All Tutorials

  • Tue Nov 8, 9:00 am - 11:00 am

    The UNIX operating system is a fundamental part of the MSI experience. Many of MSI’s scientific codes require that the user understand basic UNIX operating commands and functionality. This tutorial will give the novice user a hands-on guide to using the UNIX operating environment to navigate around and use MSI resources.


    This tutorial utilizes UMConnect and takes place entirely online. Please register as usual. Registered users will receive meeting information by email within 24 hours of the workshop start date. Please visit http://www.oit.umn.edu/umconnect/ to ensure that your system meets the minimum requirements necessary to participate in this webinar.


  • Thu Nov 3, 1:00 pm - 3:00 pm
    575
    Walter Library

    In proteomics research, label-free quantitation has emerged as a method to estimate differential expression of proteins in comparative analysis. Various modes of label-free quantitation will be introduced. Commercial software (such as Scaffold, ProteoIQ) and open source software will be discussed.


  • Tue Nov 1, 1:00 pm - 3:00 pm
    575
    Walter Library

    The Parallel Computing Toolbox software extends the MATLAB language with high-level parallel processing constructs such as parallel for-loops, distributed arrays, parallel numerical algorithms, and message-passing functions that let you exploit data and task parallelism in your applications.


    This tutorial will teach MSI's users to convert serial MATLAB programs to parallel MATLAB programs and to use the built-in functions.


    This tutorial consists of two parts:


    1) One-hour lecture to describe the MATLAB functions


    2) An optional one-hour, hands-on session focusing on the use of the Parallel Computing Toolbox


  • Tue Oct 25, 1:00 pm - 3:00 pm
    575
    Walter Library

    Microscopic images are mostly collected as stacks (3D) and often with time lapses (the fourth dimension). Huygens is a comprehensive deconvolution package for 3D and 4D microscopy.


    This tutorial will introduce users to image processing algorithms for wide-field and confocal microscopes. It will demonstrate practical applications of Huygens in deconvolution, resolution, and noise reduction for restoring images. Users will also be introduced to batch utilities in Huygens Scripting to process large numbers of image datasets automatically.


  • Tue Oct 18, 9:30 am - 4:00 pm
    575
    Walter Library

    This one-day work shop on general purpose GPU computing (GPGPU) is hosted jointly by the Supercomputing Institute and the Department of Electrical and Computer Engineering. The workshop will consist of a lecture and hands-on exercises covering the following topics: MSI’s GPGPU resources, basic CUDA programing, use of acceleration tools, and memory hierarchy for performance enhancement.


  • Fri Oct 14, 1:00 pm - 2:30 pm
    575
    Walter Library

    SYBYL is the modeling environment for computer-aided drug design (CADD). It provides the essential tools for the manipulation, visualization and analysis of biomolecules. This tutorial will go over the fundamentals of the SYBYL graphical user interface and its key features for examining protein structures and biomolecular interactions.


  • Thu Oct 13, 1:00 pm - 3:00 pm
    575
    Walter Library

    Weka is a freely available software package for knowledge discovery and data mining that contains tools for data pre-processing, classification, regression, clustering, association rules, and visualization. In this tutorial, we will go through the basic steps involved in loading data into Weka, exploring and filtering data, and applying Weka data mining

    tools. The emphasis will be on techniques for classification, such as decision trees, nearest neighbors, naive Bayes, and artificial neural networks. However, as time allows, we will briefly discuss other capabilities of Weka, such as clustering, association analysis, and variable selection.


  • Fri Oct 7, 2:00 pm - 3:30 pm
    575
    Walter Library

    Weka is a freely available software package for knowledge discovery and data mining that contains tools for data pre-processing, classification, regression, clustering, association rules, and visualization. In this tutorial, we will go through the basic steps involved in loading data into Weka, exploring and filtering data, and applying Weka data mining tools. The emphasis will be on techniques for classification, such as decision trees, nearest neighbors, naive Bayes, and artificial neural networks. However, as time allows, we will briefly discuss other capabilities of Weka, such as clustering, association analysis, and variable selection.


  • Thu Oct 6, 1:00 pm - 3:00 pm
    575
    Walter Library

    MATLAB is a general computational platform for rapid development of programs. It also has several toolboxes that allow specialized computation on images. One such toolbox, the Image Processing Toolbox, has hundreds of functions that can be used to perform operations on images.


    The various image processing operations can be classified in to reading, processing and writing images. We will begin the tutorial by performing simple image reading operations on jpeg, gif, etc. We will also discuss reading complex image formats like DICOM. We will then perform various image processing operations like filtering, visualization and analysis. We will then output these images to different formats to be read by other applications.


    Finally, we will conclude with hands-on practice using various example images. You are also welcome to bring specific questions and problems that you would like to discuss.


  • Fri Sep 30, 1:00 pm - 2:30 pm
    402
    Walter Library

    The Schrodinger software suite is a full-featured molecular modeling package designed for pharmaceutical, biotechnology, and materials science research. It provides essential tools for the manipulation, visualization and analysis of biomolecules. This tutorial will go over the fundamentals of its graphical user interface and its key features for molecular mechanics and dynamics calculations, preparation of chemical libraries, and examining biomolecular interactions.


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