Back to Table of contents

Primeur weekly 2017-04-10

Exascale supercomputing

EUROSERVER paves the way for low-power data centres ...

Intersect360 Research to provide USCC testimony for China's Pursuit of Next Frontier Tech hearing ...

Quantum computing

'Virtual' interferometers may overcome scale issues for optical quantum computers ...

Quantum-physical model system ...

Optics advance quantum information processing ...

Focus on Europe

A glance into the ISC 2017 Research Paper Session ...

OCF announce Iceotope as liquid cooling partner for research and academic market ...

Return of the mini-supercomputer in the Netherlands: Little Green Machine II ...

Max Planck Institute for Biophysical Chemistry chooses vSMP Foundation ...

PRACE opens SHAPE 5th Call for Proposals ...

IBM invests to accelerate innovation, collaboration and fast-track health care solutions in Finland ...

73% of academics say access to research data helps them in their work; 34% do not publish their data ...

Middleware

DDN Lustre powers University of Edinburgh accelerated genomics research ...

Hardware

Supercomputer growth drives record HPC revenue in 2016, Hyperion Research reports ...

Canada's most powerful academic supercomputer will launch at Simon Fraser University ...

Silicon Mechanics Announces Recipient of 6th Annual Research Cluster Grant ...

U.S. businesses risk falling behind as lead in global semiconductor industry threatened ...

Fujitsu and Oracle launch Fujitsu SPARC M12 servers with world's fastest per-core performance ...

IBM Researchers advance the understanding of chip reliability at IEEE International Reliability Physics Symposium ...

Applications

Artificial intelligence: Bosch and University of Amsterdam to cooperate closely ...

Cyber gene network could speed up discoveries ...

How can network analysis lead to a new way of studying court decisions? ...

IBM patents machine learning models for drug discovery ...

Clemson scientists receive $2.95 million to improve and simplify large-scale data analysis ...

New brain-inspired cybersecurity system detects 'bad apples' 100 times faster ...

Supercomputers reveal how cell membranes keep cancer-causing proteins turned off ...

The Cloud

IBM opens Budapest Software Lab to develop Cloud Video solutions ...

IBM first to deliver latest NVIDIA GPU accelerator on the Cloud to speed AI workloads ...

University of Wyoming uses Oracle Cloud to drive core mission of teaching, research, and service ...

Industry experts discuss advantages and risks of shifting data analytics to the Cloud ...

Cyber gene network could speed up discoveries


3 Apr 2017 Pullman - A Washington State University (WSU) team has set out to digitally model how every known gene interacts with every other gene - in plants, animals, insects and people. These gene expression networks could promote development of biomarkers that breeders use to grow new crops through traditional methods. The work could aid scientists in finding new genes that influence plant and animal health.

Stephen Ficklin, a computational biologist in the WSU Department of Horticulture, and colleagues will build the networks with $895,000 from the National Science Foundation. Their project will help test the Scientific Data Analysis at Scale project, or SciDAS, a $2.9 million NSF-funded effort to improve the United States' cyber infrastructure and help scientists make better use of it.

"Improving our cyber infrastructure helps make the U.S. more competitive in research", Stephen Ficklin stated. "It keeps us in the forefront of data science."

The WSU team will collaborate with Clemson University and RENCI, the Renaissance Computing Institute, which is a collaboration between the University of North Carolina-Chapel Hill, North Carolina State University and Duke University.

The researchers will take data from the National Center for Biotechnology Information, a public repository of genomic information, for as many species as possible and create networks that show how each gene interacts with every other one.

"In the end, we will create the most complete repository of gene coexpression networks that exists anywhere", Stephen Ficklin stated.

By following network connections, he said, scientists could discover genes that benefit agriculture, medicine, animal science and other fields.

"As a WSU researcher, I hope to help plant breeders", he stated. "I want to build networks like these as tools for breeders to find traits they’re interested in. They could use biomarkers to screen their seedlings in weeks instead of months or years."

"Plant breeders can look for genes known to be associated with good or bad traits and use them to make traditional crosses", he added.

With tens of thousands of genes in every organism, the computer power required to create these gene-expression networks is vast - well beyond the capability of a single supercomputer. A single test case by Stephen Ficklin and collaborators required 1200 processors and four weeks - divided among 70,000 computation jobs.

SciDAS gives researchers an easier way to spread their computational needs across existing large-scale resources, such as the Open Science Grid or Cloud Lab, growing or shrinking their demands as needed.

The final network will be kept, as part of SciDAS, on three petabytes (3 million gigabytes) of storage at WSU, RENCI and Clemson University.
Source: Washington State University

Back to Table of contents

Primeur weekly 2017-04-10

Exascale supercomputing

EUROSERVER paves the way for low-power data centres ...

Intersect360 Research to provide USCC testimony for China's Pursuit of Next Frontier Tech hearing ...

Quantum computing

'Virtual' interferometers may overcome scale issues for optical quantum computers ...

Quantum-physical model system ...

Optics advance quantum information processing ...

Focus on Europe

A glance into the ISC 2017 Research Paper Session ...

OCF announce Iceotope as liquid cooling partner for research and academic market ...

Return of the mini-supercomputer in the Netherlands: Little Green Machine II ...

Max Planck Institute for Biophysical Chemistry chooses vSMP Foundation ...

PRACE opens SHAPE 5th Call for Proposals ...

IBM invests to accelerate innovation, collaboration and fast-track health care solutions in Finland ...

73% of academics say access to research data helps them in their work; 34% do not publish their data ...

Middleware

DDN Lustre powers University of Edinburgh accelerated genomics research ...

Hardware

Supercomputer growth drives record HPC revenue in 2016, Hyperion Research reports ...

Canada's most powerful academic supercomputer will launch at Simon Fraser University ...

Silicon Mechanics Announces Recipient of 6th Annual Research Cluster Grant ...

U.S. businesses risk falling behind as lead in global semiconductor industry threatened ...

Fujitsu and Oracle launch Fujitsu SPARC M12 servers with world's fastest per-core performance ...

IBM Researchers advance the understanding of chip reliability at IEEE International Reliability Physics Symposium ...

Applications

Artificial intelligence: Bosch and University of Amsterdam to cooperate closely ...

Cyber gene network could speed up discoveries ...

How can network analysis lead to a new way of studying court decisions? ...

IBM patents machine learning models for drug discovery ...

Clemson scientists receive $2.95 million to improve and simplify large-scale data analysis ...

New brain-inspired cybersecurity system detects 'bad apples' 100 times faster ...

Supercomputers reveal how cell membranes keep cancer-causing proteins turned off ...

The Cloud

IBM opens Budapest Software Lab to develop Cloud Video solutions ...

IBM first to deliver latest NVIDIA GPU accelerator on the Cloud to speed AI workloads ...

University of Wyoming uses Oracle Cloud to drive core mission of teaching, research, and service ...

Industry experts discuss advantages and risks of shifting data analytics to the Cloud ...