October 15, 2013
A team of scientists within the University of South Wales' Genomics and Computational Biology research group are using HPC Wales' supercomputing resources to develop new cancer treatments. Led by Dr. Tatiana Tatarinova, the team is engaged in an area of research known as personalized medicine, which starts with an improved understanding of each patient's unique genetic makeup.
The researchers use mathematical modeling and computational simulation to help them understand the biological processes that occur within a cell. In this way, they transform the genetic information into observable physical characteristics and traits.
Like so many, Dr. Tatarinova has been personally affected by this disease, adding greater relevancy to her work. "One of the saddest moments of my life was when my mother was diagnosed with cancer," the researcher reports. "She had surgery, but developed secondary cancer and subsequently died five years later. One of the problems with cancer treatment is that drugs are not made specifically for individual patients: medicine should take into account a person's genotype, not just age and gender, and should be tailored to their needs."
Ideally, a clinician should be able to develop individualized treatment plans for each patient, optimizing drug effect and minimizing toxicity. This is where computational biology comes in. This research area uses the power of computing to understand biological processes with profound implications for genetics and healthcare. According to Dr. Tatarinova, "computational biology has the potential to become one of the most important areas of scientific research in the twenty-first century."
"In the very near future, when every person is genotyped, the notion of personalised medicine will become a reality," says Dr. Tatarinova. "Healthcare decisions and practices will be tailored to the individual patient by integrated use of genotypic and phenotypic information as well as medical and family history. At the University of South Wales we have developed a novel method for identifying a person's ancestry based on DNA analysis. Understanding an individual's origins is essential to choosing the correct medical treatments and the best diet for that person."
Personalized medicine represents a large portion of the global bioinformatics market. Experts anticipate this market will grow from £1.9 billion (US$3.04 billion) in 2012 to £5 billion (US$8 billion) in 2017. Wales has a booming £1.3 million (US$2.08 million) life sciences sector, which comprises approximately 10 percent of the total life sciences employment in the UK.
Making sense of the huge tide of biological information is both compute and data-intensive. For this reason, a commitment to life sciences must be matched by an investment in HPC and big data technologies. As Dr. Tatarinova explains, there are challenges with regard to processing, analyzing, storing and transferring information, which all require HPC-level solutions.
"High performance computing is an essential part of computational biology research," notes Dr. Tatarinova. "Our research would be slow and difficult – maybe even impossible – without access to it. HPC Wales have given us training, support and access to their technology and services. They have motivated me to aim higher and to make my projects more ambitious. They have installed all of the software that we required, fixed any problems that we had with our codes and scripts, and even liaised with third-party software developers to improve their codes."
10/30/2013 | Cray, DDN, Mellanox, NetApp, ScaleMP, Supermicro, Xyratex | Creating data is easy… the challenge is getting it to the right place to make use of it. This paper discusses fresh solutions that can directly increase I/O efficiency, and the applications of these solutions to current, and new technology infrastructures.
10/01/2013 | IBM | A new trend is developing in the HPC space that is also affecting enterprise computing productivity with the arrival of “ultra-dense” hyper-scale servers.
Ken Claffey, SVP and General Manager at Xyratex, presents ClusterStor at the Vendor Showdown at ISC13 in Leipzig, Germany.
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