All Tutorials

  • Thu Nov 8, 1:00 pm - 3:00 pm
    575
    Walter Library

    Tecplot is a software package for 2D or 3D visualization of technical data obtained from analysis, experiments, and simulations. The objective of this tutorial is to teach users how to use Tecplot. This tutorial consists of three parts:


    1. A lecture describing the capabilities of Tecplot.

    2. An introduction to different graphing capabilities.

    3. A hands-on session focusing on the use of this tool for your practical applications.


  • Tue Nov 6, 1:00 pm - 3:00 pm
    402
    Walter Library

    The GCG Wisconsin Package is an integrated collection of tools for molecular biology. It includes more than 130 programs/applications for sequence analysis, database searching, DNA/RNA secondary structure, fragment assembly, gene identification, pattern analysis, and many others.


    This tutorial will cover: UNIX basic for using GCG, overview of GCG, how to get started, command line with GCG, and seqLab GUI interface for GCG.


  • Thu Nov 1, 10:00 am - 4:00 pm
    575
    Walter Library

    OpenMP is a parallel programming interface for shared-memory architectures and is available on the IBM Regatta, the Blade Center, the SGI Altix and Calhoun. This workshop will help users to use OpenMP programming more productively for high-performance computing by addressing the different aspects of OpenMP, such as parallel and worksharing constructs, data scope attribute clauses, and synchronization constructs. In addition, the new features in the OpenMP II standard will be covered. A hands-on practice will follow the lecture. Provided examples will enable users to insert OpenMP directives for different parallel tasks and data scope attribute clauses. Users are also encouraged to bring in their serial application codes. The User Support staff will help you parallelize the code with OpenMP.


  • Tue Oct 30, 1:30 pm - 3:00 pm
    402
    Walter Library

    CHARMM (Chemistry at HARvard Macromolecular Mechanics) is an academically and commercially distributed software for molecular dynamics (MD) simulations. It is used extensively to simulate the dynamic behavior of molecular and biomolecular systems as well as free energy calculations. This tutorial will cover the basic fundamental theory of MD simulation and how an MD simulation can be used to study the conformational dynamics of a biomolecular system. This tutorial will also show you how to write simple command files for doing a simple MD simulation and how to carry out a typical analysis in CHARMM.


  • 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.


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