Sectors » Life Sciences

New File System from PSC Tackles Image Processing on the Fly

Jul 25, 2016 |

Processing the high-volume datasets, particularly image data, generated by modern scientific instruments is a huge challenge. Last week, a team of researchers from the Pittsburgh Supercomputing Center reported a novel approach to coping with the data flood – the Virtual Volume File System (VVFS) – which they say significantly reduces storage capacity requirements and facilitates Read more…

Briefing Alert: SoftBank will Purchase ARM Ltd for $32B

Jul 18, 2016 |

ARM Ltd has agreed to be bought by Japanese technology company SoftBank for $32B according to both companies. ARM-based chips are already dominant players in the mobile computing market and recently efforts to push ARM processors into servers, including HPC, have gained momentum. For example, Japan’s next flagship supercomputer, the post K Computer, will be Read more…

Life in a Drop: Ohio Supercomputer Helps Prove Hydration’s Role in Protein Folding

Jul 14, 2016 |

It’s perhaps fitting that in the middle of the summer, when water management is a common challenge, that a paper in the Proceeding of the National Academy of Sciences (PNAS) offers more proof that life as we know it can’t occur without water. Using Ohio Supercomputing Center resources, researchers have shown the critical role water plays in actively guiding protein folding and movement. “For a long time, scientists have been trying to figure out how water interacts with proteins…

Obama, NIH Announce Big Data Gathering Push for Precision Medicine

Jul 7, 2016 |

One could be forgiven for experiencing a bit of hopeful, skepticism in response to U.S. President Barack Obama Administration’s statement in May regarding re-energizing the “War Against Cancer.” The war against cancer is a many-decades old effort with mixed results – great progress in many areas but matched with disappointment in others. Winning the war Read more…

Genomic Sequencing at Children’s Mercy: Saving Time to Save Lives

Jul 1, 2016 |

Genomic sequencing – that is, rapid sequencing – is instrumental to diagnosing and treating critically ill patients, and managing the high data volumes involved in genomics is essential to the process. Children’s Mercy Hospital in Kansas City, MO, (354 beds, not-for-profit, treating children from birth through the age of 21) operates what it says is the world’s first whole genome sequencing center in a pediatric setting, where physicians, clinical laboratory scientists, molecular geneticists, bioinformaticians and software engineers work to sequence and analyze rare inherited diseases.

DDN Claims Bragging Rights (Again) in TOP500 Share

Jun 29, 2016 |

Once again, storage system supplier DataDirect Networks has the top market share – roughly 70 percent – in the TOP500, said the company today. This is the eighth consecutive year DDN has been the top storage system supplier to the Top500, according to Molly Rector, DDN CMO. Storage is the fast growing segment of the Read more…

TGAC Changes Name to Earlham Institute

Jun 27, 2016 |

June 27 — The Genome Analysis Centre (TGAC) will be changing its name to the “Earlham Institute” on June 27 2016. The Earlham Institute (EI) will build upon the research foundation developed as TGAC and continue to help answer the most fundamental questions in biological sciences today, from its home on Norwich Research Park. The institute’s genomics Read more…

HPE Tackles Phi, Debuts Mfg. Solution and New HPC Software Environment

Jun 20, 2016 |

Hewlett Packard Enterprise (HPE), now about eight months into its transition as a separate entity, retained the prestige of fielding the most systems of any vendor on the Top500 list announced at the ISC2016. HPE had 127 systems (25.4 percent) though the number was down from 155 just six months ago. Other ISC news included Read more…

NVIDIA Debuts PCIe-based P100; Broadens Aim at CPU Dominance

Jun 19, 2016 |

NVIDIA seems to be mounting a vigorous effort to dethrone the CPU as the leader of the processor pack for HPC and demanding datacenter workloads. That’s a tall order. Introduction at ISC 2016 of a PCIe-based version of is new Tesla P100 card is one element in the strategy. It should ease the upgrade path Read more…

Heading into ISC16, OpenHPC Releases Latest Stack with 60-plus Packages

Jun 16, 2016 |

SC15 was sort of a muted launch party for OpenHPC – the nascent effort to develop a ‘plug-and-play’ software framework for HPC. There seemed to be widespread agreement the idea had merit, not a lot of knowledge of details, and some wariness because Intel was a founding member and vocal advocate. Next week, ISC16 will mark the next milestone for OpenHPC, which has since grown into a full-fledged Linux Foundation Collaborative Project and today released version 1.0.1 of OpenHPC (build and test tools).

Intel Xeon E7 Balloons In-memory Capacity, Targets Real-Time Analytics

Jun 8, 2016 |

Who crunches more data faster, wins. It’s this drive that cuts through and clarifies the essence of the evolutionary spirit in the computer industry, the dual desire to get to real time with bigger and bigger chunks of data. The locomotive: HPC technologies adapted to enterprise mission-critical data analytics. With its memory capacity of up Read more…

HPC and Big Data Convergence Takes Life at PSC’s Bridges

Jun 1, 2016 |

Roughly three months into early operations, the Bridges computing resources being deployed at the Pittsburgh Supercomputing Center is bearing fruit. Designed to accommodate traditional HPC and big data analytics, Bridges had supported 245 projects as of May 26. This ramping up of the NSF-funded ($9.6 M) Bridges project is an important step in delivering practical Read more…

GPU-based Deep Learning Enhances Drug Discovery Says Startup

May 26, 2016 |

Sifting the avalanche of life sciences (LS) data for insight is an interesting and important challenge. Many approaches are used with varying success. Recently, improved hardware – primarily GPU-based – and better neural networking schemes are bringing deep learning to the fore. Two recent papers report the use of deep neural networks is superior to typical machine learning (support vector machine model) in sieving LS data for drug discovery and personalized medicine purposes.

TACC Wrangler Supports Zika Hackathon

May 19, 2016 |

By now most people have heard of Zika, the mosquito-borne disease that can cause fever and birth defects and that threatens to spread to the United States from Latin and South America. Earlier this week more than 50 data scientists, engineers, and University of Texas students gathered for the “Austin Zika Hackathon” at big data Read more…

Machine Learning Advances Fight Against Cancer

May 18, 2016 |

Developing effective tools against cancer has been a long, complicated endeavor with successes and disappointments. Despite all, cancer remains the leading cause of death worldwide. Now, machine learning and data analytics are being recruited as tools in the effort fight the disease and show significant promise according to two recent papers. In one paper – An Analytics Approach to Designing Combination Chemotherapy Regimens for Cancer – researchers from MIT and Stanford “propose models that use machine learning and optimization to suggest regimens to be tested in phase II and phase III trials.”

Edico Genome to Make DRAGEN Available on New IBM Power Systems for HPC

May 12, 2016 |

SAN DIEGO, Calif., May 12 — Edico Genome, creator of the world’s first bio-IT processor designed to analyze next-generation sequencing data, today announced a collaboration with IBM to make DRAGEN available on the new IBM Power Systems S822LC for high performance computing (HPC). In addition, Edico is now offering the Broad Institute’s Genome Analysis Toolkit (GATK), a software package for analysis of Read more…

Barcelona Supercomputing Center Develops New Bioinformatics Tool Against HIV

May 11, 2016 |

Viruses’ natural mutational agility has long been problematic for established therapies. Determining a therapeutic compound’s effectiveness against a mutated viral pathogen mostly entails empirical screening of the mutated virus with compounds to gauge effectiveness. This week researchers from the Barcelona Supercomputing Center and IrsiCaixa, the Catalan AIDS Research Institute, reported developing a bioinformatics method to Read more…

TGAC Installs largest SGI UV 300 Supercomputer for Life Sciences

May 11, 2016 |

Two weeks ago, The Genome Analysis Centre (TGAC) based in the U.K. turned on the first of two new SGI UV300 computers. Next week, or thereabouts, TGAC will bring a second identical system online. Combined with its existing SGI UV2000, TGAC will have the largest SGI system dedicated to life sciences in the world. The upgrade will allow TGAC to significantly shorten the time required to assemble wheat genomes, a core activity in TGAC efforts to enhance worldwide food security.

Technology Test Drive: PNNL Offers Exploratory Licenses

May 10, 2016 |

Signing a two-page agreement and paying just $1,000 can get U.S. companies an opportunity to test drive promising technologies through a new, user-friendly commercialization option being offered at the Department of Energy’s Pacific Northwest National Laboratory. PNNL is the only DOE lab to offer this option, called an exploratory license, which gives companies six months Read more…

Healthcare Professionals Get Cognitive Sooner with Watson Health Financed by IBM

May 9, 2016 |

Perhaps more than any other, the healthcare industry is undergoing dramatic upheaval. Changes in reimbursement models, continued merger and acquisition activity, regulatory requirements, and the increased focus on quality of patient care are forcing many hospitals and healthcare providers to reinvent themselves.   Patients and customers are driving change, and healthcare providers struggle to follow their Read more…