MICDE Annual Symposium – Poster Competition Winners

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Fifty-six posters were submitted to the 2017 MICDE symposium poster competition.

Last week’s MICDE annual symposium included a poster competition for students and postdocs. The event featured 56 posters that highlighted the interdisciplinary nature of the institute. (Some of the posters were described in a story in the Michigan Daily). All of the titles and abstracts submitted are in this spreadsheet.

Victor Wu, Ph.D. Candidate in the department of Industrial and Operations Engineering, won first place and $500 for his poster “Multicriteria Optimization for Brachytherapy Treatment Planning.” Wu and co-authors Epelman, Sir, Pasupathy, Herman and Duefel, introduced an efficient Pareto-style planning approach and intuitive graphical user interface that enables a planner or physician to directly explore dose-volume histogram metric trade-offs for brachyotherapy treatment – a common method for treating cancer patients with radiation.

Sambit Das, Ph. D. Candidate of Mechanical Engineering, earned second place and a $250 prize for his work on “Large Scale Electronic Structure Studies on the Energetics of Dislocations in Al-Mg Materials System and Its Connection to Mesoscale Models

Third place, also with a $250 prize, went to Joseph Cicchese, Ph. D. Candidate in the Department of Chemical Engineering, for his poster titled “How to optimize tuberculosis antibiotic treatments using a computational granuloma model. Cicchese and co-authors Pienaar, Kirschner and Linderman, proposed a method of combining an agent-based and multi-scale model of tuberculosis granuloma formation and treatment with surrogate-assisted optimization to identify optimal tuberculosis treatments.

 

SC2 presents the 2017 NVIDIA Visualization Challenge

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Courtesy of S. Alben (Mathematics)The Scientific Computing Student Club (SC2) and NVIDIA are presenting a Visualization Challenge, with prizes including two NVIDIA and sponsorship to enter present your results at the Scientific Visualization Showcase at Supercomputing ’17. If you are an U-M student doing research that involves coding, simulations, or data analysis, chances are you have a lot of data to show. But what is the best way to do it? What is the best way to reach your audience and convey your message? As the old adage says “a picture is worth a thousand words”, so making your data interactive, showing it in 3D, or making a video are a few options.

More information and registration at micde.umich.edu/sc2/challenge2017. Registration deadline is March 1, 2017.

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Michigan Biological Software Team to compete at iGEM with MICDE support

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MICDE is pleased to announce its support of the Michigan Biological Software Team (MiBioSoft), for its attendance at the 2017 International Genetically Engineered Machine (iGEM) competition in Boston.

Founded in 2014, MiBioSoft is a student-run organization at the University of Michigan that develops software for use in scientific research, with a focus on synthetic biology. It seeks to provide its members with opportunities to not only improve their skills as software designers, but also to improve their communication and management skills by bringing together students from a variety of backgrounds including Biology, Mathematics, Computer Science, and Chemistry.

MiBioSoft competes annually in the software track of the iGEM competition, where research teams from around the world present their results over the course of a three-day conference. During the first two years at the competition, the team was awarded bronze medals. In 2016, MiBioSoft received Best Software Project award as well as a gold medal for their protocol catalog, ProtoCat, in a competition that featured over 300 teams from more than 40 countries, with more than 5,000 participants in total.

About Protocat

Protocat is protocol catalog software developed by MiBioSoft students to address the issue of reproducibility in synthetic biology. Like many innovative ideas, it began because of a problem. Studies have estimated that only 10-25% of published scientific results are reproducible. A 2014 survey conducted by the Michigan Software team confirmed that the repeatability problem exists in synthetic biology, with every scientist surveyed reporting prior struggles with replicating protocols.

ProtoCat 3.0 is a free database of crowd-sourced protocols designed to make existing protocols more repeatable and enable more accurate computational models of biological systems. MiBioSoft believes this can most efficiently be accomplished with a commitment to open source protocols and a broader more active community of digital troubleshooters. ProtoCat 3.0 works to establish such a community by giving anyone with an internet connection or smartphone access to a repository of synthetic biology protocols collected from all over the world. Additionally, ProtoCat 3.0 encourages the development of higher quality, more repeatable protocols by allowing users to document, rate, review, and edit existing methods.

New MICDE Catalyst Grants to fund research projects in computational science

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micde2016symposiumfrontpageThe Michigan Institute for Computational Discovery & Engineering (MICDE) seeks proposals for innovative research projects in computational science that combine elements of mathematics, computer science, and cyberinfrastructure. Of interest is computational science research in any emerging area, including but not limited to (a) applications such as neuroscience, ecology, environmental science, evolutionary biology, human-made complex systems, urban infrastructure and energy; and (b) frameworks for scientific software, and exascale computing. Priority will be given to high-impact projects with potential to attract external funding. MICDE expects to fund 3-4 one-year projects at up to $100,000 each.

An informational session will be held on Thursday, Nov. 10, 2016 at 2:00 p.m. in Room D of the Michigan League (911 N. University).

For more information go to http://micde.umich.edu/grants/catalyst-grants/

MICDE affiliated faculty Monica Valluri (Astronomy) recognized for her outstanding research and teaching achievements

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valluriMonica Valluri, a Research Associate Professor in the Department of Astronomy, has been honored with the U-M Research Faculty Achievement Award for her outstanding research and teaching career in theoretical galaxy dynamics. She uses numerical calculations and simulations to probe galactic phenomena, including supermassive black holes and dark matter halos,two types of invisible matter whose presence is inferred primarily from their gravitational effects on stars and other visible matter.

Valluri earned a Ph.D. in astrophysics at the Indian Institute of Science in Bangalore, did postdoctoral research at Columbia University and Rutgers University, and joined the U-M faculty in 2007.

In addition to developing a more accurate method to determine the masses of SMBH, Valluri has transformed our understanding of galactic bars — elongated cigar-shaped clusters of orbiting stars that exist in many spiral galaxies, including the Milky Way. She demonstrated the traditional view of how stars move in bars is incomplete and that neglecting the effects of galactic bars can cause large errors in the measurement of black hole masses and host galaxy properties. Her work soon will be applied to data being gathered by the European Space Agency’s Gaia space observatory and is expected to verify or refute important predictions of the dominant paradigm regarding the nature of dark matter.

Valluri has published 42 journal articles. In addition to creating and teaching undergraduate astronomy and earth and space science courses, Valluri has taught at the Michigan Math and Science Scholars camp for high school students on a number of occasions. She has served on five doctoral committees and mentored 17 undergraduates. She also founded and organizes Conversations on Equity and Inclusion in Astrophysics and has served on the astronomy department’s curriculum committee and Michigan Institute for Research in Astrophysics planning committee. Valluri is chair of the American Astronomical Society Division of Dynamical Astronomy and a member of the Astronomical Society of India and International Astronomical Union.

With information from the record.umich.edu

[SC2] HPC resources available to U-M students

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Brock Palen, Associate Director of Advanced Research Computing-Technology Services, joined the SC2 to talk about all the high performance computing (HPC) resources available to U-M graduate and undergraduate students. A summary of his presentation is here.

Resources:

Available at/through Michigan

  1. Flux for Undergraduates: Undergraduates can use the local flux computing cluster FOR FREE! Please visit the page for more information
    • ARC-Connect: use for Jupyter notebooks and VNC (remote desktop) access of flux resources, useful for remote visualization of big data or just getting a feel for working on linux and flux.
  2. Amazon Web Services: Michigan students get $100/year in amazon web services. While not as cost-effective for some things, very good resource to be aware of.
  3. Hadoop: Michigan’s Hadoop cluster is available for free (I believe you have to apply/demonstrate a need, but you don’t have to pay if it’s accepted). This upcoming workshop will go over the basics, read more if you are interested.

Available via Grant

Brock has an up-to-date webpage linking to and detailing various resources you can apply for.

Highlights:
  1. XSEDE:
    • Startup and teaching allocations are available continuously
    • Research allocations accepts 4x/year
  2. Great Lakes Consortium:
    • Alternate way to get some time on Blue Waters
  3. Amazon/Microsoft/Google:

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Research highlights: Running climate models in the cloud

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Xianglei Huang

Can cloud computing systems help make climate models easier to run? Assistant research scientist Xiuhong Chen and MICDE affiliated faculty Xianglei Huang, from Climate and Space Sciences and Engineering (CLASP), provide some answers to this question in an upcoming issue of Computers & Geoscience (Vol. 98, Jan. 2017, online publication link: http://dx.doi.org/10.1016/j.cageo.2016.09.014).

Teaming up with co-authors Dr. Chaoyi Jiao and Prof. Mark Flanner, also in CLASP, as well as Brock Palen and Todd Raeker from U-M’s Advanced Research Computing – Technology Services (ARC-TS), they compared the reliability and efficiency of Amazon’s Web Service – Elastic Compute 2 (AWS EC2) with U-M’s Flux high performance computing (HPC) cluster in running the Community Earth System Model (CESM), a flagship climate model in the U.S. developed by the National Center for Atmospheric Research.

The team was able to run the CESM in parallel on an AWS EC2 virtual cluster with minimal packaging and code compiling effort, finding that the AWS EC2 can render a parallelization efficiency comparable to Flux, the U-M HPC cluster, when using up to 64 cores. When using more than 64 cores, the communication time between virtual EC2 nodes exceeded the communication time in Flux.

Until now, climate and earth systems simulations had relied on numerical model suites that run on thousands of dedicated HPC cores for hours, days or weeks, depending on the size and scale of each model. Although these HPC resources have the advantage of being supported and maintained by trained IT support staff, making them easier to use them, they are expensive and not readily available to every investigator that needs them.

Furthermore, the systems within reach are sometimes not large enough to run simulations at the desired scales. Commercial cloud systems, on the other hand, are cheaper and accessible to everyone, and have grown significantly in the last few years. One potential drawback of cloud systems is that the user needs to provide and install all the software and the IT expertise needed to run the simulations’ packages.

Chen and Huang’s work represents an important firstxiangleihuangpost2016 step in the use of cloud computing in large-scale climate simulations. Now, cloud computing systems can be considered a viable alternate option to traditional HPC clusters for computational research, potentially allowing researchers to leverage the computational power offered by a cloud environment.

This study was sponsored by the Amazon Climate Initiative through a grant awarded to Prof. Huang. The local simulation in U-M was made possible by a DoE grant awarded to Prof. Huang.

Top image: http://www.cesm.ucar.edu/

2015-2016 Education Snapshot

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Students at the U-M satellite site of the XSEDE 2016 Summer Bootcamp

We have over 80 students between our Ph.D. in Scientific Computing and the Graduate Certificate in Computational Discovery and Engineering. The students come from five different schools and colleges, and 30 percent are women. We also have partnered with the Multidisciplinary Design Program to offer our Masters students the experience to work on industrial projects and gain practicum credits.

Our faculty have designed two courses that are being offered for the first time: Methods and Practices of Scientific Computing in Fall 2016 and Data-Driven Analysis and Modeling of Complex Systems in Winter 2017. Methods and Practices of Scientific Computing has gathered a tremendous amount of interest, and very quickly was over-subscribed. Data-Driven Analysis and Modeling of Complex Systems is a fast paced research area that combines scientific computing with big data to improve the existing models’ accuracy and representation of physical and biological systems.

Scientific Computing Student Club social gathering

Scientific Computing Student Club social gathering

We have brought a large community of students together by sponsoring and helping found the Scientific Computing Student Club. Its goal is to become a place for all students that use or want to use high performance computing to meet, share ideas, and find peer-to-peer help. It started in February, with social gatherings, talks from expert speakers, and more. The club has nearly 200 members, including undergraduates, graduate students, and postdocs from six U-M schools and colleges.

2015-2016 Outreach and Industrial Engagement Snapshot

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High school students at miRcore’s GIDAS 2016 Biotechnology Summer Camp working on Flux

We have been working closely with miRcorea nonprofit that supports genetics research. MICDE sponsors compute cycles on Flux for high school students learning how to conduct computational biology research. We have also approached the Society of Women Engineers, U-M chapter, with the goal of  promoting scientific computing through their outreach programs.  

Intel, Cray and Altera experts talking about FPGAs and Scientific Computing

 

 

Our connections to industry have increased and we are constantly exploring new opportunities. Our ConFlux cluster architecture was designed in collaboration with IBM’s experts, and our work with them still continues. In May, MICDE hosted an internal workshop on Field Programmable Gate Arrays (FPGAs) in collaboration with experts from Intel and Cray. We have established a software partnership with MSC Software to enable access for MICDE student projects. Together with the U-M Business Engagement Center, we are creating an affiliates program for companies to invest in our research.

 

 

2015-2016 MICDE Research Snapshot

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Professor Karthik Duraisamy (U-M Aerospace Engineering) demonstrates data-driven turbulence modeling.

The Center for Data-Driven Computational Physics was established as a place to concentrate data-driven modeling research across campus. Its activities are focused on ConFlux, a $3.5M groundbreaking cluster funded by NSF with a unique architecture that connects big-data with traditional HPC clusters. ConFlux went online in April, and several teams are already using it, with five projects participating, totaling more than $3M to advance data-driven modeling. Soon, we expect to announce even more successes that are directly attributable to our pioneering role in this research area. 

The Center for Network and Storage-Enabled Collaborative Computational Science was established to tackle the challenges of extracting scientific results collaboratively from large, distributed or diverse data. This research center is a product of the Open Storage Research Infrastructure (OSiRIS), a $5M multi-institutional NSF investment, and is led by MICDE affiliated  research faculty Shawn McKee.

We hosted 16 internationally known speakers in our seminar series, and had a very successful symposium. With speakers including NSF’s ACI Director Irene Qualters, Tom Hughes from ICES, James Sethian from UC Berkeley, Charbel Farhat from Stanford, and Peter Haas from IBM, these events outlined top priorities in our fields, latest research and computing infrastructure, and increased  awareness of the quality and trend-imposing nature of research activities going on at U-M.

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Jim Belak (Lawrence Livermore National Laboratory) delivers a talk titled “Preparing for the Future of Computing: Bridging Scales within the Exascale Materials Co-design Center” as part of MICDE Winter 2016 Seminar Series.

MICDE is coordinating or supporting several large proposal submissions to federal agencies. We offer institutional support and our established educational programs to the faculty teams writing these grants. With the backing of our parent unit, Advanced Research Computing, and their technical and consulting services (ARC-Technology Services, and Consulting for Statistics, Computing and Analytics Research), our proposals have proven stronger by virtue of this support in place behind them.

MICDE also is working with the academic units at U-M to identify compelling new directions for hiring faculty who will drive computational science in the future, and supporting these hiring processes. Many of these blue-sky ideas have come from thematic, faculty-led workshops, which we will continue to organize.