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High-throughput protein crystallization on the World Community Grid and the GPU

Yulia Kotseruba, Christian A Cumbaa, Igor Jurisica
IBM Life Sciences Discovery Centre, Ontario Cancer Institute, University Health Network, 101 College Street, Toronto, Ontario M5G 1L7, Canada
Journal of Physics: Conference Series, 341, 012027, 2012

@article{1742-6596-341-1-012027,

   author={Yulia Kotseruba and Christian A Cumbaa and Igor Jurisica},

   title={High-throughput protein crystallization on the World Community Grid and the GPU},

   journal={Journal of Physics: Conference Series},

   volume={341},

   number={1},

   pages={012027},

   url={http://stacks.iop.org/1742-6596/341/i=1/a=012027},

   year={2012}

}

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We have developed CPU and GPU versions of an automated image analysis and classification system for protein crystallization trial images from the Hauptman Woodward Institute’s High-Throughput Screening lab. The analysis step computes 12,375 numerical features per image. Using these features, we have trained a classifier that distinguishes 11 different crystallization outcomes, recognizing 80% of all crystals, 94% of clear drops, 94% of precipitates. The computing requirements for this analysis system are large. The complete HWI archive of 120 million images is being processed by the donated CPU cycles on World Community Grid, with a GPU phase launching in early 2012. The main computational burden of the analysis is the measure of textural (GLCM) features within the image at multiple neighbourhoods, distances, and at multiple greyscale intensity resolutions. CPU runtime averages 4,092 seconds (single threaded) on an Intel Xeon, but only 65 seconds on an NVIDIA Tesla C2050. We report on the process of adapting the C++ code to OpenCL, optimized for multiple platforms.
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