Proceedings ArticleDOI
Reservoir and mixer constrained scheduling for sample preparation on digital microfluidic biochips
Varsha Agarwal,Ananya Singla,Mahammad Samiuddin,Sudip Roy,Tsung-Yi Ho,Indranil Sengupta,Bhargab B. Bhattacharya +6 more
- pp 702-707
TLDR
A new scheduling scheme namely Reservoir and Mixer constrained Scheduling (RMS) is proposed that can schedule a mixing tree obtained by a mixing algorithm, while minimizing the number of switching such that the total completion time can be minimized.Abstract:
In recent years, digital microfluidic biochips are being dominantly used for implementing a wide range of biochemical laboratory protocols (bioprotocols) on hand-held devices. Accurate preparation of fluid-samples is a fundamental preprocessing step that is needed in many bioprotocols. Oftentimes, the number of reservoirs built on-chip may be far less than that of the reactant fluids to be mixed. Hence, during the execution of an assay, several fluids are to be unloaded from the reservoirs to make room for loading new fluids stored off-line. Such unload-wash-load steps (switching) may be required several times, and these steps, being manual, significantly impact assay-completion time. In this paper, we propose a new scheduling scheme namely Reservoir and Mixer constrained Scheduling (RMS) that can schedule a mixing tree obtained by a mixing algorithm, while minimizing the number of switching such that the total completion time can be minimized. Simulation results over a large number of target ratios show that given the mixing trees obtained by standard mixing algorithms such as MinMix/RMA/CoDOS, RMS reduces switching steps (on average by 40.3%/41.9%/33%) at the cost of increasing mixing time (by only 3.5%/6.2%/4.8%), compared to an existing scheduling scheme invoked with reservoir constraints.read more
Citations
More filters
Journal ArticleDOI
Secure Randomized Checkpointing for Digital Microfluidic Biochips
TL;DR: This paper defines security metrics and present techniques for improving performance through static checkpoint maps, and describes performance tradeoffs associated with static and random checkpoints.
Journal ArticleDOI
Concentration-Resilient Mixture Preparation with Digital Microfluidic Lab-on-Chip
TL;DR: This work proposes an integer linear programming--based method that terminates very fast while producing the optimum solution, considering both uniform and weighted cost of reagents, and can be used conveniently in tandem with several existing sample-preparation algorithms for improving their performance.
Journal ArticleDOI
Fluid-level synthesis unifying reliability, contamination avoidance, and capacity-wastage-aware washing for droplet-based microfluidic biochips
TL;DR: A complete fluid-level synthesis considering all the essential goals together instead of dealing with them in isolation is proposed effectively handles the trade-off scenarios and provides flexibility to the designer to decide the threshold of the individual optimisation objective leading to the construction of a good-quality solution as a whole.
Journal ArticleDOI
Scheduling algorithms for reservoir- and mixer-aware sample preparation with microfluidic biochips
Varsha Agarwal,Ananya Singla,Mahammad Samiuddin,Sudip Roy,Tsung-Yi Ho,Indranil Sengupta,Bhargab B. Bhattacharya +6 more
TL;DR: This paper proposes a Reservoir- and Mixer-constrained Scheduling (RMS) algorithm that executes a given mixing tree aiming to minimize the number of reactant-switching from input reservoirs and considers certain constraints on the availability of concurrent mixing modules.
Journal ArticleDOI
A New Fluid-Chip Co-Design for Digital Microfluidic Biochips Considering Cost Drivers and Design Convergence
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.
References
More filters
Journal ArticleDOI
Electrowetting-based droplet mixers for microfluidic systems
TL;DR: In this paper, an alternative mixing strategy is presented based on the discretization of liquids into droplets and further manipulation of those droplets by electrowetting, where interfacial tensions of the droplets are controlled with the application of voltage.
Journal ArticleDOI
A high-throughput splinkerette-PCR method for the isolation and sequencing of retroviral insertion sites
Anthony G. Uren,Harald Mikkers,Jaap Kool,Louise van der Weyden,Anders H. Lund,Catherine H. Wilson,Richard Rance,Jos Jonkers,Maarten van Lohuizen,Anton Berns,David J. Adams +10 more
TL;DR: This method has allowed us to isolate hundreds of thousands of insertion sites from mouse tumors and, unlike other methods, has been specifically optimized for the murine leukemia virus (MuLV), and can easily be performed in a 96-well plate format for the efficient multiplex isolation of insertion Sites.
Journal ArticleDOI
Abstraction layers for scalable microfluidic biocomputing
TL;DR: This paper presents BioStream, a portable language for describing biology protocols, and the Fluidic ISA, a stable interface for microfluidic chip designers, and develops abstraction layers that decouple software development from changes in the underlying device technology.
Proceedings ArticleDOI
Architectural-level synthesis of digital microfluidics-based biochips
Fei Su,Krishnendu Chakrabarty +1 more
TL;DR: A system design methodology is proposed that attempts to apply classical architectural-level synthesis techniques to the design of digital microfluidics-based biochips and develops an optimal scheduling strategy based on integer linear programming and two heuristic techniques that scale well for large problem instances.
Book
Digital Microfluidic Biochips: Synthesis, Testing, and Reconfiguration Techniques
Krishnendu Chakrabarty,Fei Su +1 more
TL;DR: A new book enPDFd digital microfluidic biochips synthesis testing and reconfiguration techniques to read, offering new opportunities to read and to support reading.