Volume 3, Number 4, December 2006



Minnesota Supercomputing Institute Users Bulletin

December 15, 2006

Vol. 3, No. 4


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 December 15, 2006 MSI Users Bulletin:

1. New Software at the CGL

2. GeneData Expressionist migration

3. IBM BladeCenter updates

4. 2007–08 Research Scholarship application deadline

5. 2007 Undergraduate Internship Program application deadline

6. Review of MSI's services and structure

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

1. Computational Genetics Lab updates:

a. Sequence Data Management System: The Supercomputing Institute has developed and deployed a Sequence Data Management System (SDMS). This system is operated by the Sequencing Facility at the Biomedical Genomics Center (BMGC) for the distribution of genomics sequence and related data to researchers at the University of Minnesota. This Web-based system uses the University of Minnesota Internet ID (x.500) for authentication. Users can log in to the system and download sequence data files individually or in batch zipped format. From the beginning of its operation in March 2006 through November 2006, approximately 570 users have made use of this system. For more information about the SDMS, visit:


In addition, there are many sequence analysis software applications available at the Supercomputing Institute including widely used ones such as GCG, DNAStar, MacVector, and Sequencher.

b. New Software—Flowmapper and Newbler Assembler for the GS-20 Genome Sequencer:Flowmapper and Newbler Assembler are available at both the Computational Genetics Lab (CGL) and the Scientific Data Management Lab (SDML). They were developed by 454 Life Sciences, an ultra-high-throughput automated DNA sequencing system, for sequencing analysis related to the sequence data generated by GS-20, the ultra-high-throughput Genome Sequencer. FlowMapper can be used for aligning flowgrams of sequences against a reference sequence that has been converted into many ideal sub-flowgrams and built into a database. Newbler Assembler can be used for de novo assembly of a complete genome using flow signals.

In addition to software access, the Institute is also providing data center and offline data processing services for GS-20 at the Biomedical Genomics Center. GS-20 at the BMGC is part of MINGEN (the Minnesota Genomics Infrastructure Initiative), founded by the Minnesota Partnership for Biotechnology and Medical Genomics.

2. GeneData Expressionist updated and migrated: Expressionist is a comprehensive microarray data analysis system that is being intensively used by more than 100 University of Minnesota researchers working with approximately 22,000 experimental datasets. In order to better serve the University, MSI had upgraded this system from Pro1.0 to Pro3.1 and migrated it to a new, dedicated HP Proliant DL 385 server with 4 GB of memory and two dual-core processors. Pro3.1 facilitates new analysis methods such as regression models, FDR estimations, and specialized analyses for time series experiments.

For more information about GeneData Expressionist, please see:


3. New IBM BladeCenter Linux Cluster Updates:

a. New MSI system listed in Top 500 Supercomputer Sites list: The BladeCenter system was listed in the November 2006 Top 500 Supercomputer Sites list at number 198 based on an assumption of 1140 processors ("processor" here means each of two cores in each dual-core processor). For more information, please visit:


b. New BladeCenter system passing tests and to be ready for use by mid-January 2007: The new IBM system has already passed the first of MSI's acceptance tests. The second level of testing, starting now and continuing for the next two weeks, involves the running of the MSI benchmark suite, compiling codes, running codes interactively, running codes in batch, and testing the scalability of the entire system. The final acceptance test will involve two weeks of open use by all MSI researchers. After that, the system will be put into production in mid-January as MSI's newest core resource.

4. 2007-08 Research Scholarships: Applications for research scholarships are due January 15, 2007 for scholarships to be awarded for the 2007-08 academic year. Nominations must be made by University of Minnesota faculty members.

5. 2007 Undergraduate Internship Program: Undergraduate Internship Program applications for Summer 2007 are due February 28, 2007. Information on available projects, eligibility requirements, stipend amount, and application instructions can be viewed at:


6. Review of MSI's services and structure: MSI has two long-range planning committees (see www.msi.umn.edu/general/people/committees.htm for more information) that are presently reviewing MSI's current status and preparing recommendations for MSI Interim Director Andrew Odlyzko regarding MSI's support for computation in the biosciences, engineering, math, and the physical sciences and how it can best continue to serve the University of Minnesota. The recommendations are due at the end of January 2007. In order to assess the collective views of PIs using MSI's resources and services, and to better understand which components are most valuable to University researchers and in which format, a questionnaire was distributed during November that asked for specific feedback regarding MSI's hardware, software, services, support in obtaining research funding, value to the University, and preferred future direction.

In addition to the above process, in Spring 2007, an external advisory board composed of persons from outside the University of Minnesota will visit the Twin Cities campus to review MSI's resources, services, and structure, interview key people, and make additional recommendations to Interim Director Odlyzko, who, after both sets of recommendations have been received, will review them with Institute of Technology Dean Steve Crouch and other key persons in the University administration to decide on a course for the future.

7. 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