Article

Tabu search-based synthesis of digital microfluidic biochips with dynamically reconfigurable non-rectangular devices

Design Automation for Embedded Systems (Impact Factor: 0.24). 09/2010; 14(3):287-307. DOI: 10.1007/s10617-010-9059-x
Source: DBLP

ABSTRACT 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 performed. So far, researchers have assumed that throughout its execution,
an operation is performed on a rectangular virtual device, whose position remains fixed. However, during the execution of
an operation, the virtual device can be reconfigured to occupy a different group of cells on the array, forming any shape,
not necessarily rectangular. 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 changing the device to
which an operation is bound during its execution, to improve the completion time of the biochemical application. Moreover,
we devise an analytical method for determining the completion time of an operation on a device of any given shape. The proposed
heuristic has been evaluated using a real-life case study and ten synthetic benchmarks.

0 Followers
 · 
53 Views
  • Source
    • "Consequently, researchers have developed a design flow for DMFBs composed of several steps such as binding, scheduling , placement, and routing (this is reviewed in more detail in Section 2.1). For each of these steps, a number of corresponding design methods have been separately developed [4] [7] [10] [15] [12]. However, design gaps among these four stages do restrict the effectiveness and feasibility of the entire DMFB realization, which reveals a demand for design convergence. "
    [Show abstract] [Hide abstract]
    ABSTRACT: With the advances of the microfluidic technology, the design of digital microfluidic biochips recently received significant attention. But thus far, the corresponding design tasks such as binding, scheduling, placement, and routing have usually been considered separately. Furthermore, often just heuristic results have been obtained. In this work, we present a one-pass synthesis scheme which directly realizes the desired functionality onto the chip and, at the same time, guarantees minimality with respect to area and/or timing. For this purpose, the deductive power of solvers for Boolean satisfiability is exploited. Experiments show how the approach leverages the design of the respective devices.
  • Source
    • "This means that the alternative paths starting with conditional edges labelled err are ignored. Thus, for the graph in Fig. 2c we obtain the graph in Fig. 4a, which is then given as input to the TS algorithm from [4] to obtain Ψ 0 . "
    [Show abstract] [Hide abstract]
    ABSTRACT: Microfluidic-based biochips are replacing the conventional biochemical analyzers, and are able to integrate on-chip all the necessary functions for biochemical analysis using microfluidics. The digital microfluidic biochips are based on the manipulation of liquids not as a continuous flow, but as discrete droplets. Researchers have presented approaches for the synthesis of digital microfluidic biochips, which, starting from a biochemical application and a given biochip architecture, determine the allocation, resource binding, scheduling, placement and routing of the operations in the application. The droplet volumes can vary erroneously due to parametric faults, thus impacting negatively the correctness of the application. Researchers have proposed approaches that synthesize offline predetermined recovery subroutines, which are activated online when errors occur. In this paper, we propose an online synthesis strategy, which determines the appropriate recovery actions at the moment when faults are detected. We have also proposed a biochemical application model which can capture both time-redundant and space-redundant recovery operations. Experiments performed on three real-life case studies show that, by taking into account the biochip configuration when errors occur, our online synthesis is able to reduce the application times.
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: Microfluidic biochips are replacing the conventional biochemical analyzers, and are able to integrate on-chip all the basic functions for biochemical analysis. The "digital" microfluidic biochips are manipulating liquids not as a continuous flow, but as discrete droplets on a two-dimensional array of electrodes. Basic microfluidic operations, such as mixing and dilution, are performed on the array, by routing the corresponding droplets on a series of electrodes. So far, researchers have assumed that these operations are executed on rectangular virtual devices, formed by grouping several adjacent electrodes. One drawback is that all electrodes are considered occupied during the operation execution, although the droplet uses only one electrode at a time. Moreover, the operations can actually execute by routing the droplets on any sequence of electrodes on the array. Hence, in this paper, we eliminate the concept of virtual modules and allow the droplets to move on the chip on any route during operation execution. Thus, the synthesis problem is transformed into a routing problem. We propose an approach derived from a Greedy Randomized Adaptive Search Procedure (GRASP) and we show that by considering routing-based synthesis, significant improvements can be obtained in the application completion time. The proposed heuristic has been evaluated using two real-life case studies and ten synthetic benchmarks.
    Proceedings of the 2010 International Conference on Compilers, Architecture, and Synthesis for Embedded Systems, CASES 2010, Scottsdale, AZ, USA, October 24-29, 2010; 01/2010
Show more