The Supercomputing Institute provides software, hardware, databases, and user support for Computational Biology and Genomics research at the University of Minnesota. This includes, but is not limited to, Bioinformatics, Biostatistics, Microarray Data Analysis, Proteomics, Structural Biology, and Database Project Development.
The Supercomputing Institute has most popular software related to Computational Biology, Genomics, and Proteomics. For example, the sequence homology search tool NCBI BLAST, the comprehensive package for molecular biology GCG Wisconsin Package, the microarray data analysis and visualization tools Expressionist and GeneSpring, database search for mass spectrometry Mascot, and the molecular simulation package InsightII. Please check the software page for more information.
We also have high-performance supercomputers to support scientific computation related to Biology and Genomics.Examples are the following, Parallel BLAST search is available on our IBM Power4, SGI, and SUN servers. A 16-processor SUN Fire6800 and a 8-CPU SUN Fire v890 are dedicated for Computational Genomics/Genetics. The Basic Science Computer Lab (BSCL) in 1-280 Nils Hasselmo Hall, the Biomedical Modeling, Simulation and Design Lab (BMSDL) in room 414, 717 Delaware Building and the Computational Genetics Lab ( CGL) in the Microbial and Plant Genomics Building are focused on Computational Biology and Genomics work.
In co-operation with the Biomedical Genomics Center (BMGC) and the Center for Mass Spectrometry and Proteomics (MSP), Institute provides the centralized data management hubs for Sanger and 454 Genomic Sequencing Data, Microarray and Genotyping Data, and Mass Spectrometry and Proteomics Data.
In addition, many biological databases are installed locally. These include nucleotide and protein sequence databases, many genome databases, and protein structural databases. They come from GenBank, EMBL, Protein Data Bank, or other sources. These databases are accessible directly or by related tools and are also updated regularly.
The Supercomputing Institute also supports large-scale web-based relational database project development. MySQL, Oracle, and Microsoft SQL Server are available. Most of these projects are hosted at the Scientific Data Management Lab (SDML) in Walter Library.
The Systems and Operations Staff provides assistance with all aspects of scientific computing and visualization. This assistance includes -- but is not limited to -- general user support, development of scripts or user-friendly procedures, assistance with software packages, tutorials, user training, and user assistance with specific software and database requirements. The User Support Staff can provide technical assistance in their areas of expertise, which include Computational Chemistry, Structural and Molecular Biology, Bioinformatics, Computational Genomics, Proteomics, and Scientific Visualization.
The Institue has many machines and laboratories, including the BSCL, the CGL, the SDML, the SDVL, the BMSDL, the IBM Power4, and the Netfinity Linux Cluster (Retired June 30, 2008.).The above links will give you information about applying for access to a specific machine or laboratory. For information about the machine, laboratory or software that works best for you or your research group, contact help@msi.umn.edu or call 612.626.0802.
Access to programs and computers at the Supercomputing Institute is possible from a computer laboratory such as the CGL or the SDML, using Web browsers, or by remote login from client machines.
The CGL (Computational Genetics Laboratory) is located in the Cargill Microbial and Plant Genomics Building on the St. Paul Campus. The BSCL (Basic Science Computing Laboratory) and BMSDL (Biomedical Modeling, Simulation and Design Lab) are on the Minneaplis Campus. All three are equipped with UNIX/Linux workstations, PCs, and Macintosh computers. The laboratories are open to the Institute's users and are 24-hour accessible with a UCard. For the web-accessible programs, you can use your web browser to access the software. Please check our Web Accessbile Software for the web addresses.
You can connect to machines at the Supercomputing Institute by Secure Shell (ssh). Click this link for instructions on how to setup and configure ssh on your machine. If you using a Macintosh or PC running Microsoft Windows and want to run an X Window application (i.e. If you see a message such as "can't open display ...." when you try to run a UNIX X Window application such as Netscape), you need to install an X Window emulator and set environment variable DISPLAY. If you need assistance, please contact help@msi.umn.edu
Need directly help?
Send an email to help@msi.umn.edu
or call (612) 626-0802.For information on Computational Biology and Bioinformatics at the University of Minnesota, see www.compbio.umn.edu.
This information is available in alternative formats upon request by individuals with disabilities. Please send email to alt-format@msi.umn.edu or call 612-624-0528. |
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