All Tutorials

  • 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.


  • Tue Apr 1, 1:00 pm - 3:00 pm
    575
    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 interactive visualization.


  • Thu Mar 27, 1:00 pm - 3:00 pm
    402
    Walter Library

    Proteomics research includes the characterization of protein mixtures in order to understand complex biological systems and determine relationships between proteins, their function, and protein-protein interactions. Established methods for relative quantitation of proteins involve growth on isotope-enriched medium or chemical or enzymatic modifications. Recently, an MS/MS-based quantitation method (iTRAQ) has been developed. This tutorial will cover overview of iTRAQ technology and the software for iTRAQ data analysis, ProteinPilot. Sample iTRAQ data, analysis and how to work with the results for each of the searches available in ProteinPilot software will be described. Some other computational tools to compare multiple iTRAQ experiments and the integration of protein annotations into a ProteinPilot protein summary will also be discussed.


  • Tue Mar 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


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