awz/Open-Omics-Acceleration-Framework

Intel lab's open sourced data science framework for accelerating digital biology

Open Omics Acceleration Framework

Intel lab's open sourced data science framework for accelerating digital biology

Blogs & Related News

• Intel Xeon is all you need for AI inference: Performance Leadership on Real World Applications. Blog under Intel Communities/Blogs/Tech Innovation/Artificial Intelligence (AI); July, 2023.
• Intel and Mila Join Forces for Responsible AI. Intel newsroom, September, 2022.
• Accelerating Genomics Pipelines Using Intel’s Open Omics Acceleration Framework on AWS. AWS HPC blog, Aug, 2022.
• Intel Labs Accelerates Single-cell RNA-Seq Analysis. Blog under Intel Communities/Blogs/Tech Innovation/Artificial Intelligence (AI); June, 2022.
• Intel and MILA Join Forces to Put AI to Work in Medical Research. HPCwire, April, 2021.

Publications

• GenDP: A Framework of Dynamic Programming Acceleration for Genome Sequencing Analysis. Yufeng Gu, Arun Subramaniyan, Tim Dunn, Alireza Khadem, Kuan-Yu Chen, Somnath Paul, Md Vasimuddin, Sanchit Misra, David Blaauw, Satish Narayanasamy, Reetuparna Das. Proceedings of the 50th Annual International Symposium on Computer Architecture (ISCA); June, 2023. https://dl.acm.org/doi/abs/10.1145/3579371.3589060.
• Accelerating Barnes-Hut t-SNE Algorithm by Efficient Parallelization on Multi-Core CPUs. Narendra Chaudhary, Alexander Pivovar, Pavel Yakovlev, Andrey Gorshkov and Sanchit Misra. arXiv preprint arXiv:2212.11506; Dec, 2022; doi: https://doi.org/10.48550/arXiv.2212.11506.
• Accelerating Deep Learning based Identification of Chromatin Accessibility from noisy ATAC-seq Data. Narendra Chaudhary, Sanchit Misra, Dhiraj Kalamkar, Alexander Heinecke, Evangelos Georganas, Barukh Ziv, Menachem Adelman and Bharat Kaul. 21st IEEE International Workshop on High Performance Computational Biology (HiCOMB) May 30, 2022. https://ieeexplore.ieee.org/abstract/document/9835674
• Accelerating minimap2 for long-read sequencing applications on modern CPUs. Saurabh Kalikar, Chirag Jain, Md Vasimuddin, Sanchit Misra. Nature Computational Science 2 (2), 78-83, Feb, 2022. https://rdcu.be/cHVAK.
• GenomicsBench: A Benchmark Suite for Genomics. Arun Subramaniyan, Yufeng Gu, Timothy Dunn, Somnath Paul, Md Vasimuddin, Sanchit Misra, David Blaauw, Satish Narayanasamy, Reetuparna Das. IEEE International Symposium on Performance Analysis of Systems and Software (ISPASS), 2021.https://ieeexplore.ieee.org/document/9408208.
• LISA: Learned indexes for sequence analysis. Darryl Ho, Saurabh Kalikar, Sanchit Misra, Jialin Ding, Vasimuddin Md, Nesime Tatbul, Heng Li, Tim Kraska. bioRxiv 2020.12.22.423964; doi: https://doi.org/10.1101/2020.12.22.423964.
• Efficient Architecture-Aware Acceleration of BWA-MEM for Multicore Systems. Vasimuddin Md, Sanchit Misra, Heng Li, Srinivas Aluru. IEEE Parallel and Distributed Processing Symposium (IPDPS), 2019. https://ieeexplore.ieee.org/document/8820962.
• Performance extraction and suitability analysis of multi- and many-core architectures for next generation sequencing secondary analysis. Sanchit Misra, Tony Pan, Kanak Mahadik, George Powley, Priya N Vaidya, Md Vasimuddin, Srinivas Aluru. International Conference on Parallel Architectures and Compilation Techniques (PACT), 2018. https://dl.acm.org/doi/abs/10.1145/3243176.3243197.
• Identification of Significant Computational Building Blocks through Comprehensive Deep Dive of NGS Secondary Analysis Methods. Md Vasimuddin, Sanchit Misra, Srinivas Aluru. BioRxiv 2018 301903. https://www.biorxiv.org/content/10.1101/301903v3.abstract.