posted on October 7, 2013

An MSI Principal Investigator is part of a new project to study diagnostic methods and treatments for meningitis. The University of Minnesota Medical School’s Division of Infectious Diseases and International Medicine have received a $3.2 million grant for this project. They will partner with Uganda’s Makerere University, with whom the U has been working for nearly ten years. The University’s story can be found in the People section of the University Relations website (October 2, “$3.2 million grant to diagnose/treat meningitis”).

Associate Professor Kirsten Nielsen (Microbiology, Medical School/College of Biological Sciences) is one of the collaborators on the project to study how sertraline, an antidepressant with antifungal properties, can be used to treat cryptococcal meningitis, which is caused by a fungal pathogen. Professor Nielsen uses MSI to study how the fungus Cryptococcus neoformans is able to cross the blood-brain barrier.

posted on September 30, 2013

On Wednesday 2 October 2013, 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:

  • Network firmware updates and modifications will be performed affecting internal and external connectivity for up to 1 hour
  • Koronis will be offline for system maintenance
  • Cascade will be unavailable (system updates)
  • MSI login nodes (including NX) will be rebooted and patched
  • Hosted websites will be unavailable (disk migration to the Panasas storage system)
  • Galaxy will be offline for system maintenance


Systems status is always available on our Status page.

Please email if you have any questions.


posted September 24, 2013

Several MSI PIs have been awarded patents over recent months. These PIs are among a large number of University of Minnesota faculty receiving patents, as shown in the OVPR Research blog’s story, “Recent Patents Roundup.”

Professor Michael Murtaugh (Veterinary and Biomedical Sciences), and colleague: Identifying Virally Infected and Vaccinated Organisms

Professor Murtaugh and his group use MSI resources to support their investigations of molecular mechanisms of disease resistance in swine, with particular attention on persistent viral infections and enteric immunity.

Professor Marc Hillmyer (Chemistry) and colleague: Nano-structured Polymer Composites and Process for Preparing Same

Professor Hillmyer’s group is using MSI to study poly(thienylene vinylenes), a photoactive polymer that can be used in organic photovoltaics.

Professor Carston Wagner (Medicinal Chemistry): Necleosides with Antiviral and Anticancer Activity

Professor Wagner uses MSI to model and design protein-protein interfaces.

Professor Perry Li (Mechanical Engineering): Open Accumulator for Compact Liquid Power Energy Storage

Professor Li’s group uses computational fluid dynamics (CFD) methods to develop innovative fluid power components and to develop an efficient compression/expander for compressed air energy storage. The CFD and heat-transfer studies allow the group to gain understanding of the physics and lead to improved designs.

Professor Ned Mohan (Electrical and Computer Engineering) and colleagues: Soft Switching Power Electronic Transformer

Professor Mohan’s group uses finite-element analysis programs available through MSI for their design projects.

Professor Friedrich Srienc (BioTechnology Institute): Systems and Methods of Analyzing a Particulate

Professor Srience uses MSI to run elementary mode analyses of metabolic networks. These analyses are highly computationally intensive, and the Srienc group is working with MSI staff to parallelize the algorithms.

Professor Daniel Voytas (Genetics, Cell Biology, and Development): TAL Effector-medicated DNA Modification (three patents)

Professor Voytas’s Zinc Finger Database, a web-accessible database that houses information on individual C2H2 zinc fingers and engineered zinc finger arrays, is housed at MSI.

Associate Professor Chengguo Xing (Medicinal Chemistry) and colleague: Therapeutic Compounds

Professor Xing’s group uses MSI’s computational resources and software for pathway analysis to study drug resistance in cancer, especially leukemia.


posted September 19, 2013

St. Anthony Falls Laboratory announced recently that they are collaborating with industry on a project to harness the power of the East River in New York City. This effort, which is being funded by a two-year grant from the National Science Foundation, will involve high-performance computational modeling that will further a deeper understanding of how turbines work in real-life aquatic environments. The University's press release can be read on the University News website.

Professor Fotis Sotiropoulos, SAFL Director, is the project leader for this research. He and his research group in the Computational Hydrodynamics and Biofluids Lab use MSI resources to create high-resolution, fluid-structure interaction CFD models. These models are used for a wide variety of simulations of fluid flow. The simulations for the East River project will be performed using MSI’s high-performance computers.



posted on September 17, 2013

The Department of Biomedical Engineering, in the College of Science and Engineering, announced recently that they had a “Summer of Grants” in their department – several of their faculty were awarded grants from various funding agencies. Some of these faculty are MSI Principal Investigators and the grants will support research that they are performing at MSI.

Professor Victor Barocas (MSI Fellow) was awarded three grants. One, from the National Institutes of Health (NIH), funds a collaborative project with the University of Pennsylvania (Philadelphia, Pennsylvania) and Rensselaer Polytechnic Institute (Troy, New York). The Barocas group will study how certain ligaments in the spine respond to normal and abnormal loads, which could eventually help us understand spinal injuries and pain. The second grant, this one from the National Science Foundation (NSF), will fund a project to determine how different structural proteins contribute to the function and dysfunction of the filtration apparatus in the kidney and could contribute to our knowledge of kidney disease. Finally, Professor Barocas received a four-year extension of NIH funding for his long-term research into the mechanical behavior of bio-artificial tissues.

Professor Barocas and his group use MSI resources for their computer models of tissues. Systems they have studied and continue to study include a collagen gel model system and co-gels of collagen with fibrin, agarose, and hyaluronic acid. The computer models are also being applied to tissues such as ligaments and blood vessels.

Assistant Professor Shai Ashkenazi received two grants this summer. The first, a grant from NIH, will fund a collaborative project with faculty from the Department of Chemical Engineering (College of Science and Engineering) and Department of Laboratory Medicine and Pathology (Medical School). This project will develop a new method for non-invasive, photoacoustic imaging of Maxtrix Metalloproteinases (MMPs) activity in tissue. MMPs are linked to cancer metastatsis, among other diseases. This method might lead to better, more individualized diagnoses and treatments for cancer patients. The second award, from NSF, will develop Optical Micromachined Ultrasound Transducers (OMUT) technology. The researchers are developing ultrasound probes for high-resolution imaging that can be mounted on the tip of a needle.

Professor Ashkenazi uses MSI resources to run molecular dynamics simulations. These simulations help the research group in their work to design molecular probes.

Assistant Professor Pat Alford received funding from NIH to study whether the changes in vascular smooth muscle cells, caused by disease or vascular stents, can result in degraded ability of those muscles to contract. Professor Alford’s group uses software available through MSI as part of their research into the mechanical properties of tissues.

Professor Dave Odde received a new grant from the National Cancer Institute, a part of NIH, for a collaborative project with the Cleveland Clinic in Cleveland, Ohio. The researchers will develop a computer simulator to show how brain cancer cells invade tissue, which may result in the creation of new therapies. Professor Odde uses MSI resources for Monte Carlo simulations of various cytoskeletal and signaling processes involved in cell division and growth.