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Dell EMC Does Supercomputing Genomics Down Under

The Garvan Institute of Medical Research has selected Dell EMC to deliver an HPC system for Garvan’s Data Intensive Computer Engineering (DICE) group, designed to push scientific boundaries and transform the way genomic research is currently performed in Australia. “Genomics, the study of information encoded in an individual’s DNA, allows researchers to study how genes impact health and disease. When the first human genome was sequenced, the project took over 10 years and cost almost US$3 billion. In recent years, extraordinary advancements in DNA sequencing have made the analysis of whole human genomes viable, and today, Garvan can sequence up to 50 genomes a day at a base price of around US$1,000.”

DDN and Parabricks Accelerate Genome Analysis

Today DDN announced a Parabricks technology solution that provides massive acceleration for analysis of human genomes. The breakthrough platform combines GPU supercomputing performance with DDN’s Parallel Flash Data Platforms for fastest time to results, and enables unprecedented capabilities for high-throughput genomics analysis pipelines. The joint solution also ensures full saturation of GPUs for maximum efficiency and provides analysis capabilities that previously required thousands of CPUs to engage.

Broad Institute and Intel Advance Genomics

The Broad Institute of MIT and Harvard in collaboration with Intel, is playing a major role in accelerating genomic analysis. This guest post from Intel explores how the two are working together to ‘reach levels of analysis that were not possible before.’

SpaRC: Scalable Sequence Clustering using Apache Spark

Zhong Wang from the Genome Institute at LBNL gave this talk at the Stanford HPC Conference. “Whole genome shotgun based next generation transcriptomics and metagenomics studies often generate 100 to 1000 gigabytes (GB) sequence data derived from tens of thousands of different genes or microbial species. Here we describe an Apache Spark-based scalable sequence clustering application, SparkReadClust (SpaRC) that partitions reads based on their molecule of origin to enable downstream assembly optimization.”

Intel Select Solutions: BigStack 2.0 for Genomics

BIGstack 2.0 incorporates our latest Intel Xeon Scalable processors, Intel 3D NAND SSD, and Intel FPGAs while also leveraging the latest genomic tools from the Broad Institute in GATK 3.8 and GATK 4.0. This new stack provides a 3.34x speed up in whole genome analysis and a 2.2x daily throughput increase. It is able to deliver these performance improvements with a cost of just $5.68 per whole genome analyzed. The result: researchers will be able to analyze more genomes, more quickly and at lower cost, enabling new discoveries, new treatment options, and faster diagnosis of disease.

Radio Free HPC Looks at Biohacking

In this podcast, the Radio Free HPC team looks alarming new hacks of health care data. With news that Biohackers have successfully inserted malware into DNA, security is becoming a matter of concern for everything from scanners to gene sequencers. After that, we do our Catch of the Week.

DOE Helps Tackle Biology’s Big Data

Six proposals have been selected to participate in a new partnership between two U.S. Department of Energy (DOE) user facilities through the “Facilities Integrating Collaborations for User Science” (FICUS) initiative. The expertise and capabilities available at the DOE Joint Genome Institute (JGI) and the National Energy Research Scientific Computing Center (NERSC) – both at the Lawrence Berkeley National Laboratory (Berkeley Lab) – will help researchers explore the wealth of genomic and metagenomic data generated worldwide through access to supercomputing resources and computational science experts to accelerate discoveries.

Supercomputing the Secrets of the Snake Genome at TACC

Researchers at the University of Texas at Arlington are using TACC supercomputers to study the unique traits of snake evolution. Led by assistant professor of biology Todd Castoe, the team is exploring the genomes of snakes and lizards to answer critical questions about these creatures’ evolutionary history. For instance, how did they develop venom? How do they regenerate their organs? And how do evolutionarily-derived variations in genes lead to variations in how organisms look and function? “Some of the most basic questions drive our research. Yet trying to understand the genetic explanations of such questions is surprisingly difficult considering most vertebrate genomes, including our own, are made up of literally billions of DNA bases that can determine how an organism looks and functions,” says Castoe. “Understanding these links between differences in DNA and differences in form and function is central to understanding biology and disease, and investigating these critical links requires massive computing power.”

Next-Generation Sequencing Altering the Patient Care Landscape

Next-generation sequencing (NGS) tools produce vast quantities of genetic data which poses a growing number of challenges to life sciences organizations. Accelerating analytics, providing adequate storage and memory capacity, speeding time-to-solution, and reducing costs are major concerns for IT department operating on traditional computing systems. In this week’s Sponsored Post, Bill Mannel, Vice President & General Manager of HPC Segment Solutions and Apollo Servers, Data Center Infrastructure Group at Hewlett Packard Enterprise, explains how next-generation sequencing is altering the patient care landscape.

Bull Atos Powers New Genomics Supercomputer at Pirbright Institute

“Atos is determined to solve the technical challenges that arise in life sciences projects, to help scientists to focus on making breakthroughs and forget about technicalities. We know that one size doesn’t fit all and that is the reason why we studied carefully The Pirbright Institute’s challenges to design a customized and unique architecture. It is a pleasure for us to work with Pirbright and to contribute in some way to reduce the impact of viral diseases”, says Natalia Jiménez, WW Life Sciences lead at Atos.