posted on May 8, 2014

The College of Science and Engineering held the Grand Opening of their newest building, the Physics and Nanotechnology Building, on April 24, 2014. This building provides office and lab space to the School of Physics and Astronomy and the Minnesota Nano Center.

The University’s Discover blog ran a story about the building and some of the research that will benefit from the new facilities. MSI Principal Investigators Professor Shaul Hanany (Minnesota Institute for Astrophysics) and Professor C. Daniel Frisbie (Chemical Engineering and Materials Science) are quoted.

posted on May 7, 2014

The Minnesota Medical Foundation’s Medical Bulletin recently published a story describing research being performed at the University of Minnesota’s Leatherdale Equine Center. The staff at the Equine Center includes MSI Principal Investigators from the College of Veterinary Medicine who use MSI resources to support this research. The work being done there will not only help horses, but may also provide insights to human disease.

Associate Professor Molly McCue (Veterinary Population Medicine) studies equine genomics and is using MSI for several projects, including genome-wide association studies, developing new SNP genotyping arrays for the horse, and using RNA-seq to transcriptome and gene-expression analysis. Professor Jim Mickelson (Veterinary and Biomedical Sciences) studies heritable disorders in horses and dogs and is using advanced software available through MSI, including the Galaxy suite. Professors McCue and Mickelson both have published numerous papers that include research performed using MSI.

posted on May 6, 2014

The Virtual School of Computational Science and Engineering (VSCSE) is hosting two courses this summer. These courses are open to graduate students, post-docs, and young professionals who want to expand their skills with advanced computational resources. The courses are offered at institutions around the country, allowing participants to go to the most convenient location.

Descriptions of the courses are shown below. You can register at the XSEDE portal. Questions can be mailed to sent to the VSCSE organizing team at


Summer 2014 VSCSE Courses

Summer School 2014 Website

Harness the Power of GPUs: Introduction to GPGPU Programming (June 16 - 20, 2014)

From the VSCSE website: GPGPU Programming is a mixture of lectures and labs and introduces all levels of parallelism as well as common approaches for parallelization in order to achieve the following goals: Better utilization of the GPUs by enabling more scientists to use them, better understanding of the efficiency in the GPU utilization by the application developers and a higher job throughput by enabling more resources and shortening job runtimes. In addition, participants will understand and avoid the common pitfalls of parallel computing, learn CUDA and OpenACC, understand the basic principles of data parallel computing, tap into enormous computing power, even on a laptop, and speed up research.

Data Intensive Summer School (June 30 - July 2, 2014)

From the VSCSE website: The Data Intensive Summer School focuses on the skills needed to manage, process and gain insight from large amounts of data. It is targeted at researchers from the physical, biological, economic and social sciences that are beginning to drown in data. We will cover the nuts and bolts of data intensive computing, common tools and software, predictive analytics algorithms, data management and non-relational database models. Given the short duration of the summer school, the emphasis will be on providing a solid foundation that the attendees can use as a starting point for advanced topics of particular relevance to their work.



posted on May 5, 2014

On Wednesday, May 7, from 04:00 - 15:00, MSI staff will perform scheduled maintenance and upgrades to the network and various systems.

During this maintenance period, we will be performing the following updates:

• The MSI central filesystem, Panasas, will be upgraded to the latest software version. Clients will also be upgraded during this maintenance period. Most MSI resources will be unavailable during this period. 
• NX, the no-machine server, will be upgraded to the latest version.
• MSI printers will be unavailable as the service migrates to a new instance.
• Itasca will be unavailable for system updates of core services and to physically move some systems.
• Calhoun will be unavailable for system kernel updates.

Systems status is always available on our Status page.

If you have any questions, please email


posted on April 28, 2014

MSI held its Fifth Annual Research Exhibition on April 24, 2014. This event showcases research being performed using MSI resources and includes a poster competition.

poster presenters at Research Exhibition

We had 44 posters submitted to the Exhibition this year, in a wide variety of disciplines. Posters were judged in two categories, Biological and Medical Sciences, and Physical Sciences and Engineering. The winners in the competition received travel awards made possible by generous donations from our sponsors: Matrix Integration, a partner of HP; SGI in partnership with Comnetco; and Cray.

Pictures of the prize winners can be found on the event webpage.



Grand Prizes ($1,500 travel award)

Grand Prize Winner, Biological and Medical Sciences:

Inferring gene regulatory networks in cardiac differentiation by integrating temporal RNA-seq and ChIP-seq data
Lead author: Wuming Gong
MSI Principal Investigator: Daniel Garry (Medicine)
Award Sponsor: Cray

Grand Prize Winner, Physical Sciences and Engineering:

Multi-scale mechanical modeling of the Pacinian corpuscle
Lead author: Julia Quindlen
MSI Principal Investigator: Victor Barocas (Biomedical Engineering)
Award Sponsor: Matrix Integration, a partner of HP


Finalist Prizes ($1,000 travel award)

Finalists, Biological and Medical Sciences:

Impulsivity, adolescence, and reward-related brain activation: A monozygotic twin fMRI study
Lead author: Merav Silverman
MSI Principal Investigator: Kathleen Thomas (Institute of Child Development)
Award Sponsor: Matrix Integration, a partner of HP

Fast, fully Bayesian spatiotemporal inference for fMRI data
Lead author: Donald Musgrove
MSI Principal Investigator: John Hughes (Biostatistics)
Award Sponsor: SGI in partnership with Comnetco

Finalists, Physical Sciences and Engineering:

Using high performance computing to examine the effects of thermal gradients in carbonate CCUS reservoirs
Lead author: Benjamin Tutolo
MSI Principal Investigator: Martin Saar (Earth Sciences)
Award Sponsor: Matrix Integration, a partner of HP

1D nanodusty plasma sectional model with pulsing for the study and control of particle generation and growth
Lead author: Carlos Larriba-Andaluz
Presenting author (pictured): Romain Le Picard
MSI Principal Investigator: Steven Girshick (Mechanical Engineering)
Award Sponsor: SGI in partnership with Comnetco


Thank you to our judges!

Kevin DorfmanChemical Engineering and Materials Science

Tim GriffisSoil, Water, and Climate

George KarypisComputer Science and Engineering

Dan KnightsComputer Science and Engineering

Kelvin LimPsychiatry

Chad MyersComputer Science and Engineering


Refreshments were sponsored by Cray and by Matrix Integration, a partner of HP.