Unlocking the Full Potential of Health Data

The health care industry is facing a challenging transition as it tries to use data more effectively. Gathering, sharing and analyzing patient information is an incredibly challenging process that is contributing to a technological revolution across the health care sector. One of the main challenges in our health care system today is the difficulty in working with patient data, because it exists in a variety of formats, both structured and unstructured, and it often exists in large volumes, making it difficult to handle in many data centers. This is where supercomputing comes into play, and the Oak Ridge National Laboratory (ORNL) is leading a project that is taking key steps forward in driving innovation. According to a recent ... [ Read More ]

Using HPC Techniques to Accelerate NGS Workflows

Next-generation sequencing (NGS) describes the modern nucleotide sequencing technologies that allow analysis of genetic material with unprecedented speed and efficiency. Its advent is shifting genome assembly from a problem of laboratory-based chemistry to one well suited to high performance computing (HPC). In simple terms, NGS involves breaking up long DNA or RNA molecules into millions of small, fragments (50 to 200 nucleotides), defined as a “reads” to be assembled into larger fragments called contigs. The process of taking genetic material, processing it on a sequencer, passing it to an HPC system for assembly, and outputting digital information in a form useful for research is contained in a “workflow,” the end-to-end flow of ... [ Read More ]

The Definition of Insanity

Almost ten years ago, when I was working at Pfizer, I wrote a position paper for a W3C Workshop on Semantic Web in Life Sciences. In that paper, I pointed out several vexing problems then faced by pharmaceutical researchers that I thought could be alleviated by use of a powerful knowledge architecture such as that enabled by Semantic Web technologies. Among these problems were those you might classify as knowledge management problems, and they had much to do with effectively sharing information throughout a large research organization where specialized vocabularies and varied purposes can easily get in the way. Other problems I described were just good, old-fashioned informatics problems, in particular the creation of so-called "data ... [ Read More ]

Video Blog: Solutions that Enable Life Sciences Advances

Advanced IT solutions are transforming the life sciences industry, and there are few better places to learn about how this is happening than the Bio-IT World Conference & Expo in Boston. The conference is coming up soon, and at Cray, we're excited to highlight our computing, storage and analysis solutions. Ted Slater, senior solutions architect for life sciences at YarcData, a Cray company, will present on Wednesday, April 30, and talk about how YarcData’s Urika technology is fueling major advances. Ted's presentation, "Learn How YarcData's Graph Analytics Appliance Makes It Easy to Use Big Data in Life Sciences," is about how data-intensive research is rising in life sciences and how YarcData systems provide the functionality ... [ Read More ]

Optimizing Next Generation Sequencing Environments with Graph Analytics

Last week, I discussed using the right tool in your technological environment, and today I’d like to note the importance of this when it comes to life sciences, specifically bioinformatics and next generation sequencing (NGS). In this video on Cray’s blog, I describe some of the problems that pharmaceutical and biotech organizations are plagued with, and how a graph analytics solution can resolve them. In the video I answer many key questions that I’ve heard working with scientists, including: How can graph analytics address the data challenges seen in an NGS environment? What power does a graph representation give you that a traditional RDBMS does not give you? Where does a graph analytics solution fit in an NGS ... [ Read More ]