U-M, Yottabyte partner to accelerate data-intensive research

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CONTACT: Dan Meisler, ARC Communications Manager, 734-764-7414, dmeisler@umich.edu

A strategic partnership between the University of Michigan and software company Yottabyte promises to unleash a new wave of data-intensive research by providing a flexible computing cloud for complex computational analyses of sensitive and restricted data.

The Yottabyte Research Cloud will provide scientists high performance, secure and flexible computing environments that enable the analysis of sensitive data sets restricted by federal privacy laws, proprietary access agreements, or confidentiality requirements. Previously, the complexity of building secure and project-specific IT platforms often made the computational analysis of sensitive data prohibitively costly and time consuming.

The system is built on $5.5 million worth of hardware and software donated to the University by Yottabyte; U-M will provide $2 million to support delivery of services to researchers and general operations.

Brahmajee Nallamothu, professor of internal medicine, tested a pilot installation of the Yottabyte Research Cloud at the U-M Institute of Healthcare Policy and Innovation for his research on such topics as predictors of opioid use after surgery and the costs and uses of cancer screenings under the Affordable Care Act.

“We recently moved a healthcare claims database, which is multiple terabytes in size and requires a great deal of memory and fast storage to process, onto the pilot platform,” Nallamothu said. “The platform allows us to immediately increase or decrease computing resources to meet demand while permitting multiple users to access the data safely and remotely. Our previous setup relied on network storage and self-managed hardware, which was extremely inefficient compared to what we can do now.”

“The Yottabyte Research Cloud will improve research productivity by reducing the cost and time required to create the individualized, secure computing platforms that are increasingly necessary to support scientific discovery in the age of Big Data,” said Eric Michielssen, associate vice president for advanced research computing at U-M.

“With the Yottabyte Research Cloud, researchers will be able to ask more questions, faster, of the ever-expanding and massive sets of data collected for their work,” said Yottabyte CEO Paul E. Hodges, III. “We are very pleased to be a part of the diverse and challenging research environment at U-M. This partnership is a great opportunity to develop and refine computing tools that will increase the productivity of U-M’s world class researchers.”

Many U-M scientists are working on a variety of research projects that could benefit from use of the Yottabyte Research Cloud:

  • Healthcare research, for example in precision medicine, often requires working with sensitive patient information and large volumes of diverse data types. This research can yield results that positively impact patients’ lives, but often involves the analysis of millions of clinical observations that can include genomic, hospital, outpatient, pharmaceutical, laboratory and cost data. This requires a secure high performance computing ecosystem coupled to massive amounts of multi-tiered storage.
  • In the social sciences, U-M research requires secure, remote access to sensitive research data about substance abuse, mental health, and other topics.
  • Transportation researchers who mine large and sensitive datasets — for example, a 24 Terabyte dataset that includes videos of drivers’ faces and GPS traces of their journeys — also stand to benefit from the security features and computing power.
  • In learning analytics, studies of the persistence of teacher effects on student learning could benefit from the enclaves to store and analyze data that includes observational measures scored from classroom videos, and elementary and middle school students’ scores on standardized tests.
  • Researchers in brain science will be able to use the Yottabyte Research Cloud to investigate a wide range of topics including  the effects of aging on brain function and structure and how we focus our attention in the presence of distraction.

The Yottabyte Research Cloud is U-M’s first foray into software-defined infrastructure for research, allowing on-the-fly personalized configuration of any-scale computing resources, which promises to change the way traditional IT infrastructure systems are deployed across the research community.  

More about Yottabyte:  www.yottabyte.com.

More about Yottabyte Research Cloud: arc-ts.umich.edu/yrc

Questions: dmeisler@umich.edu

MICDE Fall 2016 Seminar Series speakers announced

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The Michigan Institute for Computational Discovery and Engineering (MICDE) is proud to announce its fall lineup of seminar speakers. In cooperation with academic departments across campus, the seminar series brings nationally recognized speakers to campus.

This fall’s speakers are:

Sept. 13: Nathan Kutz, Professor of Applied Mathematics, University of Washington

Sept. 22: Rob Gardner, Senior Scientist at the Computation Institute, University of Chicago

Sept. 29: Jeremy Lichstein, Assistant Professor of Biology, University of Florida

Oct. 6: Jonathan Freund, Professor of Mechanical Science and Engineering and of Aerospace Engineering, University of Illinois, Urbana-Champaign

Oct. 14: Anthony Wachs, Assistant Professor of Mathematics and of Chemical and Biological Engineering, University of British Columbia

Oct. 26: Andrea Lodi, Professor of Mathematical and Industrial Engineering, Polytechnique Montreal

Nov. 11: David Higdon, Professor of the Biocomplexity Institute, Virginia Tech

Dec. 9: Ann Almgren, Staff Scientist at the Center for Computational Sciences and Engineering, Lawrence Berkeley National Laboratories

For more information, including links to bios and abstracts as available, please visit micde.umich.edu/seminar-series/.

Students in the Graduate Certificate in Computational Discovery and Engineering program are required to attend at least half of the seminars.

miRcore’s high school biotechnology camp a success

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GIDAS Biotechnology camp’s high school students learning about microRNA targeted predictions using Flux, with support from MICDE and U-M’s Scientific Computing Student Club members.

 

From Aug. 8-12, 2016, MICDE and ARC-TS donated a Flux allocation and computational support to miRcore and its GIDAS’ Biotechnology Camp for high school students. All the students were able to log in the cluster, and use the command line to run RNAhybrid, a tool for finding the minimum free energy hybridization of a long and a short RNA. The students learned about microRNA target predictions that complemented the camp’s wet lab experiments. Scientific Computing Student Club members Joe Paki and Blair Winograd provided support to the students.

MICDE is partnered with miRcore, a non-profit organization whose mission is to democratize medical research by building funds for microgrants to support innovative genetic research.

U-M team uses Flux HPC cluster for pre-surgery simulations

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Last summer, Alberto Figueroa’s BME lab at the University of Michigan achieved an important “first” – using computer-generated blood flow simulations to plan a complex cardiovascular procedure.

“I believe this is the first time that virtual surgical planning was done for real and not as a retrospective theoretical exercise ,” says Figueroa.

Using a patient’s medical and imaging data, Figueroa was able to create a model of her unique vasculature and blood flow, then use it to guide U-M pediatric cardiologists Aimee Armstrong, Martin Bocks, and Adam Dorfman in placing a graft in her inferior vena cava to help alleviate complications from pulmonary arteriovenous malformations (PAVMs). The simulations were done using the Flux HPC cluster.

Read more…

Video, slides available: “Advanced Research Computing at Michigan, An Overview,” Brock Palen, ARC-TS

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Video (http://myumi.ch/aAG7x) and slides (http://myumi.ch/aV7kz) are now available from Advanced Research Computing – Technology Services (ARC-TS) Associate Director Brock Palen’s presentation “Advanced Research Computing at Michigan, An Overview.”

Palen gave the talk on June 27, 2016, outlining the resources and services available from ARC-TS as well as from off-campus resource providers.

New MICDE associate directors named

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MICDE is pleased to announce the appointment of three new associate directors starting July 1, 2016: Karthik Duraisamy (Aerospace Engineering),  Annette Ostling (Ecology and Environmental Biology) and Siqian Shen (Industrial and Operations Engineering). The associate directors, together with MICDE Director Krishna Garikipati and Assistant Director Mariana Carrasco-Teja, will work on initiatives to help MICDE achieve its goals. These include growing MICDE’s educational programs, the Ph.D in Scientific Computing and the Graduate Certificate in Computational Discovery & Engineering; assembling interdisciplinary research teams and helping them secure funding for their projects; engaging with industrial partners; and coordinating outreach activities.

New on-campus data-science and computational research services available

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Researchers across campus now have access to several new services to help them navigate the new tools and methodologies emerging for data-intensive and computational research.

As part of the U-M Data Science Initiative announced in fall 2015, Consulting for Statistics, Computing and Analytics Research (CSCAR) is offering new and expanded services, including guidance on:

  • Research methodology for data science.
  • Large scale data processing using high performance computing systems.
  • Optimization of code and use of Flux and other advanced computing systems.
  • Advanced data management.
  • Geospatial data analyses.
  • Exploratory analysis and data visualization.
  • Obtaining licensed data from commercial sources.
  • Scraping, aggregating and integrating data from public sources.
  • Analysis of restricted data.

“With Big Data and computational simulations playing an ever-larger role in research in a variety of fields, it’s increasingly important to provide researchers with a comprehensive ecosystem of support and services that address those methodologies,” said CSCAR Director Kerby Shedden.

As part of this significant expansion of its scope, the campuswide statistical consulting service CSCAR has been renamed Consulting for Statistics, Computing and Analytics Research. It was formerly known as the Center for Statistical Consultation and Research.

For more information, see the University Record article.

Krishna Garikipati appointed Director of MICDE

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Statement from S. Jack Hu, U-M Vice President for Research:

krishnaGarikipatiI’m very pleased to announce that Prof. Krishna Garikipati (Mechanical Engineering and Mathematics) has been appointed the new Director of the Michigan Institute for Computational Discovery and Engineering (MICDE). The Institute has grown significantly since its establishment in 2013 as the interdisciplinary home for the development and use of mathematical algorithms on high performance computers at U-M. Prof. Garikipati has been involved as associate director for research since Fall 2014 and is uniquely positioned to take the institute to the next level.

MICDE is a joint initiative of UMOR, the College of Engineering, and the College of Literature, Science and the Arts. In the past year, it has seen many new and important developments, including the launching of two centers focused on network and storage-enabled collaborative science and data-driven computational physics; new planned course offerings for the PhD in Scientific Computing and the Graduate Certificate in CDE; new initiatives on industrial engagement; and the establishment of the Scientific Computing Student Club. A number of new research initiatives are also being planned, with broadening participation of MICDE-affiliated faculty, whose numbers continue to grow.

Prof. Garikipati will take over the directorship of MICDE from Prof. Eric Michielssen (EECS) who founded the institute in Fall 2013 and served as director, in addition to his role as Associate Vice President for Advanced Research Computing. Prof. Michielssen will continue as AVP.