A framework for end-to-end verification for digital microfluidics View Full Text


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Article Info

DATE

2021-05-05

AUTHORS

Pushpita Roy, Ansuman Banerjee, Bhargab B. Bhattacharya

ABSTRACT

Modern bio-chemical protocols are complex to design, and hence, there may remain errors which need to be fixed before the protocol is taken up for synthesis. Additionally, in recent times, the task of protocol synthesis is becoming increasingly difficult as well, and prone to errors for reactions involving multiple reagents and their intricate interactions. In this paper, we propose a framework for easy specification and efficient verification of a bio-chemical protocol description, which operates in 2 stages of microfluidic protocol design, pre- and post-synthesis. We propose a simple and intuitive description template for specifying a biochemical reaction that is easy to adopt for expressing protocol descriptions. Once that is done, our framework (a) presents a visualization of the protocol description for easy comprehension, and (b) automatically translates the description to a high-level C program, for analysis. This program, along with a set of properties on the final reaction concentration, is passed on to a verification engine, which checks if the protocol description can indeed generate the desired concentrations on the final outputs. Further, given a synthesized protocol description, our tool analyzes the synthesis output for possible design errors that may have entered due to incorrect synthesis. We present experimental results on a few bioassay protocols and show the utility of our framework for verifiable protocol design in digital microfluidics. More... »

PAGES

231-245

References to SciGraph publications

  • 2010-11-08. Biocoder: A programming language for standardizing and automating biology protocols in JOURNAL OF BIOLOGICAL ENGINEERING
  • 2007-05-05. Abstraction layers for scalable microfluidic biocomputing in NATURAL COMPUTING
  • 2020-02-18. A Methodology for Root-Causing In-field Attacks on Microfluidic Executions in TRANSACTIONS ON COMPUTATIONAL SCIENCE XXXV
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    http://scigraph.springernature.com/pub.10.1007/s11334-021-00398-3

    DOI

    http://dx.doi.org/10.1007/s11334-021-00398-3

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