SGI Altix and InfiniteStorage Systems, and PipelineFX Qube!, Deliver the Processing Power and Speed to Map the First Fruit Genome Ever Sequenced
"Sequencing the papaya genome is the first large scale genome project done in Hawaii with international collaboration from 22 research institutes and will benefit the papaya research community, papaya farmers, and consumers for years to come," said Maqsudul Alam, Director of the Center for Advanced Studies in Genomics, Proteomics, and Bioinformatics, College of Natural Sciences, lead institute of the International Papaya Genome Consortium. "We chose the SGI Altix because of the configuration of the memory system, how quickly we can use the random memory, and also the scalability of the system, and of course, the price/performance. SGI technology has been instrumental in achieving this technological and scientific milestone."
The second largest crop in Hawaii, papaya was almost wiped out by the papaya ringspot virus a decade ago. Genetically modifying the papaya to create a ringspot-resistant transgenic or "hermaphrodite" variety such as the SunUp saved the papaya from extinction on the islands. The Papaya Genome Project mapped papaya genes to improve the efficiency of agricultural cultivation, and to discover new applications for one of the most important edible fruit crops of tropical and subtropical regions worldwide. Papaya is also used in a wide range of medical, biotechnological and cosmetic applications that can be further developed now that a complete picture of the genomic sequence has been drawn.
When the project began over two years ago, Dr. Alam, who heads the multi-institution project housed at the UH Maui High Performance Computing Center (MHPCC) at
The SGI Altix system, with 32 CPUs of processing power, gave the team high throughput to their computing needs, allowing them to run highly multi-threaded applications concurrently. PipelineFX Qube!, used widely in digital media for game build engines and animation rendering, was uniquely set up as the Center's backend software environment. PipelineFX Qube!, which handles distribution tasks, also managed the interactive Web site, Gbrowse, for national and international collaborators on the project.
"Because the SGI system architecture allows very large memory to be shared across all the processors, the Center personnel were able to write their own software that, every night, downloaded all the versions of the genomic databases, and the most common were uploaded into the Altix system's shared memory for immediate access," said Deepak Thakkar, Higher Education and Research Solutions Manager, SGI. "SGI Altix systems and scalable storage solutions, with PipelineFX Qube!, made a unique genome analysis tool that got the job done. This is an exciting combination that has many other applications in biosciences."
The Hawaii Papaya Genome Project is a multi-institutional bioinformatics project. In Hawaii, participants include MHPCC, Hawaii Agricultural Research Center (HARC), Hawaii Papaya Industry Association, USDA Pacific Basin Agricultural Research Center, Pacific Telehealth and Technology Hui, and Hawaii Biotech. Nankai University in China is a major collaborator, as is
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