Graph-Covering-Based Architectural Synthesis for Programmable Digital Microfluidic Biochips

Graph-Covering-Based Architectural Synthesis for Programmable Digital Microfluidic Biochips

Daiki Kitagawa (College of Information Science and Engineering, Ritsumeikan University, Kusatsu, Japan), Dieu Quang Nguyen (College of Information Science and Engineering, Ritsumeikan University, Kusatsu, Japan), Trung Anh Dinh (Facebook, Mountan View, CA, USA) and Shigeru Yamashita (College of Information Science, Ritsumeikan University, Kusatsu, Japan)
Copyright: © 2017 |Pages: 13
DOI: 10.4018/IJBCE.2017070103
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Digital microfluidic technology has been extensively applied in various biomedical fields. Different from application-specific biochips, a programmable design has several advantages such as dynamic reconfigurability and general applicability. Basically, a programmable biochip divides the chip into several virtual modules. However, in the previous design, a virtual module can execute only one operation at a time. In this paper, the authors propose a new multi-functional module for programmable digital microfluidic biochips, which can execute two operations simultaneously. Moreover, they also propose a binding and scheduling algorithm for programmable biochips, which is motivated from a graph-covering problem. Experiment demonstrates that their algorithm can reduce the completion time of the applications compared with the previous approaches.
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1. Introduction

Thanks to the recent advance of microfluidic technology, digital microfluidic biochips (DMFBs) have been replacing conventional laboratory experiments in a number of biomedical applications including drug discovery, high throughput DNA sequencing, and environmental toxicity monitoring. By manipulating discrete picoliter biochemical droplets, this kind of biochips offers a number of advantages over traditional procedures such as high sensitivity, high throughput, low power consumption, less human intervention, fast and precise execution (Ho & Chakrabarty, 2011; Su, Chakrabarty, & Fair, 2006).

A typical digital microfluidic biochip consists of a two-dimensional electrode array, peripheral devices such as input/output ports, detectors, etc., as shown in Figure 1. By controlling voltage values of on-chip electrodes, droplets can be moved on the electrode array due to the principle of the electrowetting-on-dielectric (Pollack, Shenderov & Fair, 2002).

Figure 1.

A schematic view of a digital microfluidic biochip

A traditional application-specific biochip can be used to perform only one single biochemical application. Several attempts have been made in the research of high-level synthesis for application-specific biochips (Alistar et al., 2010; Alistar, Pop, & Madsen, 2013; Su & Chakrabarty, 2004; Su & Chakrabarty, 2008; Xu, Chakrabarty, & Su, 2008). Such an application-specific biochip cannot be re-programmed in order to execute different applications. This not only limits the general applicability of the chip, but also increases the cost of production significantly. To deal with such issues, a programmable architecture of DMFBs, which is based on the concept of a traditional field-programmable gate array (FPGA), is proposed in (Grissom & Brisk, 2012). Such a programmable DMFB allows users to reconfigure the chip to execute different applications, and even dynamically modify the synthesis during the execution. Basically, the design in (Grissom & Brisk, 2012) divides the chip into several modules, which behave as similar to look-up tables (LUTs) in an FPGA. However, at each time step, a module can execute only one operation, and thus the completion time of the applications mapped to such a chip may be unnecessarily long. Moreover, the scheduling method proposed in (Grissom & Brisk, 2012) is based on a simple list scheduling algorithm, and thus it further increases the completion time of applications.

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