A novel droplet routing algorithm for digital microfluidic biochips

Roy, Pranab; Rahaman, Hafizur; Dasgupta, Parthasarathi

doi:10.1145/1785481.1785583

Cited by 38 publications

(44 citation statements)

References 10 publications

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“…The placement defined by the virtual topology provides dedicated routing cells which ease the router's job. We simplify an existing router [22] to compute droplet paths very quickly. (Fig.…”

Section: Contributionmentioning

confidence: 99%

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Fast Online Synthesis of Digital Microfluidic Biochips

Grissom

Brisk

2014

IEEE Trans. Comput.-Aided Des. Integr. Circuits Syst.

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Abstract-We introduce an online synthesis flow, focusing primarily on the virtual topology and operation binder, for digital microfluidic biochips, which will enable real-time response to errors and control flow. The objective of this flow is to facilitate fast assay synthesis while minimally compromising the quality of results. In particular, we show that a virtual topology, which constrains the allowable locations of assay operations such as mixing, dilution, sensing, etc., in lieu of traditional placement, can significantly speed up the synthesis process without significantly lengthening assay execution time. We present a base virtual topology and show how it can be leveraged to reduce algorithmic runtimes and guarantee rout ability. We later present several variations of the virtual topology and present experimental results demonstrating best-design practices. We present two binding solutions. The first is a left-edge binding algorithm, while the second is a more intelligent path-based binding algorithm that leverages spatial and temporal locality to produce superior results.

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Section: Contributionmentioning

confidence: 99%

“…Bio Route [34] and Huang's algorithm [12] both report runtimes below one second on a desktop PC. The router used in our online flow, a modified version of Roy's maze router [22], achieves comparable runtimes, while achieving deadlock freedom.…”

Section: Routingmentioning

confidence: 99%

Fast Online Synthesis of Digital Microfluidic Biochips

Grissom

Brisk

2014

IEEE Trans. Comput.-Aided Des. Integr. Circuits Syst.

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“…Within a 10-week period, the students were able to implement two genetic scheduling algorithms [12][14], a simulated annealing-based placer [15], and one router of nontrivial complexity [13]. Several of the students have continued to work with the simulator, either as volunteer researchers or for independent-studies course projects, and other students (mostly undergraduates and M.S.…”

Section: Implementation Status and Usability Studymentioning

confidence: 99%

“…As the schedules and placements may differ as well, we did not obtain the same routing instances as prior work [13], so the routing times are likewise different. Unsurprisingly, the schedulers based on genetic algorithms [12][14] achieve better quality results than standard list scheduling [14]; however, the runtime of the genetic algorithms is significantly higher, as they are iterative improvement algorithms, whereas, list scheduling is a greedy heuristic.…”

Section: Implementation Status and Usability Studymentioning

confidence: 99%

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A digital microfluidic biochip synthesis framework

Grissom¹,

O’Neal²,

Preciado³

et al. 2012

2012 IEEE/IFIP 20th International Conference on VLSI and System-on-Chip (VLSI-SoC)

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Abstract-Synthesis of digital microfluidic biochips (DMFBs) is a crucial to the advancement and realization of miniaturized, automated, programmable biochemistry solutions; synthesis is performed in three steps: scheduling, placement and routing. In principle, algorithms for specific steps should be interchangeable with one another; however, different research groups typically develop algorithms for each step in isolation from one another. Thus, it is difficult to compare algorithms against one another, or to determine which algorithms for different steps share synergies.We introduce an open source DMFB synthesis framework to encourage collaboration between researchers working in the area. We introduce a common interface and describe the internal data structures that must be updated to ensure that the interfaces are adhered to. We also present and describe a number of highquality 2D and 3D debugging tools that provide graphical output for each stage of synthesis.

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Introduction

Zhao

Chakrabarty

2012

Design and Testing of Digital Microfluidic Biochips

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A novel droplet routing algorithm for digital microfluidic biochips

Cited by 38 publications

References 10 publications

Fast Online Synthesis of Digital Microfluidic Biochips

Fast Online Synthesis of Digital Microfluidic Biochips

A digital microfluidic biochip synthesis framework

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