GPU-Accelerated Big Data Pipelines for Desktop, HPC and Cloud Dr. Melissa Smith 1 , Ben Shealy 1 , Josh Burns 2 , Dr. Alex Feltus 3 , Dr. Stephen Ficklin 2 1 Department of Electrical and Computer Engineering, Clemson University 2 Department of Horticulture, Washington State University 3 Department of Genetics and Biochemistry, Clemson University
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Desktop, HPC and Cloud Big Data Pipelines for GPU-Accelerated...GPU-Accelerated Big Data Pipelines for Desktop, HPC and Cloud Dr. Melissa Smith1, Ben Shealy1, Josh Burns2, Dr. Alex
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GPU-AcceleratedBig Data Pipelines for
Desktop, HPC and CloudDr. Melissa Smith1, Ben Shealy1, Josh Burns2, Dr. Alex Feltus3, Dr. Stephen Ficklin2
1 Department of Electrical and Computer Engineering, Clemson University2 Department of Horticulture, Washington State University
3 Department of Genetics and Biochemistry, Clemson University
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Overview
- KINC
- KINC Nextflow Pipeline
- Running KINC Pipeline on Kubernetes
- Demo
- Challenges / Opportunities
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The Gene Co-Expression Network (GCN)
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Knowledge Independent Network Construction (KINC)
→
Gene expression matrix
Gene co-expression network
Similarity matrix
Pairwise scatter plot
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Human Brain Tissue-Specific Network
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Human Kidney Tumor-Specific Network
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KINC GPU Implementation
Shealy, Burns, et. al., “GPU Implementation of Pairwise Gaussian Mixture Models for Multi-Modal Gene Co-Expression Networks”, IEEE Access
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KINC Pipeline
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Pipeline Portability with Nextflow
# Local
nextflow run systemsgenetics/KINC-nf -with-docker
# HPC
nextflow run systemsgenetics/KINC-nf -profile pbs -with-singularity