Volume 1, Number 1, December 2004

Minnesota Supercomputing Institute Users' Bulletin

December 15, 2004

Vol. 1, No. 1


Published by the Minnesota Supercomputing Institute

Editor: Tracey 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 sent quarterly to all users. To view this publication online, go to:


Be sure to submit your research reports for research that includes use of MSI resources in the work reported.  Please send your reports to msisubmissions@msi.umn.edu, or for more information, see:


Table of Contents for December 15, 2004 MSI Users' Bulletin:

1. New medicinal chemistry software in MSI laboratories

2. Software for proteomics

3. New visualization/computation server

4. New 3D LCD display

5. Deadline for submission of research scholarship nominations

6. Deadline for submission of undergraduate internship applications

7. Useful links

1. MSI has recently acquired a state-of-the-art software package called Sybyl for drug design and cheminformatics research. This software enables researchers to study in atomistic details interactions between drug molecules and proteins, as well as screen large chemical databases for alternative drug leads. Sybyl will be available in the SDVL, BSCL, VWL, and CGL on all SGI and Linux workstations.

2. The Computational Genetics Laboratory (CGL) has teamed with the Mass Spectrometry Consortium for the Life Sciences (MSCLS) to provide software and database support for Proteomics research. The CGL already provides support for Bioinformatics and Genomics researchers in the State of Minnesota and has added two more software packages, ProTS Data from Efeckta and Mascot from Matrix Science, for Mass Spectrometry. These packages will enhance research in Proteomics, as well as Bioinformatics and Microarray Data Analysis.

3. The Scientific Development and Visualization Laboratory (SDVL) recently purchased a SunFire V440 Visualization/Computation Server. It is a 4-processor shared memory system with 16 GB of memory. Each processor is a 1.28GHz UltraSPARC IIIi. The system has a Sun XVR-1200 graphics accelerator for high-quality visualization.

The system will help users to run large memory visualizations applications interactively. The resource will especially benefit researchers working in areas of computational fluid dynamics and other engineering disciplines.

4. The SDVL also purchased a 3D LCD display called True View MkIII from Ampronix Inc. This 20" display allows glasses-free real-time viewing of 3D images. The display is attached to a dual 3.2 GHz processor workstation with NVIdia Quadro FX 3400 graphics and runs Windows XP. The technology will assist researchers in visualizing volumetric data from various fields in medicine, engineering, seismology, geochemistry, atmospheric research, fluid dynamics and molecular structures.

5. Deadline for submission of research scholarship nominations:
Nominations for MSI research scholarships to do supercomputing research at the University of Minnesota must be received by January 15, 2005 for scholarships in the following fiscal year (July 1 to June 30). The current upper limit on research scholarship grants is $23,000 (including fringe benefits), with a required match of no less than 1:1 from non-State funds.  All nominations must be made by a University of Minnesota faculty member. The Research Scholarship Peer Review Panel makes research scholarship awards based upon a competitive review of faculty-initiated nominations. Nominees for research scholarships are expected to hold the Ph.D. degree and usually are considered potential postdoctoral research associates. More senior visitors may also be nominated. The review criteria for this program are available on the World Wide Web at:


or from Bill Hellriegel, at (612) 624-1356 or hellr@msi.umn.edu.

Late nominations cannot be accepted.

6. Deadline for submission of undergraduate internship applications:
Deadline for applications is February 28, 2005 for full-time, 10-week internships, running June 6 - August 12. 

The focus of the program is the application of computational approaches and visualization methods to supercomputing research, including digital simulation and advanced computation and all aspects of high-performance computing and scientific modeling and simulation as well as graphics, visualization, informatics, and high-performance network communications.

Interns work with faculty members and their research groups on projects using high-performance computing environments to address problems in science and engineering that could not otherwise be attempted. This program provides an opportunity for a challenging and enriching educational experience for undergraduate students interested in pursuing graduate or professional education.

The stipend provided is $4,800, and interns are responsible for their own travel and living expenses. Interns must be undergraduates at the time of the internship and must be citizens or permanent residents of the United States and its possessions.

Projects are available in the following areas:

Aerospace Engineering and Mechanics; Astronomy; Biochemistry; Biomedical Engineering; Chemical Engineering; Chemistry; Civil Engineering; Electrical and Computer Engineering; Geology and Geophysics; Laboratory Medicine and Pathology; Materials Science; Mathematics; Mechanical Engineering; Molecular Biology; Pharmaceutics; Physics

For more information, please visit:


7. Useful links:

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

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

www.msi.umn.edu/llsda -- Laboratory for Large-Scale Data Analysis (LLSDA)

Useful email addresses:

help@msi.umn.edu -- for all requests for user assistance

zirbes@msi.umn.edu -- for all questions concerning account renewal, new principal investigators, and service units

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

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

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