All Tutorials

  • Tue Nov 29, 10:00 am - 3:00 pm
    414
    University Square

    Schedule


    10 am - 12 am - Use of Matlab for computation


    1 pm - 3 pm - Image processing and visualization using Matlab


    Use of Matlab for computation


    MATLAB is an integrated technical computing environment that combines numeric computation, graphics and visualization into a high-level programming language. MATLAB includes hundreds of functions for data analysis, numeric and symbolic computation, and scientific graphics modeling and simulation. This portion of the tutorial consists of (1) a 60-minute lecture describing the basics of using Matlab for computing and (2) a 60-minute hands-on session focusing on the use of the basic functions for your application.


    Image processing and Visualization using Matlab


    Matlab has powerful capabilities to perform 2D and 3D visualization. It also has the Image Processing Toolbox with hundreds of functions that can be used to perform operations on images.


    First we will discuss the various 2D and 3D visualization functions. We will execute examples to cement the understanding.


    We will then discuss image processing using Matlab. The various image processing operations can be classified into reading, processing and writing images. We will begin with reading and writing images. 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 intersperse the lecture with hands-on exercises, so you can better understand the material. You are also welcome to bring specific questions and problems that you would like to discuss.


  • Tue Nov 22, 9:00 am - 12:00 pm
    138
    Cargill Building

    Illumina Genome Analyzer (GA) can generate up to 100 million

    sequence reads per lane with 5 to 10 gigabase DNA sequences.

    It has been widely used in biological research including

    genome sequencing, gene expression analysis, variation

    detection, etc.


    This tutorial will first introduce the new terminologies

    and data types associated with Illumina genome analyzer.

    Then we will discuss general strategies about data

    analysis including sequence assembly, mapping, SNP

    detection, and data visualization.


  • Thu Nov 17, 1:00 pm - 3:00 pm
    585
    Walter Library

    Microscope images are a complex dataset consisting of multiple structures and intensities spread across various channels. Hence, visualizing and analyzing this data becomes paramount.


    Imaris helps in visualizing all standard microscope formats. It can also be used to create iso-surfaces, perform statistical analysis based on the pixel intensities and perform co-localization (identifying pixels and entities that are present in more than one channel.) In addition to these operations, it has other modules to perform specialized functions like movie generation, etc.


  • Tue Nov 8, 9:00 am - 11:00 am
    138
    Cargill Building

    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 tool well-suited for biological data manipulation and analysis.


    This tutorial will introduce the fundamental concepts and

    mechanisms of Perl programming. We will use practical examples

    to demonstrate how to write Perl codes to do transcription,

    translation, batch sequence retrieval, promoter sequence

    extraction from genomic DNA, motif scanning, query gene ontology

    database, etc. Through these examples, you will learn how

    Perl programming can make you work easier and more

    efficient.


  • 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.


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