All Tutorials

  • Tue Jul 12, 10:00 am - 4:00 pm
    585
    Walter Library

    This one-day workshop on MPI will help researchers write better and portable parallel codes for distributed-memory machines, like Linux clusters. 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.


    The workshop will combine 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 Jul 7, 1:00 pm - 3:00 pm
    402
    Walter Library

    The SAS system is a collection of programs originally designed to perform statistical analysis of data. The SAS software started out in the 1970s as a package for statistical analysis. By the early 1980s SAS had already branched out into graphics and spreadsheets. The SAS system now has a diverse family of products. Most of its products are integrated together and can be used as building blocks to construct a seamless system.


    MSI has the SAS system installed on its supercomputers. In this tutorial, we will help you get your data into the SAS system. We will cover the topics and techniques ranging from reading data in different formats into the SAS software, to writing a basic SAS code to use some statistical procedure


  • Thu Jun 30, 1:00 pm - 3:00 pm
    402
    Walter Library

    The GeneSpring software package is the most widely used microarray software tools. In this tutorial, we will focus on the advanced features of GeneSpring based on the newest version, v7.2. These features include signal condense and normalizations (RMA, GC-RMA), quality control, gene list manipulation(external list, Venn diagram, filters), 1-way and 2-way ANOVA, Class Prediction Tool, regulatory element, gene ontology, pathway, and scripts.


  • Tue Jun 28, 10:00 am - 4:00 pm
    585
    Walter Library

    OpenMP is a parallel programming interface for shared memory architectures and is available on the IBM Regatta, IBM SP, and the SGI Altix. For better use of OpenMP programming in high performance computing, the Supercomputing Institute will have a one-day workshop addressing the different aspects of OpenMP, such as parallel and worksharing constructs, data scope attribute clauses, and synchronization constructs.


    A hands-on practice will follow the lecture. Provided examples will enable the users to insert OpenMP directives for different parallel tasks and data scope attribute clauses. The users are also encouraged to bring in their serial application codes. The User Support Staff members will help you parallelize the code with OpenMP.


  • Thu Jun 23, 12:00 pm - 4:00 pm
    585
    Walter Library

    Molecular modeling is a general term that covers a wide range of molecular graphics and computational chemistry techniques that are used to build, display, manipulate, simulate and calculate molecular properties. InsightII is a graphic user interface that acts as a front-end to many of these molecular modeling tools. This tutorial covers the basic biomolecular building and visualization features within InsightII, in addition to demonstrating its interface to some of its molecular modeling modules.


  • Wed Jun 22, 1:00 pm - 3:00 pm
    585
    Walter Library

    MATLAB is an integrated, technical computing environment that combines numeric computation, graphics and visualization, and a high-level programming language. MATLAB includes hundreds of functions for data analysis and visualization, numeric and symbolic computation engineering, scientific graphics modeling, and simulation. This tutorial will demonstrate the use of some of these functions. It will consist of two parts:

    1) A 90-minute lecture describing the use of computation and visualization functions and tools.

    2) An optional one-hour, hands-on session focusing on the use of these functions for your application.


  • Tue Jun 21, 1:00 pm - 3:00 pm
    402
    Walter Library

    Gaussian is a program that can be used to calculate a variety of chemical properties. Gaussian 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 here at the Institute, and tips on how to run jobs efficiently.


  • Thu Jun 16, 1:00 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 command files for doing a simple MD simulation and carry out a typical analysis in CHARMM.


  • Wed Jun 15, 1:00 pm - 3:00 pm
    402
    Walter Library

    The Supercomputing Institute has a wide variety of software packages, many supercomputers, and a technical user support staff dedicated to bioinformatics and proteomics research.


    This tutorial will introduce the hardware, software, databases, and user support options available at the Supercomputing Institute. The main focus will be on the 70-plus software tools available in Bioinformatics, Microarray Data Analysis, Evolution, and Proteomics. Specific application programs that the Institute staff has developed will also be introduced. Database application and web interface settings will also be discussed.


  • Tue Jun 14, 1:00 pm - 3:00 pm
    402
    Walter Library

    Computational chemistry is a broad area of research that spans from quantum scattering to biomolecular modeling to nanotechnology. This tutorial will give a general overview of some of the major areas of research in computational chemistry. We will give brief explanations of the theory used as a basis for predictive modeling in each area discussed. We will also mention some real-life applications and the more popular programs used to carry out these calculations.


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