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IBM POWER8 and OSU advance genomics research through porting

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IBM POWER8 is serving a major role in an immensely significant field of science, genomics. Genomics is the study of the genome, the complete DNA within a single cell of an organism. Advances in genomics research have triggered a revolution in understanding the most complex biological systems. Researchers can use DNA sequencing to search for variation and/or mutations that may play a role in the development or progression of a disease.

Chris Sullivan, assistant director for biocomputing at Oregon State University’s (OSU) Center for Genomic Research and Biocomputing, has made significant contributions to the advancement of genomic research by porting over 1000 valuable software tools and applications to IBM POWER8 systems. Chris and his team’s research are extremely valuable in the forestry and plant genomics areas but, more important, they work with developers to make the code available to others in an open source environment. Clients can accelerate their research and boost productivity by getting more work done in far less time at a much lower cost. The porting and ability to take advantage of application performance available on the Power architecture are major wins for the research and scientific communities.

OSU’s Center for Genomic Research and Biocomputing created the High Performance Computing Software Center, which provides a platform to work with software developers to port their code to the POWER8 architecture. There have been several success stories:

  • Collaboration between IBM, OSU and the Julia Language mathematical software community enabled developers to have access to graphics processing unit (GPU) technology, which made the software ready for the new CAPI and NVLink acceleration technologies. This was an instrumental step in getting independent software vendors to port to Power.
  • Collaboration with NVIDIA to develop a process to create dockers that work with GPUs on the POWER8 architecture accelerated the deployment of applications onto their cluster.
  • Benjamin Buchfink, creator of the DIAMOND Sequence alignment tool, helped port this software onto the IBM POWER8 architecture based on requests from the research community. DIAMOND is a sequence aligner for protein and translated DNA searches, and it functions as a drop-in replacement for the NCBI Basic Local Alignment Search Tool.
  • Sequence alignment tools CASHX and pipeline were ported to work on the IBM POWER8 to take full advantage of higher thread count machines. CASHX is one of the few non-BWA based high throughput genome alignment tools.
  • Mark Borodovsky and Alexandre Lomsadze from GeneMark are currently working on porting tools onto the POWER8 platform. GeneMark and its associated tools are used throughout the genomics field for gene prediction.

OSU’s Chris Sullivan was asked about the impact of his work on the scientific community in terms of research acceleration, flexibility and the order of magnitude. He says, “With the large system cache, incredible I/O and the massively threaded processors, our researchers are able to find answers extremely fast. The POWER8 runs circles around other server technologies we have on campus. Genomic researchers can submit a job into OSU’s cluster and run on their choice of Intel, AMD or POWER8 platforms since the genomic codes are all ported to POWER8.”

Be sure to contact Oregon State University if you would like to collaborate or want more information.

Also, visit IBM Power Systems to learn more about POWER8.

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