All Tutorials

  • 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.


  • Fri Jun 10, 1:00 pm - 3:00 pm
    402
    Walter Library

    PERL is a scripting language that can make the task of writing and maintaining scripts for various UNIX tasks considerably easier than trying to use one of the many shell languages. PERL is very useful, for example, for retrieving output from files of completed jobs for use in reports, input to subsequent jobs, and so forth. Since PERL is supported on virtually all computer platforms, PERL scripts are often very portable. PERL scripts can be extremely simple or complicated and powerful.


  • Thu Jun 9, 1:00 pm - 3:00 pm
    585
    Walter Library

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


    1. A lecture to describe the capabilities of Tecplot


    2. A hands-on part focusing on the use of this tool for your practical applications.


    Users are encouraged to contact Seema(seemaj@msi.umn.edu) to format their data to make the workshop more effective. Data sets will be available to use if you want to learn Tecplot, but do not have a dataset ready.


  • Wed Jun 8, 1:00 pm - 2:00 pm
    402
    Walter Library

    The majority of the most powerful scientific research computers in the world use Linux or UNIX for their operating system. Learning the basics of UNIX/Linux is the first step to utilizing these powerful resources effectively for your research.


    This tutorial is designed to introduce you to the Linux/UNIX operating system. We will discuss some of the most commonly used commands, some helpful shortcuts, and some of the key elements of using Linux/UNIX for your research efforts.


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