Glenn Lockwood writes that the world of high-throughput sequencing is becoming increasingly dependent on HPC, and many of the problems being solved in genomics and bioinformatics are stressing aspects of system architecture and cyberinfrastructure that haven’t gotten a tremendous amount of exercise from the more traditional scientific domains in computational research.
The human body is host to 100 trillion microorganisms, ten times the number of cells in the human body, and these microbes contain 100 times the number of DNA genes that our human DNA does. UC San Diego CSE Professor, Larry Smarr, discusses how data from these trillions of DNA bases are fed into supercomputers, resulting in innovative scalable visualization systems that allow for the examination of patterns that can be used to suggest new hypotheses for clinical application.
A new computational method has made it possible to detect genetic changes responsible for the onset and progression of tumors in a simple, quick and precise way. The SMUFIN (Somatic Mutations Finder) method is capable of analyzing the complete genome of a tumor and identifying its mutations in a few hours. In addition, it is able to identify alterations which had previously not been revealed, even using methods which require the use of supercomputers over several weeks.
In this video from the 2014 HPC User Forum in Seattle, Jack Collins from the National Cancer Institute presents: Genomes to Structures to Function: The Role of HPC. “Dr. Collins is the director of the Advanced Biomedical Computing Center at the Frederick National Laboratory for Cancer Research. Dr. Collins’ research focuses on biomedical computing applications pertaining to cancer. His research group develops and applies high-performance algorithms to solve data-intensive computational biology problems in the areas of genomic analysis, pattern recognition in proteomics and imaging, molecular modeling, and systems biology.”
“The Center for Pediatric Genomic Medicine at Children’s Mercy was the first genome center in the world inside a children’s hospital. It is also one of the first to focus on genome sequencing and analysis for inherited children’s diseases. While most genome centers focus on research, the Center for Pediatric Genomic Medicine develops new clinical tests as a starting point for next-generation medical treatments to improve outcomes in patients at Children’s Mercy and around the world.”
Working with DNAnexus and Amazon Web Services, we were able to rapidly deploy a cloud-based solution that allows us to scale up our support to researchers at the HGSC, and make our Mercury pipeline analysis data accessible to the CHARGE Consortium, enabling what will be the largest genomic analysis project to have ever taken place in the cloud.