Spectra Logic and Arcitecta team up for Genomics Data Management

Spectra Logic is teaming with Arcitecta for tackling the massive datasets used in life sciences. The two companies will showcase their joint solutions at the BioIT World conference this week in Boston. “Addressing the needs of the life sciences market with reliable data storage lies at the heart of the Spectra and Arcitecta relationship,” said Spectra CTO Matt Starr. “This joint solution enables customers to better manage their data and metadata by optimizing multiple storage targets, retrieving data efficiently and tracking content and resources.”

Custom Atos Supercomputer to Speed Genome Analysis at CNAG-CRG in Barcelona

Atos will soon deploy a Bull supercomputer at the Centro Nacional de Análisis Genómico (CNAG-CRG) in Barcelona for large-scale DNA sequencing and analysis. To support the vast process and calculation demands needed for this analysis, CNAG-CRG worked with Atos to build this custom-made analytics platform, which helps drive new insights ten times faster than its previous HPC system. “Atos helped us to set up a robust platform to conduct in-depth high-performance data analytics on genome sequences, which is the perfect complement to our outstanding sequencing platform”, stated Ivo Gut, CNAG-CRG Director.

Parabricks and SkyScale Raise the Performance Bar for Genomic Analysis

“In the modern world of genomics where analysis of 10’s of thousands of genomes is required for research, the cost per genome and the number of genomes per time are critical parameters. Parabricks adaption of the GATK4 Best Practice workflows running seamlessly on SkyScale’s Accelerated Cloud provides unparalleled price and throughput efficiency to help unlock the power of the human genome.”

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.