posted on August 21, 2014

The Office of the Vice President for Research recently announced that a record 15 start-up companies based on University inventions were formed in Fiscal Year 2014, which ended on June 30, 2014. Several of these start-ups are headed up by MSI Principal Investigators. These include:

James Cloyd, Experimental and Clinical Pharmacology (College of Pharmacy): CURx Pharmaceuticals

Allison Hubel, Mechanical Engineering (College of Science and Engineering): Meso-Flow

Larry Wackett, Biochemistry, Molecular Biology, and Biophysics (College of Biological Sciences and Medical School); Michael Sadowsky, Soil, Water, and Climate (College of Food, Agricultural, and Natural Resource Sciences); and colleague Al Aksan, College of Science and Engineering: Minneputa

Michael Garwood, Center for Magnetic Resonance Research (Medical School) and colleague Donald Nixdorf, School of Dentistry: MinnScan

Jian-Ping Wang, Electrical and Computer Engineering (College of Science and Engineering): Niron Magnetics and Zepto Life Technology

John Bischof, Mechanical Engineering (College of Science and Engineering): Vigilant Diagnostics

These start-ups were assisted through the OVPR’s Office for Technology Commercialization. A complete list of start-ups and their descriptions can be found on the OVPR Inquiry blog.


posted on August 19, 2014

The demo license for the MATLAB Distributed Compute Server (MDCS) has been extended to September 17!

The MDCS allows MATLAB jobs to launch parfor and SIMD loops across multiple nodes on Itasca. With MDCS there is no need to run pbsdsh or another parallel shell environment to span nodes. Also, jobs can be interactive or batched, and are controlled from within the MATLAB UI. More information about the software can be found on the MathWorks website

MSI users are invited to test this demo and provide feedback. Please email Evan Bollig at to get a settings file and instructions if you wish to participate. MATLAB jobs running on Itasca will burn SUs at the standard rate of 1.5 CPU hours per SU scaled by the size of your job. (So, using this demo assumes you have enough SUs.) The demo has a 256 concurrent process limit (i.e., 32 nodes), shared by all users.

Your feedback and interest will help MSI decide whether the MDCS is worth pursuing. We would also like to know the upper limit on job size that you need.

Contact Evan ( with any questions.

posted August 15, 2014

On Wednesday, August 20, 2014, from 4:00am to 5:00pm, MSI systems will be part of a construction downtime and MSI staff will perform scheduled maintenance and upgrades to the network and various systems. The construction will be simultaneously mechanical and electrical work. The electrical work will require all MSI systems to be powered-off and unavailable during this period. Some key systems will remain online during the process but user (ssh) access to key systems will not be allowed until the electrical work is complete. The mechanical work will affect only the Itasca system and is expected to last until 5:00pm on August 20 and may be extended should any issues arise.

In addition to the site-wide outage, we will be performing the following updates:
• New resource manager versions for lab queue and Galaxy systems
• All infrastructure Linux systems will be updated and rebooted
• NICE drivers will be upgraded
• Network hardware will be replaced affecting all external network connections

Due to this late August downtime, we will skip the September downtime and our next scheduled maintenance will be on October 1.

Systems status is always available on our Status page.

If you have any questions, please email

posted on August 15, 2014

MSI Principal Investigator Len Kne and a team of graduate students in Geographical Information Science (GIS) have created an app that allows users to evaluate the solar potential of any given location in the state of Minnesota. The web-based app uses Lidar data and GIS technology. It was awarded first place in the Climate Resilience App Challenge at the 2014 Esri User Conference, which was held in July 2014 in San Diego, California.

Kne is on the research staff of the Minnesota Population Center and is the Coordinator of the U-Spatial Initiative. An article about the new app appeared recently on the Rochester website.

posted on August 11, 2014

A paper co-authored by several MSI PIs reveals a relationship between a key cancer-causing gene and another nearby gene that could have implications for treating the disease. The cancer gene, MYC, appears to pair up with one of its neighbors, which allows MYC to spread. The paper appeared in the prestigious journal Nature. The lead author of the paper is PI Anindya Bagchi, an assistant professor in the Department of Genetics, Cell Biology, and Development (College of Biological Sciences; Medical School) and member of the Masonic Cancer Center. The paper is discussed on the U’s Discover blog

Professor Bagchi is using MSI for his research investigating genetics in breast cancer. He was recently interviewed by the College of Biological Sciences (CBS) about his work with students who are discovering the excitement of doing research and making discoveries. The interview can be found on the CBS-Connect blog

Co-authors on the Nature paper include several other MSI PIs: Professor David Largaespada, Assistant Professor Yasuhiko Kawakami, and Associate Professor York Marahrens (all Genetics, Cell Biology, and Development - CBS; Medical School), and Assistant Professor Kathryn Schwertfeger (Laboratory Medicine and Pathology - Medical School). Professors Largaespada and Schwertfeger are also members of the Masonic Cancer Center; Professor Kawakami is a member of the Stem Cell Institute