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Primeur weekly 2011-12-19

Special

SARA supercomputers today 600.000 times faster than its first 100 Mflop/s Cyber 205 supercomputer in 1983 ...

SC'11 bigger than ever ...

The Cloud

Atos leads the OPTIMIS project for the optimisation of services in Cloud ...

ISGC 2012 registration opens now ...

ConteXtream launches software-defined network virtualization solution for Cloud and hosting providers ...

BGI-BOX terminal server debut operation in China Agricultural University ...

Amazon Web Services launches Brazil data centres for its Cloud computing platform ...

Office 365 becomes first and only major Cloud productivity service to comply with leading EU and U.S. standards for data protection and security ...

EuroFlash

Counting the cost of research computing infrastructures ...

Bull taps Nimsoft to expand its Vision Services ...

ATLAS and CMS experiments present Higgs search status ...

New supercomputer for Bielefeld's high-energy physicists ...

Slovak Academy of Science selects IBM Power Systems and Storage for National Supercomputing Project ...

Multi-purpose photonic chip paves the way to programmable quantum processors ...

USFlash

Cray XMT supercomputer arrives at the Noblis Center for Applied High Performance Computing ...

SDSC welcomes 'Gordon' supercomputer as a research powerhouse ...

Triton resource helps track how kinesin molecules move ...

Astronomical amount of data travels across Western Canada to support space research ...

Jacket v2.0 for faster code in MATLAB ...

GPU-accelerated engineering simulation application to enable highest quality products for aerospace and other mission critical fields ...

BGI tackles DNA data deluge using NVIDIA Tesla GPUs ...

Chinese Ministry of Education to integrate CUDA programming curriculum in universities nationwide ...

NVIDIA opens up CUDA Platform by releasing compiler source code ...

High-energy physicists set record for network data transfer ...

Rogue Wave announces support for upcoming Intel Many Integrated Core architecture based products ...

Rogue Wave announces Stingray Studio 11.0 release ...

TotalView selected for China's National Supercomputing Centre in Shenzhen ...

New application makes supercomputing simple ...

HP enables organisations worldwide to expand data centre resources with HP POD ...

Oracle delivers record performance result for a two processor Intel-based system with TPC-C benchmark ...

Early black holes grew big eating cold, fast food ...

BGI tackles DNA data deluge using NVIDIA Tesla GPUs

13 Dec 2011 Beijing - BGI, one of the world's largest genomics institutes, has slashed the time to analyze batches of DNA sequencing data from nearly four days to just six hours using a NVIDIA Tesla GPU-based server farm.

The speed up is considered a critically important step in determining, in an affordable manner, the chemical building blocks that make up a DNA molecule. This is key for the genomics industry to achieve its target of the $1,000 genome - the point at which genomics can be used in clinical diagnostic tests as a practical component of patient care.

"We are drowning in the genome data that our high-throughput sequencing machines create every day", stated Dr. Bingqiang Wang, head of high performance computing from BGI. "GPU acceleration of our genome analysis applications enables our scientists to crunch through data and gain insights into bacteria, plants and humans faster than was ever possible. It offers the potential for researchers and health care professionals to identify highly effective and affordable individualized medicines and treatments."

BGI researchers and collaborators have developed three genome data analysis applications that are accelerated by NVIDIA Tesla GPUs:

  • SOAP3 aligner: Aligns short reads from the sequencing machine against existing reference genome sequences. Through GPU acceleration, the SOAP3 aligner can find all three-mismatch alignments in tens of seconds per one million reads, instead of tens of minutes without GPU acceleration. This means that sequencing and assembling of individual genomes for comparison to those previously sequenced and studied can be performed quickly to understand potential future disease states and treatments.
  • GSNP (SNP detection): A GPU-accelerated version of the widely used SOAPsnp software that detects variation of a single nucleotide polymorphism (SNP) in the DNA of a genome. These DNA SNP variations can be used to study how individuals develop diseases differently and respond to bacteria, viruses and medicines.
  • GAMA (high resolution genotyping tool): Finds the distribution of the occurrence or frequency of particular gene variants, such as eye color or the propensity for prostate cancer in a set of genes.

"The only way for science to reach the $1,000 genome milestone is through technologies that make analyzing DNA data easier, faster and more affordable", stated Sumit Gupta, manager of the Tesla business at NVIDIA. "GPU computing enables researchers to achieve game-changing speedups in their scientific applications, which can help reduce the cost and complexity of all types of critical research."

BGI does groundbreaking work in sequencing the genomes of a wide range of life forms, ranging from plants and E.coli to the giant panda, to develop better medicines, improve health care and develop genetically enhanced food. BGI's sequencing output is expected to soon surpass the equivalent of more than 700,000 human genomes per year, a dramatic increase over initial efforts, which took 13 years to sequence a single genome.

Tesla GPUs are massively parallel accelerators based on the NVIDIA CUDA parallel computing architecture. Application developers can accelerate their applications either by using CUDA C, CUDA C++, CUDA Fortran, or by using the simple, easy-to-use directive-based compilers.

Source: NVIDIA

Back to Table of contents

Primeur weekly 2011-12-19

Special

SARA supercomputers today 600.000 times faster than its first 100 Mflop/s Cyber 205 supercomputer in 1983 ...

SC'11 bigger than ever ...

The Cloud

Atos leads the OPTIMIS project for the optimisation of services in Cloud ...

ISGC 2012 registration opens now ...

ConteXtream launches software-defined network virtualization solution for Cloud and hosting providers ...

BGI-BOX terminal server debut operation in China Agricultural University ...

Amazon Web Services launches Brazil data centres for its Cloud computing platform ...

Office 365 becomes first and only major Cloud productivity service to comply with leading EU and U.S. standards for data protection and security ...

EuroFlash

Counting the cost of research computing infrastructures ...

Bull taps Nimsoft to expand its Vision Services ...

ATLAS and CMS experiments present Higgs search status ...

New supercomputer for Bielefeld's high-energy physicists ...

Slovak Academy of Science selects IBM Power Systems and Storage for National Supercomputing Project ...

Multi-purpose photonic chip paves the way to programmable quantum processors ...

USFlash

Cray XMT supercomputer arrives at the Noblis Center for Applied High Performance Computing ...

SDSC welcomes 'Gordon' supercomputer as a research powerhouse ...

Triton resource helps track how kinesin molecules move ...

Astronomical amount of data travels across Western Canada to support space research ...

Jacket v2.0 for faster code in MATLAB ...

GPU-accelerated engineering simulation application to enable highest quality products for aerospace and other mission critical fields ...

BGI tackles DNA data deluge using NVIDIA Tesla GPUs ...

Chinese Ministry of Education to integrate CUDA programming curriculum in universities nationwide ...

NVIDIA opens up CUDA Platform by releasing compiler source code ...

High-energy physicists set record for network data transfer ...

Rogue Wave announces support for upcoming Intel Many Integrated Core architecture based products ...

Rogue Wave announces Stingray Studio 11.0 release ...

TotalView selected for China's National Supercomputing Centre in Shenzhen ...

New application makes supercomputing simple ...

HP enables organisations worldwide to expand data centre resources with HP POD ...

Oracle delivers record performance result for a two processor Intel-based system with TPC-C benchmark ...

Early black holes grew big eating cold, fast food ...