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Primeur weekly 2018-04-16

Focus

GO FAIR initiative to create implementation networks for stewardship of data ...

Quantum computing

Atos Quantum Learning Machine can now simulate real qubits ...

UCSB/Google researchers in quantum computing professor John Martinis' group outline their plan for quantum supremacy ...

New qubit now works without breaks ...

Prototype of most advanced quantum memory presented by two Kazan universities ...

The thermodynamics of computing ...

Focus on Europe

GÉANT confirms Erik Huizer as CEO ...

ISC launches Travel Grant Programme to enable students and young researchers to attend the conference ...

Student develops gaming technology for environmental and scientific research ...

Prof. Dr. Xiaoxiang Zhu wins the 2018 PRACE Ada Lovelace Award for HPC ...

Academia and industry collaborate to drive UK supercomputer adoption ...

Middleware

Queen Mary University of London HPC cluster performance increases several orders of magnitude, saving time and cost ...

Hardware

University of Texas hires next director of no. 1 ranked computational institute ...

James Ang joins Pacific Northwest National Laboratory as chief scientist for computing ...

Fujitsu commences sales of PRIMERGY x86 server aimed at data centre companies ...

Tohoku University deploys vSMP Foundation for "The Supercomputer System" ...

Chinese leading weather research institute selected Mellanox InfiniBand, replacing OmniPath in an existing data centre ...

Valleytronics discovery could extend limits of Moore's Law ...

Top HPC clusters and workstations for AI, ML developed by Nor-Tech ...

Demonstration of world record: 159 Tb/s transmission over 1,045 km with 3-mode fiber ...

Applications

Boston partners with Excelero and Pixit Media at NAB to demo joint solution for media workflows ...

Fujitsu launches "Heart Explorer" to study heart behaviour ...

U.S. Department of Energy supports doctoral research into on-site analysis of supercomputer simulations ...

Scientists use machine learning to speed discovery of metallic glass ...

Machine learning could help search for gravitational waves ...

Artificial Intelligence can now detect gravitational waves ...

Jon Bashor retires after 27 years of service to national labs ...

Research and software: perspectives from different communities ...

The background hum of space could reveal hidden black holes ...

How to catch a fish genome with Big Data ...

Translational research community debates on the EGA and its impact on health ...

The Cloud

Capitalizing on the opportunity of hybrid cloud in HPC ...

St. Jude Cloud launches for researchers worldwide ...

St. Jude Cloud launches for researchers worldwide

Researchers worldwide are able to interact with paediatric cancer genomic data through St. Jude Cloud. The individuals pictured are exploring interactive genomic visualizations by using ProteinPaint within St. Jude Cloud. Credit: Peter Barta / St. Jude Children's Research Hospital.12 Apr 2018 Memphis - St. Jude Children's Research Hospital, in collaboration with Microsoft and DNAnexus, offers extensive next-generation sequencing data and unique analysis tools to accelerate research and cures for life-threatening pediatric diseases.

"Sharing research and scientific discoveries is vital to advancing cures and saving lives, especially in rare diseases like pediatric cancer", stated James R. Downing, M.D., St. Jude president and chief executive officer. "St. Jude has shared data and resources since its founding, and collaboration with researchers across the world is at the core of our mission. St. Jude Cloud offers researchers access to genomics data and analysis tools that will drive faster progress toward cures for catastrophic diseases of childhood."

St. Jude Cloud is a unique resource in the fight to advance cures for paediatric diseases, offering researchers:

  • the Largest Public Repository of Pediatric Cancer Genomics Data

The interactive data-sharing platform allows scientists to explore more than 5,000 whole-genome (WGS), 5,000 whole-exome (WES) and 1,200 RNA-Seq datasets from more than 5,000 pediatric cancer patients and survivors. By 2019, St. Jude expects to make 10,000 whole-genome sequences available on St. Jude Cloud.These data have been generated from three large St. Jude-supported genomics initiatives: the St. Jude - Washington University Pediatric Cancer Genome Project, designed to understand the genetic origins of childhood cancers; the Genomes for Kids clinical trial, focused on moving whole genome sequencing into the clinic; and the St. Jude Lifetime Cohort study (St. Jude LIFE), which conducts comprehensive clinical evaluations on thousands of pediatric cancer survivors throughout their lives.

Access to data is simple, fast and does not require downloading prior to exploration. Researchers may also upload their own data in a private, password-protected environment to explore using tools available on the St. Jude Cloud platform.

  • Interactive Data Tools

As well as high-quality next-generation sequencing data, St. Jude Cloud features a collection of bioinformatics tools to help both experts and non-specialists gain novel insights from genomics data. These tools include validated data analysis pipelines and interactive visualization tools to make it easier to make discoveries from large datasets. Data and results can be securely shared with collaborators within the platform.The platform enables researchers to explore St. Jude data or their own results using innovative, interactive visualizations powered by ProteinPaint, the genomic visualization engine developed at St. Jude. The ProteinPaint visualizations allow users to rapidly navigate through the genome and identify genetic changes linked to cancer development. St. Jude Cloud tools also produce custom visualizations of the user's own research data for exploration or comparison with St. Jude-generated data.

  • Verifying Research Discoveries Faster

A St. Jude scientist was able to use the St. Jude Cloud to replicate, in just a few days, experimental findings that originally took the research team more than two years to make. The original team discovered mutations connected to UV damage in a B-cell leukemia in work that was recently published inNature. The intriguing finding led the team to ask whether other leukemia samples not included in the original study might have similar patterns of mutations. They turned to the high-quality datasets available in St. Jude Cloud, where the rapid computing capabilities of the St. Jude Cloud platform enabled them to re-discover the same UV-linked mutational signature in pediatric B-cell leukemia patients. Identification of these additional samples will help researchers understand how UV damage could be linked to a blood cancer, and potentially point to new avenues for therapy. More details of this work were presented at the AACR annual meeting in Chicago on April 15.

  • Collaboration to Advance Cures

The data available on the St. Jude Cloud represent a key resource to understanding the genetic roots of childhood cancer. St. Jude's partnership with DNAnexus and Microsoft allows access to these data to harness the collective power of the global research community to advance precision medicine for rare paediatric diseases like cancer.

"St. Jude Cloud is a powerful resource to drive global research and discovery forward", stated Jinghui Zhang, Ph.D., chair of the St. Jude Department of Computational Biology and co-leader of the St. Jude Cloud project. "Providing genomic sequencing data to the global research community and making complex computational analysis pipelines easily accessible will lead to progress in eradicating childhood cancer. St. Jude has been committed to sequencing and understanding paediatric cancer genomes for nearly a decade, and we will continue to generate and share data with the research community in the future."

The data available through St. Jude Cloud is stored on Microsoft Azure, which can handle datasets on the massive scale required for large genomics studies such as those developed by St. Jude. Microsoft understands the complexities of large-scale genomics data and has processed half a petabyte of data for St. Jude Cloud to date.

"Health and technology partnerships are central to the advancement of scientific breakthroughs; allowing great minds and passionate hearts to work together with the common goal of ensuring one day, life-threating diseases in children are no longer a reality", stated Peter Lee, Ph.D., corporate vice president, AI + Research, Microsoft. "We are extremely proud to collaborate with our research partners at St. Jude and DNAnexus and address the challenges of technological limitations, such as storage and the speed of accessing vast amounts of pediatric cancer data, and look forward to the progress that St. Jude Cloud will bring."

DNAnexus, the biomedical informatics and data management company for St. Jude Cloud, leverages Azure to provide an open, flexible and secure Cloud platform that supports Microsoft Genomics service as well as other genomics analysis tools. Researchers around the world are able to access tools and diverse datasets in a secure and collaborative ecosystem.

"Collaboration fuels scientific advancements", stated Richard Daly, chief executive officer at DNAnexus. "Whether you are working together across hallways or international borders, researchers need a secure space to foster collaboration and share data and tools. St. Jude has long been a leader in paediatric cancer and continues to develop new approaches to revolutionize the way medicine is practiced. We are proud to serve as the technology platform bringing together St. Jude researchers and their partners to advance cures for pediatric life-threatening diseases."

Source: St. Jude Children's Research Hospital

Back to Table of contents

Primeur weekly 2018-04-16

Focus

GO FAIR initiative to create implementation networks for stewardship of data ...

Quantum computing

Atos Quantum Learning Machine can now simulate real qubits ...

UCSB/Google researchers in quantum computing professor John Martinis' group outline their plan for quantum supremacy ...

New qubit now works without breaks ...

Prototype of most advanced quantum memory presented by two Kazan universities ...

The thermodynamics of computing ...

Focus on Europe

GÉANT confirms Erik Huizer as CEO ...

ISC launches Travel Grant Programme to enable students and young researchers to attend the conference ...

Student develops gaming technology for environmental and scientific research ...

Prof. Dr. Xiaoxiang Zhu wins the 2018 PRACE Ada Lovelace Award for HPC ...

Academia and industry collaborate to drive UK supercomputer adoption ...

Middleware

Queen Mary University of London HPC cluster performance increases several orders of magnitude, saving time and cost ...

Hardware

University of Texas hires next director of no. 1 ranked computational institute ...

James Ang joins Pacific Northwest National Laboratory as chief scientist for computing ...

Fujitsu commences sales of PRIMERGY x86 server aimed at data centre companies ...

Tohoku University deploys vSMP Foundation for "The Supercomputer System" ...

Chinese leading weather research institute selected Mellanox InfiniBand, replacing OmniPath in an existing data centre ...

Valleytronics discovery could extend limits of Moore's Law ...

Top HPC clusters and workstations for AI, ML developed by Nor-Tech ...

Demonstration of world record: 159 Tb/s transmission over 1,045 km with 3-mode fiber ...

Applications

Boston partners with Excelero and Pixit Media at NAB to demo joint solution for media workflows ...

Fujitsu launches "Heart Explorer" to study heart behaviour ...

U.S. Department of Energy supports doctoral research into on-site analysis of supercomputer simulations ...

Scientists use machine learning to speed discovery of metallic glass ...

Machine learning could help search for gravitational waves ...

Artificial Intelligence can now detect gravitational waves ...

Jon Bashor retires after 27 years of service to national labs ...

Research and software: perspectives from different communities ...

The background hum of space could reveal hidden black holes ...

How to catch a fish genome with Big Data ...

Translational research community debates on the EGA and its impact on health ...

The Cloud

Capitalizing on the opportunity of hybrid cloud in HPC ...

St. Jude Cloud launches for researchers worldwide ...