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Accelerated Genomics Cloud Promotion Designed to Enhance Research Workflows

By BiotechDaily International staff writers
Posted on 13 May 2013
Convey Computer (Richardson, TX, USA) reported that Nimbix (Dallas, TX, USA), a developer of accelerated high-performance cloud computing systems, has partnered with Convey to expand its Convey hybrid-core (HC) infrastructure, as part of The Accelerated Genomics Cloud (TAGC) promotion, which provides free runtime for qualified applicants.

The Convey HC-2ex platform will be used in research projects for customers who take advantage of the promotion. A total of USD 25,000 worth of cloud processing time will be awarded to genomics researchers to increase their bioinformatics analysis. Top award recipients will each receive USD 1,000 of runtime, which is enough to map up to 3 Tbases of reads, providing the ability to analyze, for example, 12 human genomes at considerable coverage. Remaining qualified applicants will receive USD 500 of runtime.

TAGC promotion began April 30, 2013, and the first awards will be granted as soon as the application review process allows. The promotion will end July 1, 2013, or once all funding has been awarded. Therefore, interested participants may register online (please see Related Links below).

Runtime, for those applicants selected, will include a range of Nimbix resources, which includes a combination of Convey and conventional large memory systems configured to provide the best performance across a range of applications and workflows. These may include reference mapping, de novo assembly, functional annotation, variant analysis, and RNA expression profiling. Participants, for example, will have access to the full Convey Bioinformatics Suite, as well as third-party applications optimized for the hybrid-core architecture.

“Genomics is perhaps the clearest example where progress is accelerated by access to the right HPC [high-performance computing] resource and stymied when those resources are missing,” stated Dr. George Vacek, director of Convey Computer’s life sciences business unit.

“Heterogeneous computing has become a necessity in life sciences, where the data production from next-generation sequencing instruments is increasing much more quickly than traditional computing resources can handle.”

The combination of heterogeneous computing and cloud computing is a suitable approach for high performance computing demands in life sciences. Budget constraints are limiting access to vital compute resources at the very time when the incredible growth in life sciences data makes access increasingly advantageous. “HPC-oriented clouds supporting the latest heterogeneous architectures can provide even small research groups with affordable access to diverse computer resources,” said Steve Hebert, cofounder of Nimbix. “Our goal through this promotion is to give genomics researchers access to world-class HPC resources and to show them that heterogeneous cloud computing is extremely powerful, yet simple and affordable.”

Nimbix installed their first Convey system in 2011 when the two companies collaborated to offer Convey’s novel hybrid-core architecture and bioinformatics personalities as a cloud-based HPC solution. Since then, users of the Nimbix Accelerated Compute Cloud have achieved greater than 50x speed-up of sequence searches using Convey’s hybrid-core system. Users have also seen impressive acceleration, inclusive of data transfer times, for mapping and de novo assembly—both in terms of improving runtimes and increasing throughput.

Convey’s hybrid-core architecture pairs classic Intel x86 microprocessors with a coprocessor comprised of field-programmable gate arrays (FPGAs). Specific algorithms, DNA sequence assembly, for example, are optimized and converted into code that is loadable onto the FPGAs at runtime. The Convey architecture also features a highly parallel memory subsystem to additionally increase performance. Convey’s approach provides very fast access to random access memory, which is helpful for the hashing functions so widely used in bioinformatics.

Convey Computer’s world’s first hybrid-core computer—a system that fuses the low cost and simple programming model of a commodity system with the performance of a personalized hardware architecture.

Nimbix is a provider of cloud-based, HPC infrastructure and applications. Nimbix offers HPC applications as a service through the Nimbix Accelerated Compute Cloud, dramatically speeding up data processing for life sciences, oil and gas, and Rendering applications. Nimbix operates unique high performance hybrid systems and accelerated servers in its Dallas, TX, USA, datacenter.

Related Links:

Convey Computer
Nimbix
TAGC Promotion



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