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Palmetto Supercomputer Powers Genetics at Clemson

palmettoResearchers at Clemson University are using the Palmetto supercomputers to study biomass production and disease resistance. As one of the fastest supercomputers in Academia, the Palmetto2 cluster is an HP system with 12,080 compute cores and a peak performance of 739 Teraflops.

Alex Feltus, an associate professor of genetics and biochemistry, is among more than 1,500 users of the machine since its inception in 2007. He uses the supercomputer to find traits, such as biomass production and disease resistance, in the genetic material of plants.

Without the supercomputer, which nationally is among the top-five fastest at public academic institutions that don’t have federally funded centers, Feltus and other researchers would be slowed considerably. “Only a supercomputer can handle the massive numbers of DNA sequences that are generated by new DNA sequencing technology,” Feltus said. His research team recently received a $1.4 million grant from the National Science Foundation to enhance the capacity of genomic databases to process bundles of data.

According to Feltus, all crops are very complex. “For instance, there are 55,000 genes in rice. We’re trying to understand the genes and their pathways and how they are combining and interacting. You can’t examine this level of complexity without using a supercomputer.”

Feltus is working in an emerging field called systems genetics, which studies how genes in crops collectively interact using new computational technologies that Clemson University’s Public Service and Agriculture programs are helping develop. “Most agricultural traits in plants are controlled not just by one gene but by many genes,” Feltus said. “We’re trying to find the complexity ‘sweet spot,’ the balance between being too reductionist and too holistic.”

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