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Supercomputing Cancer Diagnostics with CyVerse

Adam Buntzman and his colleagues at the University of Arizona recently developed a tool that uses CyVerse supercomputing resources to create the first nearly comprehensive map of the human immunome, all the possible immune receptors our bodies can make. “When people go to a clinic, it’s usually because they’re already sick,” Buntzman said. “If doctors could detect cancerous cells before they grow drastically out of proportion to healthy cells, patients would have much higher odds of successful cancer treatment and survival.”

LLNL Collaboration to Improve Cancer Screening

Computer scientists at LLNL and Norwegian researchers are collaborating to apply high performance computing to the analysis of medical data to improve screening for cervical cancer. The team is developing a flexible, extendable model that incorporates new data such as other biomolecular markers, genetics and lifestyle factors to individualize risk assessment, according to Abdulla. “We want to identify the optimal interval for screening each patient.”

Video: Storage Architecture for Innovation & Research at the University of Florida

In this video from the DDN booth at SC15, Dr. Erik Deumens of the University of Florida describes why unpredictable and less standard architectures and system configurations are necessary to meet the agility, availability and responsiveness requirements to meet the mission of innovation and exploration. “The University of Florida’s Interdisciplinary Center for Biotechnology Research (ICBR) offers access to cutting-edge technologies designed to enable university faculty, staff and students, as well as research and commercial partners worldwide with the tools and resources needed to advance scientific research.”

Video: Using Google Compute Engine Pre-Emptible VMs for Cancer Research

In this video from the HPC in the Cloud Educational Series, Marco Novaes, Solutions Engineer with the Google Cloud Platform team explains how the Broad Institute was able to use Google Pre-Emptible VMs to leverage over 50,000 cores to advance cancer research. “Cancer researchers saw value in a highly-complex genome analysis, but even though they already had powerful processing systems in-house, running the analysis would take months or more. We thought this would be a perfect opportunity to utilize Google Compute Engine’s Preemptible VMs to further their cancer research, which was a natural part of our mission. And now that Preemptible VMs are generally available, we’re excited to tell you about this work.”

DDN Storage Speeds Genome Sequencing at University of Miami

Today DDN announced that the University of Miami’s Center for Computational Science (CCS) has deployed high-performance, DDN GS12K scale-out file storage to speed scientific discoveries and boost collaboration with researchers around the world. CCS maintains one of the largest centralized academic cyberinfrastructures in the country, which fuels vital and critical discoveries in Alzheimer’s, Parkinson’s, gastrointestinal cancer, paralysis and climate modeling as well as marine and atmospheric science research.

SGI UV Helps Decode How Mutations Rewire Cancer Cells

Linding Lab at the University of Copenhagen used an SGI UV system to discover how genetic diseases such as cancer systematically attack the networks controlling human cells. By developing advanced algorithms to integrate data from quantitative mass-spectrometry and next generation sequencing of tumor samples, the UCPH researchers have been able to uncover cancer related changes to phospho-signaling networks at a global scale. The studies are some of the early results of the strategic collaboration between SGI and the Linding Lab at UCPH. The landmark findings have been published in two back-to-back papers in today’s Cell journal.

Video: Intel Announces Collaborative Cancer Cloud

In this video from IDF 2015, Intel and Oregon Health & Science University (OHSU) announce the Collaborative Cancer Cloud, a precision medicine analytics platform that allows hospitals and research institutions to securely share patient genomic, imaging, and clinical data for potentially lifesaving discoveries.

Podcast: TACC Supercomputers Power Cancer Discovery

In this podcast, Karen Vasquez and Albino Bacolla of the University of Texas at Austin describe how TACC supercomputers have helped scientists find a surprising link between cross-shaped pieces of DNA and human cancer.

BSC Can Now Analyze Tumor Genomes in Just Hours

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.

Informatics Hub to Accelerate Cancer Research and Discovery

The National Cancer Informatics Program at NIH is building a virtual cancer informatics research community. Built on the HUBzero platform, NCIPHub.org is a ready-made open source cyberinfrastructure for research and education developed at Purdue, which, among other things, simplifies access to HPC systems and HPC workflows.