Open MP Workshop

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ARC-TS and the Scientific Computing Student Club are hosting a satellite site for XSEDE hands-on workshops during this summer. These workshops provide a convenient way for researchers to learn about the latest techniques and technologies of current interest in HPC.

This one-day event will focus on OpenMP.

Please fill out this google form if you are interested in attending either workshop and would like more information. Official registration is done through the XSEDE site and will open soon. Space is limited.

Michigan Biological Software Team to compete at iGEM with MICDE support

By | Educational, General Interest, News, SC2

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.

Big Data: Improving the Scope, Quality and Accessibility of Financial Data

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The Office of Financial Research and the University of Michigan will host a joint conference, “Big Data: Improving the Scope, Quality, and Accessibility of Financial Data” in Ann Arbor, Michigan.  The conference will bring together a wide range of scholars, regulators, policymakers, and practitioners to explore how Big Data can be used to enhance financial stability and address other challenges in financial markets.

[SC2] DEMO: Visualizations on remote resources

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Results of adaptive simulations of a three-dimensional wing undergoing flapping motion in viscous flow. The target output of interest is the lift at the end of the simulation. Tailored meshes are created by increasing the approximation order on selected elements identified by an output-sensitivity error estimate. The resulting output converges much faster in terms of total degrees of freedom used when compared to other adaptive methods, including residual-based adaptation and uniform order refinement.

Results of adaptive simulations of a three-dimensional wing undergoing flapping motion in viscous flow. K. Fidkowski (U-M Aerospace)

One of the advantages of scientific computing research is the ability to use powerful supercomputers from the convenience of your home computer, laptop, tablet, or even phone! In the next SC2 meeting club members will be demonstrating how you can use these remote resources to run and visualize simulations. Additionally, we will be demonstrating the “scientific python” stack (Python, NumPy, Scipy) to duplicate MATLAB functionality with free, open source software.

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Claude E. Shannon Centennial Symposium

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Claude E. Shannon was born in Petoskey, MI and grew up in Gaylord, MI. After graduating from the University of Michigan with degrees in electrical engineering and mathematics in 1936, he went on to publish a series of papers that laid the foundation for modern information theory. The University of Michigan is celebrating the 100th birthday of Claude E. Shannon, widely recognized as the father of information theory with a Shannon Centennial Symposium on Sept. 16, 2016.

The symposium will consist of two poster sessions and four plenary talks by eminent leaders in the field of information theory. (Promotional poster can be downloaded here.)

Registration is required; to register and to sign up to participate in the poster session, please fill out this form.

Space is limited, so please register early! The deadline for poster submission is Sept. 9. Posters will be selected based on submitted title, abstract and relevance to Shannon’s scientific contributions.

Plenary speakers are:


The Shannon Centennial Celebration is supported by the U-M College of Engineering, the ECE division of the U-M EECS Department, the Michigan Institute for Data Science (MIDAS), and the IEEE Information Theory Society.

The co-organizers are Hye Won Chung, Al Hero, David Neuhoff and Sandeep Pradhan.

miRcore’s high school biotechnology camp a success

By | Educational, General Interest, News

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.

HPC Summer Bootcamp, presented by XSEDE and the Pittsburgh Supercomputing Center

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University of Michigan Satellite Site is hosted by the SC2

Please join us in this 4 day event to learn about hybrid computing including MPI, OpenMP, OpenACC and accelerators.

The event will conclude with a special hybrid exercise contest that will challenge the students to apply their skills over the following 3 weeks and be awarded the Third Annual XSEDE Summer Boot Camp Championship Trophy. The SC2 team is looking forward to this competition. It will be a fun way to learn about HPC and interact with us!

Please visit the official event page for more information and registration! (Look for the University of Michigan specific site)