GPU-based real-time detection and analysis of biological targets using solid-state nanopores

The emergence of nanoscale devices has provided robust interfaces to biomolecules that faithfully transduce and define fundamental interactions of living systems. Measuring single-event behavior of important targets like DNA, and diseased cells has been achieved with a number of devices and systems....

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Bibliographic Details
Published in:Medical & biological engineering & computing 2012-06, Vol.50 (6), p.605-615
Main Authors: Hafeez, Abdul, Asghar, Waseem, Rafique, M. Mustafa, Iqbal, Samir M., Butt, Ali R.
Format: Article
Language:English
Subjects:
Algorithms
Automation
Bioengineering
Biomedical and Life Sciences
Biomedical engineering
Biomedical Engineering and Bioengineering
Biomedicine
Computer Applications
Computer engineering
Decision making
Diagnosis, Computer-Assisted - methods
Diagnostic tests
Human Physiology
Humans
Imaging
Nanomedicine - instrumentation
Nanomedicine - methods
Nanopores
Nanotechnology
Original Article
Pattern recognition systems
Pattern Recognition, Automated - methods
Radiology
Real time
Sensors
Signal Processing, Computer-Assisted
Software
Studies
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Summary:The emergence of nanoscale devices has provided robust interfaces to biomolecules that faithfully transduce and define fundamental interactions of living systems. Measuring single-event behavior of important targets like DNA, and diseased cells has been achieved with a number of devices and systems. An important dimension to these systems, often discounted, is real-time computational decision-making from measured data. This paper describes an adaptive approach that can record single-molecule or single-cell events in real-time and automatically analyze patterns from the measured data. The automated analysis of measured data is done using a static threshold technique and two variations of a dynamic threshold technique: baseline-tracker and moving average filtering. Dynamic techniques for threshold detection enable noise suppression in the measured data and precise detection of patterns, but at the cost of more complex software as compared to static technique. To mitigate the computational overhead, a real-time system is implemented that uses advanced I/O techniques to minimize the execution stalls, thus enabling the system to process data significantly faster than the electrical measurement setup. Furthermore, the algorithms are implemented on programmable graphics processing units for parallel pattern detection. Our implementation provides five times faster data acquisition and pattern detection than the maximum sampling rate of the electrical measurement setup.
ISSN:0140-0118
1741-0444
DOI:10.1007/s11517-012-0893-9