Genomics & Life Sciences

With the advent of more powerful and effective scientific instrumentation including more affordable next generation sequencers for genomics, the complexity and amount of data being generated, managed, studied and interpreted is exploding. High performance computing has kindled a revolution in genomics and life sciences in recent years because gene sequencing and assembly, as well as complex modeling and analysis tasks, require high-performance compute capability not available with commodity servers and clusters. The ability to process, analyze, manage and ultimately act on this data is quickly becoming a critical element of research success.

In line with this trend, there is increasing demand for loading all data into memory for more efficient and accelerated computational analysis. For example, the assembly algorithms that build final cell sequences are all memory-limited, and thus utilizing shared memory systems that can handle massive parallelization is critical. Additionally, research areas such as gene sequence analysis, cluster comparisons, homology modeling, Hidden Markov Models and genetic algorithms require significant storage resources to achieve outstanding results. SGI solutions for genomics and life sciences address these computational and data storage challenges.

Life sciences research often requires significant chip memory (>2TB), accessible by all processes, to efficiently parallelize heterogeneous sets of equations. The SGI® UV platform, built on the Intel® Xeon® processor E7 family, is the world's most robust single system image computer. It can drive huge efficiency gains in time-to-discovery for compute- and data-intensive applications like computational biology, genome reconstruction, high content analysis and systems biology. This performance and versatility means excellent TCO/ROI for ongoing work, as well as exciting new possibilities for breakthrough discoveries. With directly attached active archive, RAID, MAID or JBOD storage solutions from SGI, SGI UV enables immediate access to any number of CPUs on the system, delivering maximum computational dynamic range.

The SGI® ICE X bladed cluster and Rackable™ cluster product lines also deliver top performance and superior configuration flexibility in cost-effective solutions that are easy to build and deploy.

SGI system management software supercharges the capabilities of the operating system to maximize performance on SGI computer systems, while enabling researchers to run jobs when resources become available, based upon an array of parameters that datacenter managers set up.

With SGI solutions, researchers gain a competitive advantage. Larger complex modeling and analyses can be completed in record time and at higher theory levels. SGI solutions shrink time-to-market and reduce costs by providing:

• Scaling superiority for all model sizes and theory levels
• Flexibility to handle large and small simulations on a single server
• Fastest performance for genome sequencing and assembly algorithms, as well as computational biology applications
• Ease of management
• Industry standards
• Shared and transparent access to archive data without administrator intervention: Workflow is improved with scalable storage systems, with the I/O capability necessary to move data to and from storage without impeding productivity.

SGI systems have proven superiority in the following areas:

• 3D data classification, segmentation and manipulation, which allow surgeons to visualize key portions of patient data to enable less invasive procedures and treatments
• Patient data and CAD model integration, which combine patient-specific information with implant models to assist in pre-operative planning of implant procedures
• Sub-cellular analysis, enabling both a microscopic and macroscopic understanding of the behavior of cancer or other cells, both at the cellular level and within the context of tissue sections

SGI customers such as the Technical University of Denmark (CBS, DTU), NNF Center for Protein Research (CPR), Institute of Cancer Research, BBSRC Genome Analysis Center (TGAC), Imperial College London, Biogemma, Novo Nordisk A/S and Merck have all adopted SGI solutions to accelerate their research in life sciences.

Additional Information

• Case Study: Queensland Centre for Medical Genomics (PDF 725K)
• Technical Whitepaper: SGI High Throughput Computing (HTC) Wrapper Program for Bioinformatics (PDF 713K)
• Press Release: DTU Accelerates Metagenomic Research with SGI UV