MICDE announces 2017-2018 Fellowship recipients

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MICDE is pleased to announce the recipients of the 2017-2018 MICDE Fellowships for students enrolled in the PhD in Scientific Computing or the Graduate Certificate in Computational Discovery and Engineering. We had 91 applicants from 25 departments representing 6 schools and colleges. Due to the extraordinary number of high quality applications we increased the number of fellowships from 15 to 20 awards. See our Fellowship page for more information.

AWARDEES

Diksha Dhawan, Chemistry
Negar Farzaneh, Computational Medicine & Bioinformatics
Kritika Iyer, Biomedical Engineering
Tibin John, Neuroscience
Bikash Kanungo, Mechanical Engineering
Yu-Han Kao, Epidemiology
Steven Kiyabu, Mechanical Engineering
Christiana Mavroyiakoumou, Mathematics
Ehsan Mirzakhalili, Mechanical Engineering
Colten Peterson, Climate and Space Sciences & Engineering
James Proctor, Chemical Engineering
Evan Rogers, Biomedical Engineering
Longxiu Tian, S. Ross School of Business
Jipu Wang, Nuclear Engineering and Radiological Sciences
Yanming Wang, Chemistry
Zhenlin Wang, Mechanical Engineering
Alicia Welden, Chemistry
Anna White, Industrial & Operations Engineering
Chia-Nan Yeh, Physics
Yiling Zhang, Industrial & Operations Engineering

HONORABLE MENTIONS

Geunyeong Byeon, Industrial & Operations Engineering
Ayoub Gouasmi, Aerospace Engineering
Joseph Kleinhenz, Physics
Jia Li, Physics
Changjiang Liu, Biophysics
Vo Nguyen, Computational Medicine & Bioinformatics
Everardo Olide, Applied Physics
Qiyun Pan, Industrial & Operations Engineering
Pengchuan Wang, Civil & Environmental Engineering
Xinzhu Wei, Ecology & Evolutionary Biology

ARC-TS seeks input on next generation HPC cluster

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The University of Michigan is beginning the process of building our next generation HPC platform, “Big House.”  Flux, the shared HPC cluster, has reached the end of its useful life. Flux has served us well for more than five years, but as we move forward with replacement, we want to make sure we’re meeting the needs of the research community.

ARC-TS will be holding a series of town halls to take input from faculty and researchers on the next HPC platform to be built by the University.  These town halls are open to anyone and will be held at:

  • College of Engineering, Johnson Room, Tuesday, June 20th, 9:00a – 10:00a
  • NCRC Bldg 300, Room 376, Wednesday, June 21st, 11:00a – 12:00p
  • LSA #2001, Tuesday, June 27th, 10:00a – 11:00a
  • 3114 Med Sci I, Wednesday, June 28th, 2:00p – 3:00p

Your input will help to ensure that U-M is on course for providing HPC, so we hope you will make time to attend one of these sessions. If you cannot attend, please email hpc-support@umich.edu with any input you want to share.

Job Opening: Research Cloud Administrator

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Advanced Research Computing – Technology Services (ARC-TS)  has an exciting opportunity for a Research Cloud Administrator.

This position will be part of a team working on a novel platform for research computing in the university for data science and high performance computing.  The primary responsibilities for this position will be to develop and create a resource sharing environment to enable execution of Data Science and HPC workflows using containers for University of Michigan researchers.

For more details and to apply, visit: http://careers.umich.edu/job_detail/142372/research_cloud_administrator_intermediate

HPC training workshops begin Monday, May 15

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series of training workshops in high performance computing will be held May 15, May 17 and May 24, 2017, presented by CSCAR in conjunction with Advanced Research Computing – Technology Services (ARC-TS). All sessions are held at East Hall, Room B254, 530 Church St.

Introduction to the Linux command Line
This course will familiarize the student with the basics of accessing and interacting with Linux computers using the GNU/Linux operating system’s Bash shell, also known as the “command line.”
• Monday, May 15, 9 a.m. – noon. (full descriptionregistration)

Introduction to the Flux cluster and batch computing
This workshop will provide a brief overview of the components of the Flux cluster, including the resource manager and scheduler, and will offer students hands-on experience.
• Wednesday, May 17, 1 – 4:30 p.m. (full description | registration)

Advanced batch computing on the Flux cluster
This course will cover advanced areas of cluster computing on the Flux cluster, including common parallel programming models, dependent and array scheduling, and a brief introduction to scientific computing with Python, among other topics.
• Wednesday, May 24, 1 – 5 p.m. (full description | registration)

NOTE: Additional workshops may be scheduled if demand warrants. Please sign up for the waiting list if the workshops are full, and you will be given first priority for any additional sessions.

ARC-TS contributes to successful fNIRS workshop

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The Center for Human Growth and Development (CHGD) held a workshop on functional near-infrared spectroscopy (fNIRS), a form of neuroimaging, with a special focus on pediatric applications. The workshop was sponsored by units at U-M, as well as units from Eastern Michigan University and Gallaudet University. It was attended by 50 people from as far away as Texas, and included research talks, instructional sessions, and hands-on experience with fNIRS data processing. The workshop was the first of its kind at U-M.

CHGD, ARC-TS, and LSA IT staff collaborated to provide a remote neuroimaging computing environment, which included a graphical interface, access to Matlab, and a suite of fNIRS software, that was accessed from participants’s laptops during the workshop. The attendees rated the practice exercises done via the computing environment one of the most important components of the workshop.

ARC-TS was pleased to be able to contribute to training in computational tools needed for emerging methods in neuroimaging. For more information about the fNIRS workshop, please see http://chgd.umich.edu/facilities-resources/developmental-neuroscience-laboratories/fnirs/fnirs-workshop/

New private insurance claims dataset and analytic support now available to health care researchers

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The Institute for Healthcare Policy and Innovation (IHPI) is partnering with Advanced Research Computing (ARC) to bring two commercial claims datasets to campus researchers.

The OptumInsight and Truven Marketscan datasets contain nearly complete insurance claims and other health data on tens of millions of people representing the US private insurance population. Within each dataset, records can be linked longitudinally for over 5 years.  

To begin working with the data, researchers should submit a brief analysis plan for review by IHPI staff, who will create extracts or grant access to primary data as appropriate.

CSCAR consultants are available to provide guidance on computational and analytic methods for a variety of research aims, including use of Flux and other UM computing infrastructure for working with these large and complex repositories.

Contact Patrick Brady (pgbrady@umich.edu) at IHPI or James Henderson (jbhender@umich.edu) at CSCAR for more information.

The data acquisition and availability was funded by IHPI and the U-M Data Science Initiative.

Designing optimal shunts for newborns with heart defects using computational modeling

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shuntFor babies born with hypoplastic left heart syndrome, several open-heart surgeries are required. During Stage I, a Norwood procedure is performed to construct an appropriate circulation to both the systemic and the pulmonary arteries. The pulmonary arteries receive flow from the systemic circulation, often by using a Blalock-Taussig (BT) shunt between the innominate artery and the right pulmonary artery. This procedure causes significantly disturbed flow in the pulmonary arteries.

A group of researchers led by U-M Drs. Ronald Grifka and Alberto Figueroa used computational hemodynamic simulations to demonstrate its capacity for examining the properties of the flow through and near the BT shunt. Initially, the researchers constructed a computational model which produces blood flow and pressure measurements matching the clinical magnetic resonance imaging (MRI) and catheterization data. Achieving this required us to determine the level of BT shunt occlusion; because the occlusion is below the MRI resolution, this information is difficult to recover without the aid of computational simulations. The researchers determined that the shunt had undergone an effective diameter reduction of 22% since the time of surgery. Using the resulting geometric model, they showed that we can computationally reproduce the clinical data. The researchers then replaced the BT shunt by with a hypothetical alternative shunt design with a flare at the distal end. Investigation of the impact of the shunt design revealed that the flare can increase pulmonary pressure by as much as 7%, and flow by as much as 9% in the main pulmonary branches, which may be beneficial to the pulmonary circulation.

Read more in Frontiers in Pediatrics.

MIDAS starting research group on mobile sensor analytics

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The Michigan Institute for Data Science (MIDAS) is convening a research working group on mobile sensor analytics. Mobile sensors are taking on an increasing presence in our lives. Wearable devices allow for physiological and cognitive monitoring, and behavior modeling for health maintenance, exercise, sports, and entertainment. Sensors in vehicles measure vehicle kinematics, record driver behavior, and increase perimeter awareness. Mobile sensors are becoming essential in areas such as environmental monitoring and epidemiological tracking.

There are significant data science opportunities for theory and application in mobile sensor analytics, including real-time data collection, streaming data analysis, active on-line learning, mobile sensor networks, and energy efficient mobile computing.

Our working group welcomes researchers with interest in mobile sensor analytics in any scientific domain, including but not limited to health, transportation, smart cities, ecology and the environment.

Where and When:

Noon to 2 pm, April 13, 2017

School of Public Health I, Room 7625

Lunch provided

Agenda:

  • Brief presentations about challenges and opportunities in mobile sensor analytics (theory and application);

  • A brief presentation of a list of funding opportunities;

  • Discussion of research ideas and collaboration in the context of grant application and industry partnership.

Future Plans: Based on the interest of participants, MIDAS will alert researchers to relevant funding opportunities, hold follow-up meetings for continued discussion and team formation as ideas crystalize for grant applications, and work with the UM Business Engagement Center to bring in industry partnership.

Please RSVP.  For questions, please contact Jing Liu, Ph.D, MIDAS research specialist (ljing@umich.edu; 734-764-2750).

Dr. Greg Wilson, founder of Software Carpentry, to speak on U-M campus Oct. 12-13

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The founder of Software Carpentry, Dr. Greg Wilson, will be on the U-M campus to give two public talks. Over the past 18 years, The Software and Data Carpentry organizations have sought to improve the data analysis and computing skills of researchers around the world. The organizations’ materials are developed collaboratively under the Creative Commons-Attribution license and taught by hundreds of trained volunteer instructors. Dr. Wilson will present two talks that you are invited to attend. Both talks will be in the Clark Library presentation space on the second floor of Hatcher South:

“Software Carpentry: Lessons Learned”
1:00 pm on Wednesday, 10/12, Clark Library
Since its start in 1998, Software Carpentry has evolved from a week-long training course at the US national laboratories into aworldwide volunteer effort to improve researchers’ computing skills. This talk will explore the lessons we’ve learned along the way about applying open source software development techniques to teaching at scale, and about getting people and institutions to change the way they work.

“Not on the Shelves: What Nonexistent Books, Tools, and Courses Can Tell Us About Ourselves”
11 am on Thursday, 10/13, Clark Library
Hundreds of books about writing compilers are currently on the market, but there are only three about writing debuggers. Spreadsheets are used to do calculations more often than every other kind of tool combined, but thirty-five years after their invention, version control systems still can’t handle them. Everyone thinks we should teach children how to program, but undergraduate courses on computing education are practically nonexistent.  This talk will explore what
these gaps in our books, tools, and courses tell us about the state of computing today, and about what it could look like tomorrow.

For more information: pschloss@umich.edu