, and P. Brisk. 2015. An open-source compiler and pcb synthesis tool for digital microfluidic biochips. Integration: the VLSI Journal 51 (Sep. 2015). 169-193.

Digital Library

[57]

A. J. Ricketts, K. M. Irick, N. Vijaykrishnan, and M. J. Irwin. 2006. Priority scheduling in digital microfluidics-based biochips. In Proceedings of Design, Automation and Test in Europe (DATE'06). 329-334.

Digital Library

[58]

F. Su and K. Chakrabarty. 2008. High-level synthesis of digital microfluidic biochips. ACM JETC 3, 4 (Jan. 2008). Article #1.

Digital Library

[59]

D. Grissom and P. Brisk. 2012. Path scheduling on digital microfluidic biochips. In Proceedings of the Design Automation Conference (DAC'12). 26-35.

Digital Library

[60]

K. O'Neal, D. Grissom, and P. Brisk. 2012. Force-directed list scheduling for digital microfluidic biochips. in Proceedings of the 20th IEEE/IFIP International Conference on VLSI and System-on-Chip (VLSI-SoC'12). 7-11.

[61]

C. Liu, K. Liu, and J. Huang. 2013. Latency-optimization synthesis with module selection for digital microfluidic biochips. In Proceedings of the IEEE International SOC Conference (SOCC'13). 159-164.

[62]

A. Yadav, T. A. Dinh, D. Kitagawa, and S. Yamashita. 2016. ILP-based synthesis for sample preparation applications on digital microfluidic biochips. In Proceedings of the 29th International Conference on VLSI Design (VLSID'16).

Digital Library

[63]

F. Su and K. Chakrabarty. 2006. Module placement for fault-tolerant microfluidics-based biochips. ACM TODAES 11, 3 (July 2006). 682-710.

Digital Library

[64]

C. Liao and S. Hu. 2011. Multiscale variation-aware techniques for high-performance digital microfluidic lab-on-a-chip component placement. IEEE Transactions on Nanobioscience 10, 1 (Mar. 2011). 51-58.

[65]

Y. Chen, C. Hsu, L. Tsai, T. Huang, and T. Ho. 2013. A reliability-oriented placement algorithm for reconfigurable digital microfluidic biochips using 3- d deferred decision making technique. IEEE TCAD 32, 8 (Aug. 2013). 1151- 1162.

Digital Library

[66]

D. Grissom and P. Brisk. 2014. Fast online synthesis of digital microfluidic biochips. IEEE TCAD 33, 3 (Mar. 2014). 356-369.

Digital Library

[67]

F. Su, W. L. Hwang, and K. Chakrabarty. 2006. Droplet routing in the synthesis of digital microfluidic biochips. in Proceedings of Design, Automation and Test in Europe (DATE'06). 323-328.

Digital Library

[68]

K. Bohringer. 2006. Modeling and controlling parallel tasks in droplet-based microfluidic systems. IEEE TCAD 25, 2 (Feb. 2006). 334-344.

Digital Library

[69]

M. Cho and D. Z. Pan. 2008. A high-performance droplet routing algorithm for digital microfluidic biochips. IEEE TCAD 27, 10 (Oct. 2008). 1714-1724.

Digital Library

[70]

P. Yuh, C. Yang, and Y. Chang. 2008. BioRoute: A network-flowbased routing algorithm for the synthesis of digital microfluidic biochips. IEEE TCAD 27, 11 (Nov. 2008). 1928-1941.

Digital Library

[71]

T. Huang and T. Ho. 2009. A fast routability- and performance driven droplet routing algorithm for digital microfluidic biochips. In Proceedings of the 27th International Conference on Computer Design (ICCD'09). 445-450.

Digital Library

[72]

P. Roy, H. Rahaman, and P. Dasgupta. 2010. A novel droplet routing algorithm for digital microfluidic biochips. In Proceedings of the 20th ACM Great Lakes Symposium on VLSI (GLSVLSI'09). 441-446.

Digital Library

[73]

P. Roy, H. Rahaman, and P. Dasgupta. 2012. Two-level clustering-based techniques for intelligent droplet routing in digital microfluidic biochips. Integration: The VLSI Journal 45, 3 (June, 2012). 316-330.

Digital Library

[74]

O. Keszocze, R. Wille, and R. Drechsler. 2014. Exact routing for digital microfluidic biochips with temporary blockages. In Proceedings of the IEEE/ACM International Conference on Computer-Aided Design (ICCAD'14). 405-410.

Digital Library

[75]

O. Keszocze, R. Wille, K. Chakrabarty, and R. Drechsler. 2015. A general and exact routing methodology for digital microfluidic biochips. In Proceedings of the IEEE/ACM International Conference on Computer-Aided Design (ICCAD'15). 874-881.

Digital Library

[76]

O. Keszocze, Z. Li, A. Grimmer, R. Wille, K. Chakrabarty, and R. Drechsler. 2017. Exact routing for micro-electrode-dot-array digital microfluidic biochips. In Proceedings of the 22nd Asia and South Pacific Design Automation Conference (ASP-DAC'17).

[77]

T. Huang, C. Lin, and T. Ho. 2010. A contamination aware droplet routing algorithm for the synthesis of digital microfluidic biochips. IEEE TCAD 29, 11 (Nov. 2010). 1682-1695.

Digital Library

[78]

Y. Zhao and K. Chakrabarty. 2012. Cross-contamination avoidance for droplet routing in digital microfluidic biochips. IEEE TCAD 31, 6 (June 2012). 817-830.

Digital Library

[79]

H. Yao, Q. Wang, Y. Shen, T. Ho, and Y. Cai. 2016. Integrated functional and washing routing optimization for cross-contamination removal in digital microfluidic biochips. IEEE TCAD 35, 8 (Aug. 2016). 1283-1296.

Digital Library

[80]

P. Yuh, C. Yang, and Y. Chang. 2007. Placement of defect-tolerant digital microfluidic biochips using the t-tree formulation. ACM JETC 3, 3 (Nov. 2007). Article #13.

Digital Library

[81]

T. Xu and K. Chakrabarty. 2008. Integrated droplet routing and defect tolerance in the synthesis of digital microfluidic biochips. ACM JETC 4, 3 (Aug. 2008). Article #11.

Digital Library

[82]

T. Xu, K. Chakrabarty, and F. Su. Defect-aware high-level synthesis and module placement for microfluidic biochips. IEEE TBioCAS 2, 1 (Mar. 2008). 50-62.

[83]

E. Maftei, P. Pop, and J. Madsen. 2010. Tabu search-based synthesis of digital microfluidic biochips with dynamically reconfigurable nonrectangular devices. Design Automation for Embedded Systems 14, 3 (Sep. 2010). 287-307.

Digital Library

[84]

E. Maftei, P. Pop, and J. Madsen. 2013. Module-based synthesis of digital microfluidic biochips with droplet-aware operation execution. ACM JETC 9, 1 (Feb. 2013). Article #2.

Digital Library

[85]

R. Wille, O. Keszocze, R. Drechsler, T. Boehnisch, A. Kroker. 2015. Scalable one-pass synthesis for digital microfluidic biochips. IEEE Design & Test 32, 6 (Dec. 2015). 41-50.

[86]

R. Cytron, J. Ferrante, B. K. Rosen, M. N. Wegman, and F. K. Zadeck. 1991. Efficiently computing static single assignment form and the control dependence graph. ACM TOPLAS 13, 4 (Oct. 1991). 451-490.

Digital Library

[87]

J-D. Choi, R. Cytron, J. Ferrante. 1991. Automatic construction of sparse data flow evaluation graphs. In Proceedings of the International Conference on Principles of Programming Languages (POPL'91). 55-66.

Digital Library

[88]

P. Briggs, K. D. Cooper, T. J. Harvey, and L. T. Simpson. 1998. Practical improvements to the construction and destruction of static single assignment form. Software: Practice & Experience 28, 8 (July 1998). 859-881.

Digital Library

[89]

M. Jebrail, R. Renzi, A. Sinha, J. Van De Vreugde, C. Gondhalekar, C. Ambriz, R. Meagher, and S. Branda. 2015. A solvent replenishment solution for managing evaporation of biochemical reactions in air-matrix digital microfluidics devices. Lab-on-a-Chip 15, 1 (Jan. 2015). 151-158.

[90]

C. S. Ananian. 1999. The Static Single Information Form. M.S. Thesis. Massachusetts Institute of Technology, Cambridge, MA, USA.

[91]

J. Singer. 2005. Static Program Analysis based on Virtual Register Renaming. Ph.D. Thesis. University of Cambridge, UK.

[92]

B. Boissinot, P. Brisk, A. Darte, and F. Rastello. 2012. SSI properties revisited. ACM TECS 11S, 1 (June 2012). Article #21.

Digital Library

[93]

K. D. Cooper and L. Torczon. 2004. Engineering a Compiler. Morgan Kaufmann 2004, ISBN 1-55860-699-8

[94]

P. Paik, V. K. Pamula, and R. B. Fair. 2003. Rapid droplet mixers for digital microfluidic systems. Lab-on-a-Chip 3, 4 (Sep. 2003). 253-259.

[95]

K. Bazargan, R. Kastner, and M. Sarrafzadeh. 2000. Fast template placement for reconfigurable computing systems. IEEE Design & Test of Computers 17, 1 (Jan-Mar.2000). 68-83.

Digital Library

[96]

G. J. Chaitin, M. A. Auslander, A. K. Chandra, J. Cocke, M. E. Hopkins, and P. W. Markstein. 1981. Register allocation via coloring. Computer Languages 6, 1 (Jan. 1981). 47-57.

Digital Library

[97]

P. Briggs, K. D. Cooper, and L. Torczon. 1994. Improvements to graph coloring register allocation. ACM TOPLAS 16, 3 (May, 1994). 428-455.

Digital Library

[98]

F. M. Q. Pereira and J. Palsberg. 2008. Register allocation by puzzle solving. In Proceedings of the 29th SIGPLAN Conference on Programming Language Design and Implementation (PLDI'08). 216-226.

Digital Library

[99]

V. C. Sreedhar, R. D-C. Ju, D. M. Gillies, and V. Santhanam. 1999. Translating out of static single assignment form. In Proceedings of the Static Analysis Symposium (SAS'99). 194-210.

Digital Library

[100]

Z. Budimlic, K. D. Cooper, T. J. Harvey, K. Kennedy, T. S. Oberg, and S. W. Reeves. 2002. Fast copy coalescing and live-range identification. In Proceedings of the 26th SIGPLAN Conference on Programming Language Design and Implementation (PLDI'02). 25-32.

Digital Library

[101]

F. Rastello, F. de Ferrière, and C. Guillon. 2004. Optimizing translation out of SSA using renaming constraints. In Proceedings of the International Symposium on Code Generation and Optimization (CGO'04). 265-278.

Digital Library

[102]

B. Boissinot, A. Darte, F. Rastello, B. D. de Dinechin, and C. Guillon. 2009. Revisiting out-of-SSA translation for correctness, code quality and efficiency. In Proceedings of the International Symposium on Code Generation and Optimization (CGO'09). 114-125.

Digital Library

[103]

F. M. Q. Pereira and J. Palsberg. 2009. SSA elimination after register allocation. In Proceedings of Compiler Construction (CC'09). 158-173.

Digital Library

[104]

UC Riverside Digital Microfluidic Biochip Static Synthesis Simulator. URL: http://microfluidics.cs.ucr.edu/dmfb_static_simulator/overview.html

[105]

Y. Luo, B.B. Bhattacharya, T-Y. Ho, and K. Chakrabarty. Design and optimization of a cyberphysical digital-microfluidic biochip for the polymerase chain reaction. IEEE TCAD 34, 1 (Jan. 2015). 29-42.

[106]

L. Freedman, I. Cockburn, and T. Simcoe. 2015. The economics of reproducibility in preclinical research. PLoS Biology 13, 6 (June 2015). e1002165.

[107]

K. Eric. Aquarium, your protocols will be assimilated. http://klavinslab.org/aquarium.html Accessed: 2011-11-13.

[108]

Autoprotocol: an open standard for life science experimental design and automation. URL: http://autoprotocol.org

[109]

Antha. URL: https://docs.antha.com

[110]

W. Thies, J. P. Urbanski, T. Thorsen, and S. Amarasinghe. Abstraction layers for scalable microfluidic biocomputing. Natural Computing 7, 2 (June 2008). 255-275.

Digital Library

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A compiler for cyber-physical digital microfluidic biochips

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Published In

cover image ACM Conferences

CGO '18: Proceedings of the 2018 International Symposium on Code Generation and Optimization

February 2018

377 pages

ISBN:9781450356176

DOI:10.1145/3179541

General Chairs:
Jens Knoop
Vienna University of Technology, Austria
,
Markus Schordan
Lawrence Livermore National Laboratory, USA
,
Program Chairs:
Teresa Johnson
Google, USA
,
Michael O'Boyle
University of Edinburgh, UK

Copyright © 2018 ACM.

Permission to make digital or hard copies of all or part of this work for personal or classroom use is granted without fee provided that copies are not made or distributed for profit or commercial advantage and that copies bear this notice and the full citation on the first page. Copyrights for components of this work owned by others than ACM must be honored. Abstracting with credit is permitted. To copy otherwise, or republish, to post on servers or to redistribute to lists, requires prior specific permission and/or a fee. Request permissions from [email protected]

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SIGPLAN: ACM Special Interest Group on Programming Languages
SIGMICRO: ACM Special Interest Group on Microarchitectural Research and Processing
IEEE-CS: Computer Society

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Association for Computing Machinery

New York, NY, United States

Publication History

Published: 24 February 2018

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National Science Foundation

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CGO '18

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CGO '18: 16th Annual IEEE/ACM International Symposium on Code Generation and Optimization

February 24 - 28, 2018

Vienna, Austria

Acceptance Rates

Overall Acceptance Rate 312 of 1,061 submissions, 29%

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Cited By

Albin DBuecherl LKochavi ENiehaus ENovack SUragoda SMyers CAlistar M(2024)PhageBox: An Open Source Digital Microfluidic Extension With Applications for Phage DiscoveryIEEE Transactions on Biomedical Engineering10.1109/TBME.2023.329541871:1(217-226)Online publication date: Jan-2024
https://doi.org/10.1109/TBME.2023.3295418
Loveless TBrisk PDubach CBruening DHardekopf B(2023)Compiling Functions onto Digital MicrofluidicsProceedings of the 21st ACM/IEEE International Symposium on Code Generation and Optimization10.1145/3579990.3580023(136-148)Online publication date: 17-Feb-2023
https://dl.acm.org/doi/10.1145/3579990.3580023
Swain JPyne S(2023)A Flooding-Based Droplet Routing Protocol for Digital Microfluidic BiochipJournal of Circuits, Systems and Computers10.1142/S021812662350302432:17Online publication date: 30-May-2023
https://doi.org/10.1142/S0218126623503024
Swain JPyne S(2023)A bidirectional droplet routing in digital microfluidics biochipMicroprocessors & Microsystems10.1016/j.micpro.2023.10477498:COnline publication date: 1-Apr-2023
https://dl.acm.org/doi/10.1016/j.micpro.2023.104774
Rajesh KPyne S(2022)Quasi-static scheduling based error recovery for Digital microfluidic biochipsMicroprocessors & Microsystems10.1016/j.micpro.2022.10468494:COnline publication date: 1-Oct-2022
https://dl.acm.org/doi/10.1016/j.micpro.2022.104684
Roy PBanerjee A(2021)A Framework for Validation of Synthesized MicroElectrode Dot Array Actuations for Digital Microfluidic BiochipsACM Transactions on Design Automation of Electronic Systems10.1145/346043726:6(1-36)Online publication date: 30-Jul-2021
https://dl.acm.org/doi/10.1145/3460437
Loveless TOtt JBrisk PMaggio MWeimer JAl Faruque MOishi M(2021)Time- and resource-constrained scheduling for digital microfluidic biochipsProceedings of the ACM/IEEE 12th International Conference on Cyber-Physical Systems10.1145/3450267.3450547(198-208)Online publication date: 19-May-2021
https://dl.acm.org/doi/10.1145/3450267.3450547
Mohammadzadeh NWille RKeszocze O(2021)Efficient One-pass Synthesis for Digital Microfluidic BiochipsACM Transactions on Design Automation of Electronic Systems10.1145/344688026:4(1-21)Online publication date: 22-Apr-2021
https://dl.acm.org/doi/10.1145/3446880
Love FLeopold JMcMillin BSu F(2021)Discriminative Pattern Mining for Runtime Security Enforcement of Cyber-Physical Point-of-Care Medical Technology2021 IEEE 45th Annual Computers, Software, and Applications Conference (COMPSAC)10.1109/COMPSAC51774.2021.00145(1066-1072)Online publication date: Jul-2021
https://doi.org/10.1109/COMPSAC51774.2021.00145
Roy PBanerjee ABhattacharya B(2021)A framework for end-to-end verification for digital microfluidicsInnovations in Systems and Software Engineering10.1007/s11334-021-00398-317:3(231-245)Online publication date: 1-Sep-2021
https://dl.acm.org/doi/10.1007/s11334-021-00398-3
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