Swedish National Infrastructure for Computing joins iRODS Consortium

Organization is now implementing new iRODS-based infrastructure

CHAPEL HILL, NC – The Swedish National Infrastructure for Computing (SNIC), a national research infrastructure hosted at universities across Sweden, is the newest member of the iRODS Consortium, the membership-based foundation that leads development and support of the integrated Rule-Oriented Data System (iRODS).

SNIC provides balanced and cost-effective resources and user support for large-scale computation and data storage to researchers in all scientific disciplines nationwide. The resources are made available through open application procedures such that the best Swedish research is supported.

SNIC services are provided by six university-based HPC centers: the High Performance Computing Center North (HPC2N) at Umeå University; the Uppsala Multidisciplinary Center for Advanced Computational Science (UPPMAX) at Uppsala University; PDC Center for High Performance Computing at KTH Royal Institute of Technology; the National Supercomputer Centre (NSC) at Linköping University; the Chalmers Centre for Computational Science and Engineering (C3SE) at Chalmers University of Technology; and LUNARC, the Center for Scientific and Technical Computing at Lund University. These SNIC partner centers provide the expert services to ensure that researchers can make optimal use of national HPC resources, resolving problems that range from compiling code to data management.

As iRODS Consortium members, SNIC is incorporating iRODS into its national service portfolio and deploy iRODS-based storage for research data. SNIC technical experts also plan to collaborate with iRODS developers and other consortium members to enable new iRODS features based on the needs of users, contribute to the development of the open source, graphical interface Kanki iRODS client, and contribute to the continuing integration of iRODS into HPC systems, including parallel file system integration and possible future high-performance transport mechanisms for iRODS.

“At SNIC, we look forward to serving the Swedish scientific research community with our new iRODS-based infrastructure and we are excited to be members of the consortium,” said Dejan Vitlacil, SNIC storage coordinator. “We see supporting the continuity of the development of iRODS as vitally important to our operation and we are happy to see a vibrant and growing community behind iRODS.”

In addition to SNIC, iRODS Consortium members include Bayer, Dell/EMC, DDN, HGST, IBM, Intel, MSC, the National Institute for Computational Science at the University of Tennessee, OCF, RENCI, the National Institute of Environmental Health Sciences (NIEHS), University College London, Utrecht University, and the Wellcome Trust Sanger Institute. Consortium members direct the technology and governance of iRODS, which is used by thousands of businesses, research institutes, universities, and governments worldwide. Consortium members also receive priority access to support, training, and consulting.

“With SNIC as members of the consortium, iRODS becomes an important piece of the technology infrastructure that supports Swedish research endeavors,” said Jason Coposky, iRODS Consortium executive director. “We are thrilled to be the data management and storage solution for SNIC and to work with them to enable research and discovery across Sweden.”

To learn more about iRODS and the iRODS Consortium, please visit https://irods.org/.

To learn more about SNIC, please visit https://www.snic.se/.

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RENCI to lead one of 12 projects to create an NIH Data Commons

The National Institutes of Health (NIH) has tapped the University of North Carolina at Chapel Hill and RENCI, a UNC technology research institute, to lead a project that is part of a nationwide effort to develop an NIH Data Commons, a shared virtual space where biomedical researchers can easily and securely work with data, analytical tools, and applications.

The Data Commons Pilot Phase provides nearly $646,000 to RENCI and UNC-Chapel Hill and another $578,000 to partners at seven institutions. The project launched in September and phase 1 will conclude in 2018. The award is one of 12 Data Commons Pilot Phase awards totaling $9 million announced by the NIH on Nov. 6.

The NIH Data Commons Pilot Phase is expected to span fiscal years 2017-2020. The pilot phase will explore the feasibility and best practices for making digital objects available through collaborative platforms. The work will be done on public clouds, which are virtual spaces where service providers make resources, such as applications and storage, available over the internet. The Data Commons aims to make biomedical research data Findable, Accessible, Interoperable, and Reusable (FAIR) for more biomedical researchers.

“Harvesting the wealth of information in biomedical data will advance our understanding of human health and disease,” said NIH Director Francis S. Collins, M.D., Ph.D. “However, poor data accessibility is a major barrier to translating data into understanding. The NIH Data Commons Pilot Phase is an important effort to remove that barrier.”

The UNC/RENCI Data Commons effort will engage multi-institutional, multidisciplinary teams to address eight key capabilities: guidelines and metrics for making data findable, accessible, interoperable and reusable; Global Unique Identifiers (GUIDs, which are numbers used to identify information in computer systems); open standard application programming interfaces (APIs); cloud agnostic architectures; workspaces for computation; research ethics, privacy and security (including authentication and authorization); indexing and searching; and use cases. RENCI is the overall lead for the UNC Data Commons Pilot Phase project and also leads the efforts on cloud agnostic architectures, workspaces for computation, and indexing and searching.

Some of the products that the RENCI teams plan to deliver include a tool called PIVOT, an acronym for Policy-driven, deeply integrated, Virtualized abstractiOn and federation. PIVOT, to be developed with partners from RTI International, will be a “cloud within clouds” architecture that integrates analytics tools, workflows, data optimization services, and other services that support FAIR principles into the core functionalities of a cloud.

A RENCI-led team also will develop and deploy cloud agnostic virtual workspaces for computation that can make use of many different scientific workflows and can dynamically provision technical infrastructure and resources across the Commons. In addition, RENCI researchers will work with partners at Lawrence Berkeley National Laboratory and Johns Hopkins University to deliver indexing and search capabilities that allow biological researchers to easily search free-form text, find digital objects, assign IDs, and search using ontology-based inference.

“We live in a time when digital biomedical data are ubiquitous, but the challenge is extracting value from those data in ways that lead to scientific breakthroughs and innovations in healthcare delivery,” said Stan Ahalt, PhD, director of RENCI and lead principal investigator for the project. “The NIH Data Commons addresses all the key questions that need to be answered in order to make biomedical data easy to find, access, analyze, share, and reuse. RENCI has been dealing with these kinds of questions for several years in other projects and we look forward to applying and leveraging what we’ve learned in this major, nationwide effort.”

RENCI’s partners in the Data Commons project include researchers at the UNC School of Medicine and the School of Information and Library Science as well as RTI International, Jackson Laboratory for Genomic Medicine, Johns Hopkins University, Lawrence Berkeley National Laboratory, Maastricht University, University of New Mexico, and Oregon Health and Science University.

“RENCI’s Innovations in data science are integral to the research we do here at UNC,” said Terry Magnuson, vice chancellor for research and NIH Council of Councils member. “The collaborative nature of our researchers, across disciplines and with other universities, creates a perfect environment in which medicine, information and data science can converge to advance discovery in biomedical research.”

For more information on the NIH Data Commons Pilot Phase, see https://go.usa.gov/xnbRX.

RENCI’s work as part the NIH Data Commons Pilot Phase is supported by award number 1OT3OD025464-01.


New project aims to bring semantics to evolutionary trees

Project team from left to right: Todd Vision, UNC-Chapel Hill; Jim Balhoff, RENCI; Wasila Dahdul, University of South Dakota; Josef Uyeda, Virginia Tech; and Hilmar Lapp, Duke University.

CHAPEL HILL, NC – Researchers at the University of North Carolina at Chapel Hill will play key roles in a new project that applies semantic technologies developed by computer and information scientists to the field of evolutionary biology.

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Chameleon Cloud Computing Project enters new phase with $10M award

Cloud computing lies behind many of today’s most popular technologies, from streaming video and music to email and chat services to storing and sharing family photos. Since 2015, the Chameleon testbed has helped researchers push the potential of cloud computing even further, finding novel scientific applications and improving security and privacy.

A new grant from the National Science Foundation will extend Chameleon’s mission for another three years, allowing the project led by University of Chicago with partners at the Texas Advanced Computing Center (TACC), Renaissance Computing Institute (RENCI), and Northwestern University to enter its next phase of cloud computing innovation. Upgrades to hardware and services as well as new features will help scientists rigorously test new cloud computing platforms and networking protocols. 

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SILS student awarded Thomas M. Carsey Scholarship in Data Science

Xueli Fan, a graduate student in the School of Information and Library Science (SILS) at UNC-Chapel Hill, was recently named 2017-2018 recipient of the Thomas M. Carsey Scholarship in Data Science.

The scholarship program gives talented UNC-Chapel Hill students the chance to work on real data science problems and domain science problems that use data and data science techniques in the discovery process. Launched by RENCI, Carsey scholars are paid for up to 20 hours per week to work with RENCI research teams and collaborators. Read more

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Data Fellows project aims to make storm surge predictions faster and more accurate

By Nelson Tull

Note: Nelson Tull is a graduate student in the Department of Civil, Construction, and Environmental Engineering at North Carolina State University. His faculty advisor, Casey Dietrich, is an NCDS Data Fellow conducting research to improve hurricane and storm surge guidance to emergency managers in North Carolina’s coastal counties. Dietrich’s Data Fellows research builds on previous work supported by the North Carolina Sea Grant program. Other collaborators are Rick Luettich, head of the Institute of Marine Sciences at UNC-Chapel Hill, Brian Blanton, a senior research scientist and oceanographer at RENCI, and Jason Fleming of Seahorse Coastal Consulting. To learn more about this research, tune into the September 2017 NCDS DataBytes webinar.

When lives are on the line, minutes count but so does accuracy
Storm surge model forecasts are a critical tool used by coastal emergency managers to plan and make decisions. These models must be both accurate and fast to give reliable information in a timely manner as a storm moves toward the coast. The forecast guidance must also be visualized in a way that is meaningful to those who need this vital information. Read more

BRAIN-I project uses RENCI cyberinfrastructure called xDCI to manage brain microscopy images

Sharing massive image files just became easier

Today’s advanced microscopes have revolutionized biology by giving scientists the ability to view 3D biological structures at the cellular and molecular level. However, that ability has created another problem: How to share and manage massive image files that can each be as large as 1 terabyte (TB), with possibly more than 50 TBs of data for the entire research project.  (A terabyte equals 1 trillion bytes of data, or about 150 hours of HD quality recording). Read more

iRODS Consortium welcomes OCF as newest member

UK-based technical support provider will now have a role in future iRODS development

CHAPEL HILL, NC – OCF, an organization that specializes in supporting the data challenges of private and public organizations in the UK, is the latest organization to join the iRODS Consortium, the membership-based foundation that leads development and support of the integrated Rule-Oriented Data System (iRODS).

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RENCI to lead $3 million project aimed at enabling safe and secure data sharing

CHAPEL HILL, NC – RENCI and partners at UNC-Chapel Hill, Duke University, Indiana University and the city of Durham, NC, will work together on a project that aims to allow scientists to share and analyze data across institutional boundaries while keeping that data safe and in compliance with regulations that control data location, availability, movement and access. Read more

Presentations at upcoming meeting highlight worldwide uses of iRODS

Go to irods.org to register for the 2017 User Group Meeting at Utrecht University

UTRECHT, The Netherlands – Users will take the spotlight during the annual iRODS User Group Meeting, which will feature at least 20 user presentations highlighting the many industries, government agencies, and research institutes who depend on iRODS to manage their data.

iRODS—the integrated Rule Oriented Data System—is free open source software for data management and discovery, workflow automation, secure collaboration, and data virtualization. iRODS software is developed and maintained through the support of the iRODS Consortium, a membership organization with industry and academic members worldwide. Read more

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