Online synthesis for operation execution time variability on digital microfluidic biochips

Alistar, Mirela; Pop, Paul

doi:10.1109/isicir.2014.7029557

“…Software algorithms were demonstrated in the context of biochemical applications, such as automating droplet routing ( [1], [10], [11]) and scheduling the operations for a variety of bioprotocols ( [12]- [15]). These algorithms allow for complex biological protocols to be executed ( [16], [17]).…”

Section: Introductionmentioning

confidence: 99%

PhageBox: An Open Source Digital Microfluidic Extension with Applications for Phage Discovery

Albin¹,

Buecherl²,

Kochavi³

et al. 2023

Preprint

0

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This work introduces an open-source hardware and software expansion for digital microfluidics (DMF) devices that integrates programmatic temperature and magnetic control. Our aim was to create a versatile, modular, extension that may aid in biomedical applications and has proven potential for use in bacteriophage research. To achieve this, we developed an accessible DMF device extension called PhageBox. PhageBox incorporates temperature and magnetic control modules at the hardware level. At the software level, it is controlled by embedded software that includes a unique model for bio-protocol programming and a graphical user interface for visual feedback and operation of the device. We evaluated PhageBox's effectiveness in biomedical applications using functional testing and validated the temperature control using thermography, achieving a range of +/-0.2 Celsius. The electromagnets produced a magnetic force of 15 milliTesla, which precisely immobilized magnetic beads. Furthermore, we demonstrate the potential of PhageBox in bacteriophage research through three initial proof of principle protocols: (1) a universal framework for PCR, (2) T7 bacteriophage restriction enzyme digestion, and (3) the concentration of PhiX174 RF genomic DNA. Overall, our study presents an open-source solution for DMF devices to integrate temperature regulation and magnetism, facilitating various applications in biomedical research and bacteriophage studies. (GitHub: <a href="https://github.com/Dreycey/PhageBox" target="_blank">https://github.com/Dreycey/PhageBox</a>)

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“…Software algorithms were demonstrated in the context of biochemical applications, such as automating droplet routing ( [1], [10], [11]) and scheduling the operations for a variety of bioprotocols ( [12]- [15]). These algorithms allow for complex biological protocols to be executed ( [16], [17]).…”

Section: Introductionmentioning

confidence: 99%

PhageBox: An Open Source Digital Microfluidic Extension with Applications for Phage Discovery

Albin¹,

Buecherl²,

Kochavi³

et al. 2023

Preprint

0

View full text Add to dashboard Cite

This work introduces an open-source hardware and software expansion for digital microfluidics (DMF) devices that integrates programmatic temperature and magnetic control. Our aim was to create a versatile, modular, extension that may aid in biomedical applications and has proven potential for use in bacteriophage research. To achieve this, we developed an accessible DMF device extension called PhageBox. PhageBox incorporates temperature and magnetic control modules at the hardware level. At the software level, it is controlled by embedded software that includes a unique model for bio-protocol programming and a graphical user interface for visual feedback and operation of the device. We evaluated PhageBox's effectiveness in biomedical applications using functional testing and validated the temperature control using thermography, achieving a range of +/-0.2 Celsius. The electromagnets produced a magnetic force of 15 milliTesla, which precisely immobilized magnetic beads. Furthermore, we demonstrate the potential of PhageBox in bacteriophage research through three initial proof of principle protocols: (1) a universal framework for PCR, (2) T7 bacteriophage restriction enzyme digestion, and (3) the concentration of PhiX174 RF genomic DNA. Overall, our study presents an open-source solution for DMF devices to integrate temperature regulation and magnetism, facilitating various applications in biomedical research and bacteriophage studies. (GitHub: <a href="https://github.com/Dreycey/PhageBox" target="_blank">https://github.com/Dreycey/PhageBox</a>)

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“…There is a significant amount of research work done at the fluid level of the DMFBs [13][14][15]. A contamination-aware physicallevel synthesis is performed in [16].…”

Section: T 1 Introductionmentioning

confidence: 99%

Fluid‐level synthesis unifying reliability, contamination avoidance, and capacity‐wastage‐aware washing for droplet‐based microfluidic biochips

Chakraborty

¹

,

Datta²,

Pal

³

2018

IET Computers & Digital Techniques

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Production of correct bioassay outcome is the foremost objective in digital microfluidic biochips (or DMFBs). In highfrequency DMFBs, continuous actuation of electrodes leads to malfunctioning or even breakdown of the system. The improper functioning of a biochip tends to produce erroneous results. On the other hand, while transporting droplets, the residues may get stuck to electrode walls and cause contamination to other droplets. To ensure proper assay outcome, washing becomes mandatory, whose incorporation may delay the bioassay completion time significantly. Furthermore, each wash droplet possesses a capacity constraint within which the residues can be washed off successfully. Evidently, the design objectives possess a large degree of trade-offs among themselves and must be attacked to prepare an efficient platform. Here, the authors propose a complete fluid-level synthesis considering all the essential goals together instead of dealing with them in isolation. The presented approach 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. The performance is evaluated over several benchmark bioassays.

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Online synthesis for operation execution time variability on digital microfluidic biochips

Cited by 7 publications

References 10 publications

PhageBox: An Open Source Digital Microfluidic Extension with Applications for Phage Discovery

PhageBox: An Open Source Digital Microfluidic Extension with Applications for Phage Discovery

PhageBox: An Open Source Digital Microfluidic Extension with Applications for Phage Discovery

Fluid‐level synthesis unifying reliability, contamination avoidance, and capacity‐wastage‐aware washing for droplet‐based microfluidic biochips

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