Volume 3, Number 2, June 2006


Minnesota Supercomputing Institute Users Bulletin

June 15, 2006

Vol. 3, No. 2


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 tomsisubmissions@msi.umn.edu, or for more information, see:


Table of Contents for June 15, 2006 MSI Users Bulletin:

1. BladeCenter delivery delayed

2. Staff changes in User Support and Systems Administration

3. Non-renewed accounts to close July 1, 2006

4. 2006 Undergraduate Internship Program

5. New members for MSI Peer Review Panels

6. Computational proteomics support at the Supercomputing Institute

7. New metabolic database search tool, MetaCore, at the CGL

8. MSI support to Academic Health Center's Center for Research in Education and Simulation Technologies (CREST)

9. Useful links, Quick Start Guides, and email addresses

1. The new IBM BladeCenter Linux Cluster will be arriving sometime in August or September.Infrastructure and a test blade of the new system will arrive by July 1st so that the system can be promptly tested and ready for use soon after set up is completed. Those PIs who would normally want to run jobs on the BladeCenter should use MSI's SGI Altix Cluster until the new IBM system arrives. For more information, please contact any of the User Support staff listed at:


2. There have been some staff changes at MSI. Former MSI Chief of Technology Barry Schaudt resigned affective April 14, 2006, and a search is being conducted for a person to fill the related but new position of Systems Administration and Technical Operations Manager. Also, searches for five new User Support staff positions continue. For more information about these positions, please see "Employment Opportunities" at:


3. The user accounts of PIs who have not submitted their Account Renewal Forms will not be accessible after July 1. The deadline for submission was April 15, 2006 to ensure maximum consideration for the awarding of service units (SUs) for the second half of 2006. You can access the Account Renewal Form at:


Submission of the form is required for maintaining access to user accounts, and the form can be submitted late. Please contact Jane Zirbes by phone at 5-0012 or by email at zirbes@msi.umn.edu for more information.

4. The 2006 Undergraduate Internship Program kicked off on June 5. Twenty-three interns are participating this year. Interns work with faculty advisors on projects related to the faculty members’ supercomputing research, and write a report and give a presentation about their work. The program runs 10 weeks, ending on August 11. Interns in this summer's program are funded by an NSF Research Experiences for Undergraduates grant, the NSF Virtual Laboratory for Earth and Planetary Materials grant, the NSF Institute for the Theory of Advanced Materials in Information Technology grant, and by the Supercomputing Institute.

5. New members have been chosen for MSI's Peer Review Panels. At the beginning of April, MSI's Nominating Committee nominated new members for its Supercomputing Resources Peer Review Panel and for its Research Scholarship Peer Review Panel. The new appointments were finalized at the beginning of May. On the Supercomputing Resources Peer Review Panel, Mitchell Luskin (Mathematics) and Fernando Porté-Agel (Civil Engineering) will replace outgoing members Ashley James (Aerospace Engineering and Mechanics) and Dong Wang (Soil, Water, and Climate). On the Research Scholarship Peer Review Panel, Yiannis Kaznessis (Chemical Engineering and Materials Science) will replace outgoing member Renata Wentzcovitch (Chemical Engineering and Materials Science) and Darrin York (Chemistry) will join the panel as a new member. These changes will take place effective September 1, 2006. For more information, please visit:


6. Mass spectrometry has become the leading technology for obtaining information at the necessary levels to better understand protein and cellular function and regulation.  The Supercomputing Institute provides hardware, software, and user support to the proteomics research community so they can efficiently analyze their data from local and remote locations. In particular, the Institute provides support to the Center for Mass Spectrometry and Proteomics (MSP). It has recently allocated 1 Terabyte of disk space for storing mass spectrometry data and will continue to allocate more disk space as needed. In cooperation with the MSP facility, the Institute has developed a Mass Spectrometry Data Management System for distributing raw and processed data to users at the University of Minnesota. See:


The Institute, and particularly the Computational Genetics Laboratory, has invested substantial resources in software to facilitate the necessary support for computational proteomics and now hosts more than ten software applications directly related to the field. The software titles include Mascot, Sequest, Peaks, ProTS Data, Clinprotools, Scaffold, Analyst QS, Bioanalysis, Pro ID, and Pro QUANT.

7. Metabolic database searches play an important role in searching for potential functional involvement of protein(s). These searches are especially useful for post-microarray data analysis.

Users can now access MetaCore through the Computational Genetics Laboratory.  MetaCore is an integrated software suite for functional analysis of microarrays, SAGE, proteomics, and other experimental data. Ingenuity Pathway Analysis (IPA), similar to MetaCore, is also available at the CGL.

8. MSI is supporting Dr. Robert Sweet of the Academic Health Center (AHC) in establishing the Center for Research in Education and Simulation Technologies (CREST). The first surgical simulator developed by Dr. Sweet's group and the Human Interface Technology Lab (HITL) at the University of Washington, TURPSim, was showcased at the American Urological Association conference at Atlanta, Georgia in May. An IRB (Institutional Review Board)-approved validation study was conducted at the conference exhibition. Several surgeons and residents participated as subjects in the study, which was conducted in partnership with Medical Education Technologies, Inc. (METI). Seema Jaisinghani from the MSI User Support group has been working with Dr. Yunhe Shen and Dr. Ann Ooms, both in Dr. Sweet's group, and helped them run the study on the simulator.

9. Useful links, Quickstart Guides, and email addresses

www.msi.umn.edu/general/coremachines.htm -- Core Computing Machines

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

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

www.msi.umn.edu/vwl -- Medicinal Chemistry/Supercomputing Institute Visualization-Workstation Laboratory (VWL)

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

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

www.msi.umn.edu/cbl -- Digital Technology Computational Biology Laboratory (DTCBL)

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

Quickstart Guides:

www.msi.umn.edu/altix/intro -- Quickstart Guide for the SGI Altix

www.msi.umn.edu/power4/quickstart.html -- Quickstart Guide for the IBM Power4

www.msi.umn.edu/netfinity/tutorials/intro.html -- Quickstart Guide for the Netfinity Linux Cluster

www.msi.umn.edu/sdml/intro/ -- Quickstart Guide for the Scientific Data Management Laboratory

www.msi.umn.edu/sdvl/hardware/quantum/quickstart.html-- Quickstart Guide for the Quantum Cube in the Scientific Development and Visualization Laboratory

Useful email addresses:

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

zirbes@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