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Tag: bioinformatics

New Genomics Pipeline Combines AWS, Local HPC, and Supercomputing

Sep 22, 2016 |

Declining DNA sequencing costs and the rush to do whole genome sequencing (WGS) of large cohort populations – think 5000 subjects now, but many more thousands soon – presents a formidable computational challenge to researchers attempting to make sense of large cohort datasets. No single architecture is best. This month researchers report developing a hybrid Read more…

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…

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.

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.

‘Biomolecular Motor-based’ Computer Promises Speed and Reduced Power

Mar 2, 2016 |

Combinatorial tasks are among the hardest for traditional computers. A good example is finding the optimum path through a large complicated network. Every possible path must be evaluated and as datasets grow the computing time grows exponentially making some tasks unfeasible. One practical example is verification of VLSI (very large scale integrated) semiconductor circuit design. Read more…

NVIDIA K80 GPU-System Speeds Up Bioinformatics Tool 12X

Jan 28, 2015 |

Not long ago, the high cost and relative slowness of DNA sequencing were the rate-limiting bottlenecks in biomedical research. Today, post-sequencing data analysis is the biggest challenge. The reason, of course, is the prodigious output from modern next-generation sequencing (NGS) instruments (e.g., Illumina and ThermoFisher/Life Technologies) overwhelming analysis pipelines. Efficiently sifting the data treasure trove Read more…

NSF Signs $1.4 Million Check to Advance Community Database

Jan 21, 2015 |

Thanks to an NSF award worth $1.4 million, bioinformatics researchers at Washington State University and Clemson University and elsewhere will soon have the kind of infrastructure capable of supporting 21st century big data genomics workloads. As part of the Tripal Gateway project, the multi-university team will work to enhance the scope and capacity of their existing Read more…

Pathogens Can’t Hide from Novel HPC Approach

Jan 21, 2015 |

In the realm of pathogenic threats, there are the usual suspects – anthrax, botulism, tuberculosis – but in reality there are a whole host of bacterial and viral pathogenic microbes that can be problematic to human and animal health. Protecting the public against these threats falls under the domain of biosecurity. While staying ahead of Read more…

Software Pinpoints Disease-Causing Genes

Oct 28, 2013 |

In what’s being heralded as a breakthrough in bioinformatics research, European researchers have developed a new software suite, called eXtasy, that automatically generates the most likely cause of a given genetic disorder. A team of scientists from iMinds, STADIUS, and Katholieke Universiteit Leuven (KU Leuven) built the new tool using advanced artificial intelligence techniques that Read more…