All Tutorials

  • Tue Dec 6, 1:00 pm - 2:00 pm

    The technology behind data acquisition and especially image acquisition have grown enormously over the years. Data sets of size greater than 1GB are common. Such datasets present a unique problem during the visualization process. They need large memory, powerful CPUs and good graphic capabilities in the form of graphics cards. Such technologies are expensive for individual researchers to buy and maintain, so MSI has been working on creating such an infrastructure.


    In this tutorial, we will introduce the remote visualization capabilities of MSI. We will discuss the details of the various visualization systems users can access. We will also discuss the software, VirtualGL, for connecting to these systems.


    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 Dec 1, 1:00 pm - 3:00 pm
    575
    Walter Library

    MSI has a new high-performance computing system named Koronis. It features an SGI Altix UV 1000, one of the largest global shared memory (GSM) systems available. Koronis offers unprecedented opportunities for NIH researchers to conduct memory-intensive calculations. At the same time, it poses great computational challenges from the system-memory complexity that - combined with the flexibility in the selection of the number of computing cores - can severely degrade the performance. This tutorial will help Koronis users improve application performance. We will show examples of programs that can take advantage of this computer. We will also describe tactics that can be used in the calculations within the CPUset regime to achieve optimal performance.


  • Tue Nov 29, 1:00 pm - 3:00 pm
    575
    Walter Library

    Image manipulation includes such functions as cropping, rotating, resizing, adding text, photo retouching, color conversion, and much more. Image manipulation can be used when preparing photos for print or the web or when creating animation. MSI has several programs that can be used for image manipulation; this tutorial will introduce you to three of those programs.


    Adobe Photoshop is the most popular commercial package for image manipulation. ImageMagick is a free collection of programs to display, manipulate and convert images from one format to another. ImageMagick can be used from a GUI or from the command line. GNU Image Manipulation Program (Gimp) is a free, general image processing program for editing images.


    This tutorial serves varying interest groups ranging from medicine, biology, chemistry, physics, material sciences, geophysics, astronomy, and engineering.


  • 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


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