Latency-optimization synthesis with module selection for digital microfluidic biochips

Liu, Chia-Hung; Liu, Kuang-Cheng; Huang, Juinn-Dar

doi:10.1109/socc.2013.6749681

Cited by 11 publications

(7 citation statements)

References 15 publications

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“…The majority of work on DMFB compilation targets devices that do not feature sensory feedback or control flow; as such, the scope of compilation was limited to programs that consisted of a single basic block. Discrete formulations of the various compilation stages of scheduling [21,30,50,63,70,80], placement [14,28,48,57,58,79,87,88,90], and droplet routing [9,15,34,41,42,71,72,81,91] were explored, along with wash-droplet [35,89,92] to eliminate contamination on the surface of the chip. The compiler described here is a general framework and could implement any of these algorithms.…”

Section: Related Workmentioning

confidence: 99%

A performance-optimizing compiler for cyber-physical digital microfluidic biochips

Loveless

Ott

Brisk

2020

Proceedings of the 18th ACM/IEEE International Symposium on Code Generation and Optimization

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This paper introduces a compiler optimization strategy for Software-Programmable Laboratories-on-a-Chip (SP-LoCs), which miniaturize and automate a wide variety of benchtop laboratory experiments. The compiler targets a specific class of SP-LoCs that manipulate discrete liquid droplets on a 2D grid, with cyber-physical feedback provided by integrated sensors and/or video monitoring equipment. The optimization strategy employed here aims to reduce the overhead of transporting fluids between operations, and explores tradeoffs between the latency and resource requirements of mixing operations: allocating more space for mixing shortens mixing time, but reduces the amount of spatial parallelism available to other operations. The compiler is empirically evaluated using a cycle-accurate simulator that mimics the behavior of the target SP-LoC. Our results show that a coalescing strategy, inspired by graph coloring register allocation, effectively reduces droplet transport latencies while speeding up the compiler and reducing its memory footprint. For biochemical reactions that are dominated by mixing operations, we observe a linear correlation between a preliminary result using a default mixing operation resource allocation and the percentage decrease in execution time that is achieved via resizing. CCS Concepts • Computer systems organization → Embedded and cyber-physical systems; Parallel architectures; Reconfigurable computing; • Software and its engineering → Compilers; • Hardware → Emerging languages and compilers; Microelectromechanical systems.

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Section: Related Workmentioning

confidence: 99%

A performance-optimizing compiler for cyber-physical digital microfluidic biochips

Loveless

Ott

Brisk

2020

Proceedings of the 18th ACM/IEEE International Symposium on Code Generation and Optimization

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“…Our papers describing force-directed list scheduling [59] and path scheduling [23] include comparisons with the other algorithms using the framework. Two algorithms that have not (yet) been implemented within the framework include optimal scheduling via integer linear programming (ILP) [15,69] and a heuristic called Latency Optimal Scheduling with MOdule Selection (LOSMOS) [43]. The ILPs that have been published thus far are specific to two different assay topologies, and we have not yet tried to generalize them.…”

Section: Schedulingmentioning

confidence: 99%

“…Under the traditional model of DMFB scheduling [15,22,23,43,59,63,69], the latency of each operation is known statically. Under routing-based synthesis, the latency of operations such as mixing and dilution is not determined until the routes are known, thus scheduling and routing must be performed together [51].…”

Section: Routing-based Synthesismentioning

confidence: 99%

“…Table 3 lists 10 benchmark DAGs that were used in our experiments, along with their origins. The first four benchmarks, PCR, In vitro 4 Â 4, Protein, and Protein Split 5 have been widely used in past literature on DMFB scheduling [15,22,23,43,59,63,69]; the remaining six are DAGs generated by four of the different sample preparation algorithms listed in Table 1: to the best of our knowledge, this is the first time that DAGs generated by any of these sample preparation algorithms have been used to evaluate the performance of the scheduling algorithms listed above.…”

Section: Experimental Comparisonmentioning

confidence: 99%

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An open-source compiler and PCB synthesis tool for digital microfluidic biochips

Grissom

Curtis

Windh

et al. 2015

Integration, the VLSI Journal

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“…Concurrent droplet routing in opposite directions is not possible using a three-phase bus (a) but becomes possible with a direct-addressing bus (b).A. Abdoli, P. Brisk Microelectronics Journal 77 (2018)[34][35][36][37][38][39][40][41][42][43][44][45][46][47][48] …”

mentioning

confidence: 99%

Stationary-Mixing Field-Programmable Pin-Constrained Digital Microfluidic Biochip

Abdoli

Brisk

2018

Microelectronics Journal

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This paper introduces a Field Programmable Pin-Constrained (FPPC) architecture for a Digital Microfluidic Biochip (DMFB) that integrates a new stationary hydrodynamic mixing technology. Compared to the traditional rotation-based mixing, stationary mixing is faster, requires fewer electrodes, and limits residue production and the likelihood of biofouling. Although the stationary mixing principle has been established, programmable DMFB architectures that feature stationary mixing have not been investigated or evaluated. Simulation results show that the Stationary Mixing FPPC (SM-FPPC) architecture introduced here outperforms existing Direct Addressing (DA) and FPPC DMFBs that employ traditional rotation-based mixing. An analysis based on a commercially available Printed Circuit Board (PCB) cost calculator demonstrates a 31% reduction in cost compared to the lowest cost PCB reported in prior literature.

show abstract

Latency-optimization synthesis with module selection for digital microfluidic biochips

Cited by 11 publications

References 15 publications

A performance-optimizing compiler for cyber-physical digital microfluidic biochips

A performance-optimizing compiler for cyber-physical digital microfluidic biochips

An open-source compiler and PCB synthesis tool for digital microfluidic biochips

Stationary-Mixing Field-Programmable Pin-Constrained Digital Microfluidic Biochip

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