Volume 6, Number 1, March 2009


Users' Bulletin Vol. 6, No. 1, March 16, 2009


Minnesota Supercomputing Institute Users Bulletin

March 16, 2009

Vol. 6, No. 1


Published by the Minnesota Supercomputing Institute

Editor: Tracey A. Bartlett

The Minnesota Supercomputing Institute (MSI) Users Bulletin provides information about news, policies, procedures, and events of interest to users of MSI resources. It is published quarterly.

Be sure to submit your research reports for research that includes use of MSI resources (hardware, software, or user support) in the work reported. Please send your reports tosubmissions@msi.umn.edu, or for more information, see:


Table of Contents for March 16, 2009 MSI Users Bulletin:

1. Regatta to be retired April 1

2. New screen in the LMVL

3. Genome sequencing at the CGL

4. Bioinformatics: Building Bridges symposium

5. MSI to participate in upcoming events

6. Useful links, Quickstart Guides, and email addresses

1. Regatta to be retired April 1: The Regatta/Power4 system will be retired on April 1, 2009 to make way for MSI's newest system, currently in a procurement process. User Support staff have been helping existing Regatta users to migrate their data to other MSI platforms. If you are an existing Regatta user and have any questions, please see our transition page:


for more information about how to move to another MSI system. Details on the new system will be published after the Board of Regents' approval in mid-March.

2. New screen in the LMVL: The LMVL has installed a new screen for the immersive projection system. The screen consists of three plexiglass panels, with each side panel set at a 135-degree angle to the center panel. Replacing the previous six-panel configuration with the new three-panel screen removes the seam from the center of each screen section and provides a more continuous image. An edge-to-edge screen coating produces a 156-degree cone of viewing, providing a high-integrity image even when viewed from an angle far offset from center. New lamps were also installed in the Christie stereo projectors to produce a brighter image.

3. Genome sequencing at the CGL: Working with the Biomedical Genomics Center, MSI is providing a computational infrastructure for University researchers using Roche/454 new generation genome technology. Using the upgraded Roche/454 Titanium, the MSI staff has successfully processed a GS Titanium run on cl1, a new Linux server at the CGL. It generated 1.22 million sequence readings: a total of 500 megabase DNA sequences with an average of 433 base pairs of length. Bioinformatics support from MSI enables University researchers to leverage the advantage of new-generation sequencing technology.

4. Bioinformatics: Building Bridges symposium: The seventh Bioinformatics: Building Bridges symposium will be held on the fourth floor of Walter Library on April 16-17, 2009. As part of this event, MSI will present five tutorials on April 16. The topics include bioinformatics programming, microarray technology, sequence analysis using BLAST, running R applications, and proteomics software. This symposium supports the field of bioinformatics and the University's Bioinformatics Graduate Program. Complete information about the symposium can be found at:


5. MSI to participate in upcoming events:

a. National American Indian Science and Engineering Fair (NAISEF): MSI will have a booth at the NAISEF, which is sponsored by AISES and other organizations. This fair provides an important opportunity for students to do hands-on science; apply their knowledge of math and science; conduct research and collect data; and interact with professional role models in science, mathematics, and engineering. Information can be found at:


b. Design of Medical Devices Conference: MSI will participate in the upcoming Design of Medical Devices conference, to be held on April 14-16, 2009 at the Radisson University Hotel. The conference promotes the medical device industry; provides a forum to bring medical device designers, manufacturers, researchers, and representatives from the public sector together to share perspectives on medical devices; and raises funds from corporate sponsorships to endow graduate fellowships in medical device design. Information about the conference can be found at:


c. Minnesota High Tech Association (MHTA) Spring Meeting: MSI will have a booth at the MHTA Spring Conference on April 15, 2009. The theme of the conference is Leadership Strategies for Today's Uncertain Economy. Information can be found on the MHTA's website:


6. Useful links, Quickstart Guides, and email addresses:

Please be sure to change your password often.

www.msi.umn.edu/hardware/ -- Core Computing Machines

www.msi.umn.edu/labs/bscl/ -- Basic Sciences Computing Laboratory (BSCL)

www.msi.umn.edu/labs/bmsdl/ -- Biomedical Modeling, Simulation, and Design Laboratory (BMSDL)

www.msi.umn.edu/labs/cgl/ -- Computational Genetics Laboratory (CGL)

www.msi.umn.edu/labs/lmvl/ -- LCSE-MSI Visualization Laboratory (LMVL)

www.msi.umn.edu/labs/sdml/ -- Scientific Data Management Laboratory (SDML)

www.msi.umn.edu/labs/sdvl -- Scientific Development and Visualization Laboratory (SDVL)

www.compbio.umn.edu/ -- One-Stop Portal for Computational Biology and Bioinformatics

Quickstart Guides:

www.msi.umn.edu/hardware/calhoun/quickstart.html -- Quickstart Guide for Calhoun (SGI Altix XE 1300 Linux Cluster)

www.msi.umn.edu/hardware/blade/quickstart.html -- Quickstart Guide for the IBM BladeCenter Linux Cluster

www.msi.umn.edu/hardware/altix/quickstart.html -- Quickstart Guide for the SGI Altix

www.msi.umn.edu/hardware/regatta/quickstart.html -- Quickstart Guide for the Regatta (IBM Power4)

Useful email addresses:

help@msi.umn.edu -- for all requests for user assistance (technical help for all users)

projects@msi.umn.edu -- for all questions concerning account renewal, new principal investigators, and service units (administrative help for all users)

accounts@msi.umn.edu -- for all questions and instructions concerning changes in users and accounts for existing users

msisubmissions@msi.umn.edu -- for submission of research reports containing work done using MSI resources

alt-format@msi.umn.edu -- to request access to information in an alternative format for individuals with disabilities