All Tutorials

  • Tue Nov 28, 10:00 am - 4:00 pm
    585
    Walter Library

    OpenMP is a parallel programming interface for shared-memory architectures and is available on the IBM Regatta and the SGI Altix. This one-day workshop will help users to use OpenMP programming more productively for high-performance computing. It will also address the different aspects of OpenMP, such as parallel and worksharing constructs, data scope attribute clauses, and synchronization constructs. In addition, the new features in the OpenMP II Standard will be covered.


    A hands-on practice will follow the lecture. Examples provided will enable the users to insert OpenMP directives for different parallel tasks and data scope attribute clauses. The users are also encouraged to bring in their serial application codes. The User Support Staff will help you parallelize the code with OpenMP.


  • Tue Nov 21, 1:00 pm - 3:00 pm
    402
    Walter Library

    Genomics has changed the face of life sciences since the first draft of the human genome sequence was released in 2000. Computational tools play an important role in this change.

    The Supercomputing Institute has some of the most powerful computational genomics software tools available. These tools allow for genomics data acquisition, quality assessment, normalization, statistical analysis, functional annotation, pathway, interaction network, structural genomics, and data management.


    This tutorial will overview around 15 of the Institute's microarray and pathway genomics software tools and will guide users in accessing these resources.


  • Thu Nov 9, 1:00 pm - 3:00 pm
    138
    Cargill Building

    Microarrays have become a very popular and important tool for understanding gene expression. Proper interpretation of the results requires a reasonable understanding of the statistics involved in analyzing the data.


    This tutorial is designed to give an explanation of the necessary statistical concepts for interpreting the results from microarray experiments. We will incorporate the most frequently used tools to demonstrate and aid in understanding the statistics behind the tools.


  • Tue Nov 7, 1:00 pm - 3:00 pm
    585
    Walter Library

    GeneData Expressionist has been widely used for microarray

    data analysis at the University of Minnesota. It offers

    many statistical analysis methods for microarray data analysis. Understanding these methods is very important in the use of the software.


    In this tutorial, we will go through some statistical methods used in Expressionist including sample comparison, similarity search, and clustering.


  • Thu Nov 2, 1:00 pm - 3:00 pm
    585
    Walter Library

    This tutorial will show how to call MATLAB routines from FORTRAN and C codes. Calling MATLAB from within a FORTRAN or C code provides a convenient method for interactive visualization

    of computational results. The tutorial will include the description of the MATLAB communication functions, which start

    and end the MATLAB process, how to send data to and from MATLAB, and how to send commands to be processed in MATLAB. The presentation will be followed by a hands-on exercise to practice the mixed programming of FORTRAN or C with MATLAB with an emphasis on the interactive visualization.


  • Tue Oct 31, 1:00 pm - 3:00 pm
    402
    Walter Library

    Schrodinger's, Inc. provides a wide range of computational chemistry and molecule modeling software tools that are used to build, display, manipulate, simulate, and calculate molecular properties. The common graphic user interface, Maestro, acts as a front-end to many of these tools. This tutorial covers the basic biomolecular building and visualization features within Maestro, in addition to demonstrating its interface to some of its molecular modeling and computational chemistry modules.


  • Thu Oct 26, 1:00 pm - 3:00 pm
    402
    Walter Library

    NWChem is a program that can be used to calculate a variety of chemical properties. NWChem is primarily used for carrying out electronic structure calculations. In particular, it is used for problems that can scale to hundreds of processors. This tutorial will give an overview of the program capabilities, a detailed description of how to run the program here at the Institute, and tips on how to run jobs efficiently.


  • Tue Oct 24, 1:00 pm - 3:00 pm
    402
    Walter Library

    With the development of genomics and proteomics, many biologists now need to handle large amounts of data for their research. Bioinformatics programming, especially Perl programming, is a well-suited tool for biological data manipulation and analysis.


    This tutorial will introduce the fundamental concepts and mechanisms of computer programs, using Perl language as an example. We will use practical program examples such as RNA transcription, promoter sequence extraction from genomic DNA, motif scanning, parse BLAST result, etc. to demonstrate how bioinformatics programming can make you work easier and more efficient.


  • Thu Oct 19, 1:00 pm - 3:00 pm
    585
    Walter Library

    Expressionist is a powerful microarray data analysis software system that is especially useful when working with affymetrix chip data. It provides a workflow for data loading and quality control. It offers comprehensive statistical methods for data analysis, as well as a database for data management. In this hands-on tutorial we will walk through this software system using sample data.


  • Tue Oct 17, 1:00 pm - 3:00 pm
    585
    Walter Library

    This is a hands-on workshop focusing on an introduction to relational databases and structural query language (SQL). People will have an opportunity to practice creating and querying databases in an Oracle environment. Topics will include a brief overview of relational database design concepts and principals, and conceptual data models and constraints.


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