Placement of digital microfluidic biochips using the t-tree formulation

Yuh, Ping-Hung; Yang, Chia-Lin; Chang, Yao-Wen

doi:10.1145/1146909.1147145

Cited by 50 publications

(56 citation statements)

References 11 publications

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“…Su and Chakrabarty [16] have proposed an integer linear programming (ILP) model for scheduling and binding, considering a given allocation, but without addressing placement and routing. During the physical-level synthesis, the placement [18,25] of each module on the microfluidic array and the droplets routes [6,23,28] have to be determined.…”

Section: Related Workmentioning

confidence: 99%

“…Their algorithm was modified in [22] to include droplet-routingaware physical design decisions. Yuh et al [25] have proposed a synthesis and placement algorithm which uses a tree-based topological representation and is able to improve on the results from [17]. The algorithm has later been extended to consider defective cells on the biochip array [26].…”

Section: Related Workmentioning

confidence: 99%

“…Yuh et al [27] use a 3D transitive closure subGraph for the 3D packing problem. Their earlier work on temporal floorplanning using a tree-based topological representation [24] has been extended for DMBs [25].…”

Section: Related Workmentioning

confidence: 99%

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Tabu search-based synthesis of dynamically reconfigurable digital microfluidic biochips

Maftei

Pop

Madsen

2009

Proceedings of the 2009 International Conference on Compilers, Architecture, and Synthesis for Embedded Systems

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Microfluidic biochips are replacing the conventional biochemical analyzers, and are able to integrate on-chip all the necessary functions for biochemical analysis. The "digital" microfluidic biochips are manipulating liquids not as a continuous flow, but as discrete droplets, and hence they are highly reconfigurable and scalable. A digital biochip is composed of a two-dimensional array of cells, together with reservoirs for storing the samples and reagents. Several adjacent cells are dynamically grouped to form a virtual device, on which operations are executed. During the execution of an operation, the virtual device can be reconfigured to occupy a different group of cells on the array. In this paper, we present a Tabu Search metaheuristic for the synthesis of digital microfluidic biochips, which, starting from a biochemical application and a given biochip architecture, determines the allocation, resource binding, scheduling and placement of the operations in the application. In our approach, we consider moving the modules during their operation, in order to improve the completion time of the biochemical application. The proposed heuristic has been evaluated using three real-life case studies and ten synthetic benchmarks.

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Section: Related Workmentioning

confidence: 99%

Section: Related Workmentioning

confidence: 99%

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Tabu search-based synthesis of dynamically reconfigurable digital microfluidic biochips

Maftei

Pop

Madsen

2009

Proceedings of the 2009 International Conference on Compilers, Architecture, and Synthesis for Embedded Systems

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“…Recent years have seen growing interest in the this area [9], [12], [13], [19], [20]. One of the first published methods for biochip synthesis decouples high-level synthesis from physical design [13].…”

Section: Related Prior Workmentioning

confidence: 99%

“…Therefore, defect tolerance must be integrated into the automated design tools to ensure high levels of system dependability. Despite the recent emergence of automated synthesis methods for biochips [9], [12], [13], defect tolerance has largely been overlooked in the literature. Fig.…”

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confidence: 99%

Defect-Aware High-Level Synthesis and Module Placement for Microfluidic Biochips

Chakrabarty

2008

IEEE Trans. Biomed. Circuits Syst.

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Abstract-Recent advances in microfluidics technology have led to the emergence of miniaturized biochip devices, also referred to as lab-on-a-chip, for biochemical analysis. A promising category of microfluidic biochips relies on the principle of electrowetting-ondielectric, whereby discrete droplets of nanoliter volumes can be manipulated using an array of electrodes. As chemists adapt more bioassays for concurrent execution on such "digital" droplet-based microfluidic platforms, system integration, design complexity, and the need for defect tolerance are expected to increase rapidly. Automated design tools for defect-tolerant and multifunctional biochips are important for the emerging marketplace, especially for lowcost, portable, and disposable devices for clinical diagnostics. We present a unified synthesis method that combines defect-tolerant architectural synthesis with defect-aware physical design. The proposed approach allows architectural-level design choices and defect-tolerant physical design decisions to be made simultaneously. We use a large-scale protein assay and the polymerase chain reaction procedure as case studies to evaluate the proposed synthesis method. We also carry out simulations based on defect injection to evaluate the robustness of the synthesized biochip designs.

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