All Tutorials

  • Thu Oct 25, 1:00 pm - 3:00 pm
    402
    Walter Library

    R and S-PLUS are powerful computing environments and languages for statistical computing and graphics that run on a wide variety of UNIX platforms, Windows and Mac OS. Both R and S-PLUS are available on the computers, including the supercomputers, at MSI.


    Bell Laboratories developed the S language and the environment in the 1980s for data analysis. S was further developed into a commercial product called S-PLUS. R, a dialect of the S language, is free. R is available on MSI's supercomputers, which are ideal for long run-time and/or large memory R applications.


    This tutorial will demonstrate how to log into MSI's computers to get started with R and S-PLUS and how to read and manipulate data in the R and S-PLUS environments. In addition, attendees will learn to perform basic statistical analysis in R and to produce graphics with the software packages.


  • Tue Oct 23, 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 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 Oct 18, 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 16, 1:30 pm - 3:00 pm
    575
    Walter Library

    The CCP4 suite is a collection of programs used in most of the computations involved in protein x-ray crystallography. The package includes programs for data processing, molecular replacement, MIR, structure refinement, and validation, as well as a graphical user interface for most of the common programs.


    This tutorial will give an overview of the programs and their use, as well as a detailed description of how to run the program here at MSI.


  • Thu Oct 11, 1:00 pm - 3:00 pm
    402
    Walter Library

    Gaussian is a program that can be used to calculate a variety of chemical properties and is primarily used for carrying out electronic structure calculations. This tutorial will give an overview of the program capabilities, a detailed description of how to run the program at the Institute, and tips on how to run jobs efficiently.


  • Tue Oct 9, 10:00 am - 4:00 pm
    575
    Walter Library

    This one-day workshop on MPI will help researchers write better and portable parallel codes for distributed-memory machines like Linux clusters, such as the Institute's IBM Power4, SGI Altix, BladeCenter and Calhoun. It will focus on basic point-to-point communication and collective communications, which are the most commonly used MPI routines in high-performance scientific computation. In addition, the advantage of using MPI non-blocking communication will be introduced. Each session of the workshop will combine a lecture with hands-on practice. The lecture introduces basic principles, and the hands-on portion focuses on the use of MPI principles via examples.


    Session One: Introduction to basic concepts of "MPI is Small," centering on point-to-point communication.


    Session Two: MPI collective communications including broadcast, gather, scatter, and Alltoall.


    Programming will be done in Fortran and C, so any background in these two languages will be helpful.


  • Thu Oct 4, 1:00 pm - 3:00 pm
    402
    Walter Library

    The Supercomputing Institute has three commercial pathway analysis software packages, Ingenuity Pathways Analysis (Ingenuity Systems), MetaCore (GeneGo) and PathwayStudio (Ariadne). These tools are used to build and examine biological association networks, including canonical pathways, protein-small molecule and protein-protein interaction networks, as well as protein distribution by diseases, for a more complete systems biology network view. This tutorial will explain how to use these software packages to analyze genomics and proteomic data.


  • Tue Oct 2, 1:00 pm - 3:00 pm
    138
    Cargill Building

    The Genome Sequencer (GS) FLX from 454 Life Sciences is the 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.


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

    Schroedinger, Inc. provides a wide range of computational chemistry and molecular modeling software packages that are used to build, display, manipulate, simulate, and calculate molecular properties. Maestro is the common graphic user-interface that acts as a front-end to many of these tools. This tutorial covers the basic biomolecular building and visualization features within Maestro. We will also demonstrate its interface with some of its molecular modeling and computational chemistry modules.


  • Wed Sep 26, 3:00 pm - 4:00 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 the 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.


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