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.

New graduate course offering: “Methods and Practice of Scientific Computing”

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The Michigan Institute for Computational Discovery and Engineering (MICDE) is pleased to announce “Methods and Practice of Scientific Computing”, the first graduate course designed and organized by MICDE faculty. The course will be taught in Fall 2016, coordinated by Dr. Brendan Kochunas. This foundational course in scientific computing has been developed as a broad introduction to the subject, and has been designed to support research in all disciplines represented in MICDE. In addition to Brendan Kochunas, the course was developed by MICDE professors Bill Martin, Karthik Duraisamy, Vikram Gavini, and Shravan Veerapaneni, and MICDE Assistant Director Mariana Carrasco-Teja.

The details follow:

NERS 590
4 credits
Prerequisites: Graduate standing and permission of instructor.

This course is designed for graduate students who are developing the methods, and using the tools, of scientific computing in their research. With the increased power and availability of computers to do massively scaled simulations, computational science and engineering as a whole has become an integral part of research that complements experiment and theory. This course will teach students the necessary skills to be effective computational scientists and how to produce work that adheres to the scientific method. A broad range of topics will be covered including: software engineering best practices, computer architectures, computational performance, common algorithms in engineering, solvers, software libraries for scientific computing, uncertainty quantification, verification and validation, and how to use all the various tools to accomplish these things. The class will have lecture twice a week and have an accompanying lab component. Students will be graded on homeworks, lab assignments, and a course project.

A draft of the syllabus can be found here. Please contact MICDE at micde-contact@umich.edu with any questions.

Software Carpentry workshop at U-M — May 2-3

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A Software Carpentry workshop will be held at the U-M Medical School May 2 and 3. These workshops are free and open to anyone on campus; the sessions are suitable for researchers in the humanities and social sciences. Register here.

This hands-on workshop will cover basic concepts and tools, including program design, version control, data management, and task automation. Participants will be encouraged to help one another and to apply what they have learned to their own research problems.

Who: The course is aimed at graduate students, postdocs, and other researchers across the University of Michigan. You don’t need to have any previous knowledge of the tools that will be presented at the workshop.

Where: Furstenberg 2710 (2nd floor of Med Sci II).

Student groups can access Flux at no charge under Flux Academic Use program

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Undergraduate groups can now access Flux, U-M’s shared computing cluster, at no cost under the new Flux Academic Use program from Advanced Research Computing (ARC). Flux Academic Use aims to provide undergraduates with experience in high performance computing and access to computational resources for their projects; it is not meant for faculty-led research. Jobs submitted under Flux Academic Use will run only when unused cycles are available. To be most efficient, student groups should use short or checkpointed jobs to take advantage of these available cycles. Student groups can also purchase Flux allocations for jobs that are higher priority or time constrained; those allocations can also work in conjunction with the free Flux Academic Use jobs. Undergraduate groups must have a faculty sponsor to be eligible for Flux Academic Use. For more information, or to request time under Flux Academic Use, please email hpc-support@umich.edu.

Midwest Big Data Hub offers early career seed funding to improve data access — April 1, May 1 deadlines

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The Midwest Big Data Hub, an NSF-funded group including U-M’s Michigan Institute for Data Science (MIDAS), is seeking proposals from early career researchers to enhance collaborations with data-producing organizations to improve access to data. Senior researchers are also welcome to apply for funding for activities that bring together data producers and researchers with significant participation from early career researchers.

The goal of the funding, provided by the Computing Community Consortium, is to improve partnerships and collaboration between data producing organizations in industry, government, and academia and researchers. Activities can include workshops, internships, hackathons at universities, data-related competitions, travel grants and lecture series. Awards will range from between $10,000 and $40,000.

Deadlines for applications are April 1 and May 1.

For more information, including how to apply, read the proposal description on the MIDAS website.

MIDAS hosting Data Science Summer Camp for high school students

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The Michigan Institute for Data Science (MIDAS) is hosting a data science summer camp for juniors and seniors in high school, from July 18 – 22, 2016.

Students in the camp, titled “From Simple Building Blocks to Complex Shapes: A Visual Tour of Fourier Series” will create art, diagnose disease, and play detective using the Fourier Series. Students will learn the basic mathematics behind Fourier series and use them to tackle data science problems by starting with simple building blocks and scaling up the complexity. Click to watch our preview video.

Any high school student can apply, with a special focus on Juniors and Seniors. Interest in mathematics and art is strongly encouraged; experience with trigonometry recommended. The camp will be full day, and attendance is expected all five days. Contact the organizers at midas-camp@umich.edu  or visit the camp’s website for more information.

REMINDER: Info Sessions: Graduate programs in computational and data science — Feb. 22, 23

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Learn about graduate programs that will prepare you for success in computationally intensive fields, and enjoy some pizza. Presentations will describe the following programs:

  • The Ph.D. in Scientific Computing is open to all Ph.D. students who will make extensive use of large-scale computation, computational methods, or algorithms for advanced computer architectures in their studies. It is a joint degree program, with students earning a Ph.D. from their current departments, “… and Scientific Computing” — for example, “Ph.D. in Aerospace Engineering and Scientific Computing.”
  • The Graduate Certificate in Computational Discovery and Engineering trains graduate students in computationally intensive research so they can excel in interdisciplinary HPC-focused research and product development environments. The certificate is open to all students currently pursuing Master’s or Ph.D. degrees at the University of Michigan.
  • The Graduate Certificate in Data Science is focused on developing core proficiencies in data analytics: 1) Modeling — Understanding of core data science principles, assumptions and applications; 2) Technology — Knowledge of basic protocols for data management, processing, computation, information extraction, and visualization; 3) Practice — Hands-on experience with real data, modeling tools, and technology resources.

Monday, February 22, 5-6 p.m., Room 2001, LS&A Building, 500 State St. 

Tuesday, February 23, 5-6 p.m., EECS 1200, 1301 Beal Ave. 


  • Krishna Garikipati, Professor of Mechanical Engineering and Mathematics, and Associate Director for Research, Michigan Institute for Computational Discovery and Engineering.
  • Ivo Dinov, Associate Professor of Computational Medicine and Bioinformatics, and Human Behavior and Biological Sciences.
  • Ken Powell, Arthur F. Thurnau Professor of Aerospace Engineering.

There will be time for questions and discussion.

MICDE Seminar: Jim Belak, Lawrence Livermore National Lab, “Bridging Scales within Exascale Materials Co-design Center” — Feb. 5

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As part of the MICDE Seminar Series, Jim Belak of the Materials Science Division at Lawrence Livermore National Laboratory will speak on campus Friday, Feb. 5.

Abstract: The advent of Advanced / Additive Manufacturing and the Materials Genome Initiative has placed significant emphasis on accelerating the qualification of new materials for use in real applications. Within these workflows lies both the engineering scale qualification through building and testing components at scale and full-scale modeling with integrated continuum computer codes and the materials scale qualification through revolutionary methods to non-destructively measure microstructure (3DXRD) and physics specific experiments coupled with meso-scale mechanics simulations of the same physics specific experiment using the same microstructure. This ICME process is one of the use cases that drives the Exascale Materials Co-design Center (ExMatEx). The goal of the Co-design Center is very analogous to the acceleration of new materials deployment within the MGI, rather co-design accelerates the deploying of laboratory concepts for future computer components to enable a productive exascale computer system. To enable better meso-scale understanding in the continuum models, ExMatEx is creating a direct coupling between the continuum integrated code and direct numerical simulation of the meso-scale phenomena. Here we review the ExMatEx project, and its use cases.

Bio: Jim Belak is an Applied Scientist in the Materials Science Division at Lawrence Livermore National Laboratory. His career has centered around the application of High Performance Computing to equilibrium and non-equilibrium problems in Condensed Matter Physics, including: order-disorder phase transition in solids; indentation, metal cutting and tribology of interfaces; shock propagation and spallation fracture; structure and dynamics of grain boundaries and defects in solids; and kinetics of phase evolution in extreme environments. These applications have required the development of new algorithms and application codes for emerging high performance parallel computers and the use of novel x-ray synchrotron techniques (3D x-ray tomography and small-angle x-ray scattering) to guide and validate the simulations. Currently, Jim co-leads the Exascale Co-design Center for Materials in Extreme Environments (ExMatEx).

MIDAS Seminar: Kevin Ward, Executive Director, Michigan Center for Integrative Research in Critical Care, “Data in Motion Phenotyping” — Feb. 5

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MIDAS is proud to announce that Kevin Ward, Professor of Emergency Medicine and Executive Director of the Michigan Center for Integrative Research in Critical Care, and Fast Forward Medical Innovation, will speak at 4 p.m., Feb. 5, 2016, in the Michigan League Ballroom, as part of the MIDAS Seminar Series. All seminars are streamed live (sign in as Guest).