A New Fluid-Chip Co-Design for Digital Microfluidic Biochips Considering Cost Drivers and Design Convergence
01 Oct 2018-Vol. 4, Iss: 4, pp 548-564
TL;DR: This paper aims to propose a fluid-chip co-design methodology in dealing with the consideration of the fluid- chip cost drivers, while reducing the design cycles in between.
Abstract: The design process for digital microfluidic biochips (DMFBs) is becoming more complex due to the growing need for essential bio-protocols. A number of significant fluid- and chip-level synthesis tools have been offered previously for designing an efficient system. Several important cost drivers like bioassay schedule length, total pin count, congestion-free wiring, total wire length, and total layer count together measure the efficiency of the DMFBs. Besides, existing design gaps among the sub-tasks of the fluid and chip level make the design process expensive delaying the time-to-market and increasing the overall cost. In this context, removal of design cycles among the sub-tasks is a prior need to obtain a low-cost and efficient platform. Hence, this paper aims to propose a fluid-chip co-design methodology in dealing with the consideration of the fluid-chip cost drivers, while reducing the design cycles in between. A simulation study considering a number of benchmarks has been presented to observe the performance.
Citations
More filters
01 Jan 2020
TL;DR: This paper presents a fluid-control co-design considering several important cost-driving issues like minimization of schedule length, control pin count, and wirelength, together with congestion-free and conflict-free wiring.
Abstract: Paper-based digital microfluidic biochips (PDMFBs) are becoming highly effective among the microfluidic platforms due to its low-cost and in-place fabrication. The designed electrodes and wiring can be fabricated on a piece of paper by an inkjet printer and conductive ink containing carbon nanotube particles (CNTs). However, due to induced control interference, the wires cannot pass by an arbitrary electrode. Each wire that is to be routed possesses its conflict electrode group, which must be avoided for a feasible droplet movement. This paper presents a fluid-control co-design considering several important cost-driving issues like minimization of schedule length, control pin count, and wirelength, together with congestion-free and conflict-free wiring. Observably, design gaps exist among the sub-tasks of the fluid-level, control-level, and fluid-control as a whole, due to their separate considerations. It indeed introduces many design cycles lengthening the design process, and thus increases the overall cost. In this context, this work integrates the sub-tasks as a prior need to obtain a low cost and efficient platform. Several benchmarks have been studied to evaluate the performance.
2 citations
TL;DR: With increasing effectiveness of flow-based microfluidic biochips in the field of biochemical experiments and point-of-care diagnosis, design automation demands enormous attention to integrate the technology into the design process.
Abstract: With increasing effectiveness of flow-based microfluidic biochips in the field of biochemical experiments and point-of-care diagnosis, design automation demands enormous attention to integrate the ...
1 citations
TL;DR: A machine learning-based model is built to predict violation in control design beforehand and accordingly guides the fluid-control codesign to tackle important cost-driving issues while attaining congestion- and conflict-free wiring and effectively eliminates the design cycles producing a low-cost platform.
Abstract: Paper-based digital microfluidic biochips (or P-DMFBs) are becoming highly impelling due to its low-cost and in-place fabrication of electrodes and control wiring on a single piece of paper having an inkjet printer and conductive ink. Despite enormous advantages, several complex design rules also subsist, such as avoidance of induced control interference, minimum separation among the control lines, and congestion-free wiring on a single layer, which is to be correlated leading toward overall feasibility of the design. Several cost raising issues, such as schedule length, control pin count, and wire length, must be considered for attaining a successful fluid-control codesign. Moreover, design gaps exist among the subtasks of the fluid level, control level, and fluid-control design as a whole, which undeniably impose expensive design cycles increasing overall cost. This article builds a machine learning-based model for the pin-constrained P-DMFBs to predict violation in control design beforehand and accordingly guides the fluid-control codesign to tackle important cost-driving issues while attaining congestion- and conflict-free wiring. This model effectively eliminates the design cycles producing a low-cost platform. The predictive model has been evaluated over a balanced data set. Several benchmarks for assessing the performance are studied.
1 citations
Cites background from "A New Fluid-Chip Co-Design for Digi..."
...Like traditional DMFBs, through analyzing the activation sequences, a compatibility graph (Gcom) for a group of electrodes can be acquired [9], [15], where an edge denotes the compatibility between the electrode pairs....
[...]
...NP-hard [15], [25], [26]) is aimed to assure a higher quality solution of the fluid level, control level, and overall codesign....
[...]
...If the associated goals for fluid- and control-level tasks are viewed in isolation, a “good” result from a phase may guide to an “unsatisfactory” outcome for the succeeding phases [15]–[17]....
[...]
...wiring in a microfluidic platform [8], [15], [16]....
[...]
TL;DR: In this article , an attack-tolerant synthesis is proposed with two-way security through integrating attack-detection and attack-recovery from various Denial of Service attacks.
Abstract: A digital microfluidic biochip (DMFB) with cyber-physical adaptation implements complex bio-protocols with high precision and high throughput dealing with safety-critical applications including point-of-care diagnosis, personalized medicine, and drug development. Having integrated sensors with network connectivity, a cyber-physical DMFB is undeniably susceptible to attacks. A number of leading research works are carried out to assess various attacks and their impacts. Several defense mechanisms are developed by arranging on-chip monitoring systems through deployment of checkpoints. As checkpoints are external resources imposing a cost-overhead to the system, a cost-effective detection mechanism is of utmost importance. Moreover, after detecting an attack, an efficient recovery process is imperative to execute the associated bioassay in a vulnerable environment. Here, an attack-tolerant synthesis is proposed with two-way security through integrating attack-detection and attack-recovery from various Denial of Service attacks. Moreover, a selective re-synthesis approach has been introduced to allow multiple recovery steps to be executed simultaneously on the biochip. The recovery strategy is closely coupled with the detection process which makes the system adaptive towards attack-tolerance. Experimental results on several benchmarks demonstrate the efficacy of the proposed two-way attack-tolerance strategy.
References
More filters
TL;DR: A novel error-recovery technique to dynamically reconfigure the biochip using real-time data provided by on-chip sensors and an integer linear programming-based method to select the optimal local- recovery time for each operation is presented.
Abstract: A digital microfluidic biochip (DMFB) is an attractive technology platform for automating laboratory procedures in biochemistry. In recent years, DMFBs based on a micro-electrode-dot-array (MEDA) architecture have been proposed. MEDA biochips can provide advantages of better capability of droplet manipulation and real-time sensing ability. However, errors are likely to occur due to defects, chip degradation, and the lack of precision inherent in biochemical experiments. Therefore, an efficient error-recovery strategy is essential to ensure the correctness of assays executed on MEDA biochips. By exploiting MEDA-specific advances in droplet sensing, we present a novel error-recovery technique to dynamically reconfigure the biochip using real-time data provided by on-chip sensors. Local recovery strategies based on probabilistic-timed-automata are presented for various types of errors. An online synthesis technique and a control flow are also proposed to connect local-recovery procedures with global error recovery for the complete bioassay. Moreover, an integer linear programming-based method is also proposed to select the optimal local-recovery time for each operation. Laboratory experiments using a fabricated MEDA chip are used to characterize the outcomes of key droplet operations. The PRISM model checker and three benchmarks are used for an extensive set of simulations. Our results highlight the effectiveness of the proposed error-recovery strategy.
23 citations
"A New Fluid-Chip Co-Design for Digi..." refers background in this paper
...able sized droplets on a chip [7], [8], [9]....
[...]
TL;DR: This paper demonstrates a scalable single-layer PCB wiring scheme for several FPPC-DMFB variations, and presents efficient algorithms for droplet routing, with and without contamination removal via wash droplets, which offer new insights on the relationship between PCB layer count, pin count, and cost.
Abstract: This paper introduces a field-programmable pin-constrained digital microfluidic biochip (FPPC-DMFB), which offers general-purpose assay execution at a lower cost than general-purpose direct addressing DMFBs and highly optimized application-specific pin-constrained DMFBs. One of the key cost drivers for DMFBs is the number of printed circuit board (PCB) layers, onto which the device is mounted. We demonstrate a scalable single-layer PCB wiring scheme for several FPPC-DMFB variations, for PCB technology with orthogonal routing capacity of at least three; for PCB technology with orthogonal capacity of two, more PCB layers are required, but the FPPC-DMFB retains its cost advantage. These results offer new insights on the relationship between PCB layer count, pin count, and cost. Additionally, to reduce the execution time of assays on the FPPC-DMFB, we present efficient algorithms for droplet routing, with and without contamination removal via wash droplets.
22 citations
25 Mar 2012
TL;DR: This work provides a comprehensive integration throughout fluidic-operation scheduling, chip layout generation, control pin assignment, and wiring solution to achieve higher design performance and feasibility in digital microfluidic biochips.
Abstract: Recently, digital microfluidic biochips (DMFBs) have revolutionized many biochemical laboratory procedures and received much attention due to many advantages such as high throughput, automatic control, and low cost. To meet the challenges of increasing design complexity, computer-aided-design (CAD) tools have been involved to build DMFBs efficiently. Current CAD tools generally conduct a two-stage based design flow of fluidic-level synthesis followed by chip-level design to optimize fluidic behaviors and chip architecture separately. Nevertheless, existing fluidic-chip design gap will become even wider with a rapid escalation in the number of assay operations incorporated into a single DMFB. As more and more large-scale assay protocols are delivered in current emerging marketplace, this problem may potentially restrict the effectiveness and feasibility of the entire DMFB realization and thus needs to be solved quickly. In this paper, we propose the first fluidic-chip co-design methodology for DMFBs to effectively bridge the fluidic-chip design gap. Our work provides a comprehensive integration throughout fluidic-operation scheduling, chip layout generation, control pin assignment, and wiring solution to achieve higher design performance and feasibility. Experimental results show the effectiveness, robustness, and scalability of our co-design methodology on a set of real-life assay applications.
20 citations
"A New Fluid-Chip Co-Design for Digi..." refers methods in this paper
...[21] first proposed a co-design method-...
[...]
...While the first design scheme (which follows the basic idea of [21]) assumes a dedi-...
[...]
...To show the effectiveness of the proposed co-design, we consider three state-of-the-art design methods for DMFBs among which one is an integrated fluid-chip co-design [21], one is a PCB layer wire routing [23], and the other one is the traditional design process....
[...]
TL;DR: Improved multiterminal escape routing algorithm for the design of printed circuit boards (PCBs) that control digital microfluidic biochips (DMFBs) can reduce both the number of PCB layers and average wirelength compared to existing DMFB escape routers.
Abstract: This paper introduces a multiterminal escape routing algorithm for the design of printed circuit boards (PCBs) that control digital microfluidic biochips (DMFBs). The new algorithm extends a negotiated congestion-based single-terminal escape router that has been shown to be superior to previous methods. It relaxes the pin assignment to allow pin groups to be broken up when doing so can reduce the number of PCB layers. Experimental results indicate that the improved method can reduce both the number of PCB layers and average wirelength compared to existing DMFB escape routers.
18 citations
"A New Fluid-Chip Co-Design for Digi..." refers background or methods or result in this paper
...Moreover, we have taken the measures of the pin count and layer count for a Naive method as presented in [23]....
[...]
...Table 4 shows the results of pin count and layer count obtained in [23] and our proposed method....
[...]
...[23] proposed a PCB constrained wire routing model for DMFBs....
[...]
...In [23], to obtain the wire routing followed by layer allocation, two methods were introduced, which are Layered Negotiated Congestion (LNC) and Layer Minimized Negotiated Congestion (LMNC)....
[...]
...We further compare our work with another design flow presented in [23] that offers chip-level solutions....
[...]
TL;DR: Experimental results based on real-life chips with obstacles demonstrate the high routability of proposed algorithm for pin-constrained EWOD chips with obstacle avoidance, based on effective integer-linear-programming (ILP) formulation as well as efficient routing framework.
Abstract: Electrowetting-on-dielectric (EWOD) chips have become the most popular actuators, particularly for droplet-based digital microfluidic biochip (DMFB) systems. In order to enable the electrical manipulations, wire routing is a key problem in designing EWOD chips. Unlike traditional very-large-scale-integration (VLSI) routing problems, in addition to routing-path establishment on signal pins, the pin-constrained EWOD-chip routing problem must address the issue of signal sharing for pin-count reduction under a practical constraint posed by a limited pin-count supply. Moreover, EWOD-chip designs might incur several obstacles in the routing region due to embedded devices for specific fluidic protocols. However, no existing work considers the EWOD-chip routing with obstacles and, therefore, lots of manual design efforts are involved. To remedy this insufficiency, we propose in this paper the first routing algorithm for pin-constrained EWOD chips with obstacle avoidance. The proposed algorithm, based on effective integer-linear-programming (ILP) formulation as well as efficient routing framework, can achieve high routability with a low design complexity. Experimental results based on real-life chips with obstacles demonstrate the high routability of proposed algorithm for pin-constrained EWOD chips with obstacle avoidance.
11 citations
"A New Fluid-Chip Co-Design for Digi..." refers background in this paper
...However, in 2013, [22] first considered the issue of multi-layer printed circuit board (or PCB) during wire routing, while in 2017, McDaniel et al....
[...]