All Tutorials

  • Tue May 6, 1:00 pm - 3:00 pm
    575
    Walter Library

    Calhoun is an SGI Altix XE that offers opportunities to run large chemical simulations using highly scalable computational chemistry programs. Programs that scale to hundreds of processors are vital to take advantage of the Altix XE architecture.


    This tutorial will give an overview of the chemistry packages available and how to run them on Calhoun. We will compare performance between the Calhoun and other MSI machines. We will also address memory usage, application-specific MPI tuning, and local scratch disk.


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

    The Genome Sequencer (GS) FLX from 454 Life Sciences is the ultra high-throughput instrument for conducting nucleotide sequencing. It can potentially generate one million sequencing readings with an average reading at about 250 bp within a single operation run. This technology has been used for small genome sequencing, mass EST sequencing, and potentially large genome analysis. This tutorial will introduce the principle of 454 sequencing technology, data preparation, and data analysis, especially in sequence assembly and mapping. We will also discuss RNA and protein identification on the assembled genome.


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

    MATLAB is a general computational platform for the rapid development of programs. It also has several toolboxes that allow specialized computations. One such toolbox, the Image Processing Toolbox, has functions that can be used to perform various operations on images. These operations can be classified into 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 such as filtering, visualization, and analysis. We will output these images to different formats to be read by other applications. Finally we will conclude with hands-on practice using various example images. Users are also welcome to bring specific questions and problems that they would like to discuss.


  • Thu Apr 24, 1:00 pm - 3:00 pm
    575
    Walter Library

    Single nucleotide polymorphisms (SNP) make individuals different (color, susceptibility to diseases, productivity, etc.). However, there are millions of SNPs in humans. Which SNPs are associated with particular phenotypes? HelixTree is a powerful software tool for studying SNP association with disease or drug response. It also analyzes single marker and haplotype, calculates LD and HWE, identifies tagging SNPs, and more.


    In this tutorial, we will walk through this software using sample data.


  • Tue Apr 22, 1:00 pm - 3:00 pm
    402
    Walter Library

    In this tutorial, we will start with some examples to show how to retrieve and handle genomic data, and how to perform some simple statistical analysis. We will introduce hidden Markov models and demonstrate how to detect change points in the statistical make-up of biological sequences. We will also discuss some applications in whole-genome analysis of multiple species. Techniques and tools for data processing, clustering, and classification for NDA microarray will also be discussed.


  • Thu Apr 17, 1:00 pm - 3:00 pm
    575
    Walter Library

    Mimics is a tool for the visualization and segmentation of CT/MR images and 3D rendering of segmented objects. It also provides an interface to create FEM meshes. In this tutorial, we will first focus on reading and writing images. We will then segment the images using various techniques, improve the quality of segmentation using mask tools, and obtain a 3D object. The 3D object will be stored in various 3D formats and then will be FEM meshed, and the FEM mesh will be refined globally and locally.


  • Tue Apr 15, 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.


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


  • Thu Apr 10, 1:00 pm - 3:00 pm
    402
    Walter Library

    In this tutorial, we will introduce some common approaches to the extraction of data in relational databases.


    The SAS/ACCESS interface provides methods to access relational database data. We will discuss how we can use these methods to interact with data residing on a remote server, say in an Oracle database.


    We will also introduce the SAS SQL procedure and learn how to complete many tasks with a single SQL statement while a more traditional SAS approach may involve several SAS procedures and DATA steps.


  • Tue Apr 8, 1:00 pm - 3:00 pm
    575
    Walter Library

    The majority of MPI codes use point-to-point and collective communication routines from the original MPI standard (MPI 1.1). MPI-2 implementations are being undertaken now by all vendors and provide a rich functionality to MPI. MPI-2 features include all MPI-1 features, dynamic process creation and management, one-sided communications, extended collective communications, parallel I/O, C++ and Fortran 90 binding, and other miscellaneous features.


    This tutorial will go over MPI-2 features and will cover in detail MPI-derived data types and parallel I/O. The I/O part will include data file partitioning among processes, transfer global data between memory and files (collective I/O), and asynchronous transfers. This tutorial will also provide examples on how to use these new features.


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

    Pymol is a free-for-academic-use modeling software program useful for viewing and creating figures and animation of protein models. This tutorial is designed to help users learn how to navigate and view protein models in Pymol with the goal of making figures and animations for presentations and publications.


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