All Tutorials

  • 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.


  • Tue Jun 7, 1:00 pm - 2:00 pm
    402
    Walter Library

    This tutorial is geared to new users and will provide an introduction to the facilities and computational resources of the Supercomputing Institute. All members of the Technical User Support staff will be introduced to facilitate assistance with all aspects of scientific computing and visualization at the Institute.


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

    MATLAB is an extremely popular programming environment with about 1,000,000 users worldwide who are primarily scientists and engineers engaged in technical computing. MATLAB is increasingly being run on clusters and grids to accelerate computations and to solve larger problems. This tutorial will present an overview of some of the most popular technologies (e.g. MatlabMPI http://www.ll.mit.edu/MatlabMPI and the Distributed Computing Toobox http://www.mathworks.com/products/distribt) for writing parallel and distributed MATLAB programs. It will also discuss some of the performance results achieved by real users using these products. The bulk of this tutorial will be an example-based, hands-on introduction to coding, running, debugging, and tuning parallel MATLAB programs. In addition, this hands-on workshop will also cover advanced topics such as how to implement and optimize complex communication patterns.


  • Thu Apr 28, 1:00 pm - 3:00 pm
    402
    Walter Library

    POLYRATE is a program designed to calculate chemical reaction rate constants on the basis of transition state theory and variational transition state theory.


    This tutorial will cover the basic knowledge required to calculate a reaction rate constant with POLYRATE. It will cover some of the reaction-path following methods as well as the methods for incorporating quantum effects. Finally, we will give a few pointers on running programs that interface with POLYRATE.


  • Tue Apr 26, 1:00 pm - 3:00 pm
    585
    Walter Library

    The SGI Altix has been a major component of computing resources at the Supercomputing Institute. With the objective of helping researchers better use this system, this tutorial will introduce some tools available on the Altix for code performance evaluation, tuning, memory usage, and application I/O characteristics. These tools include pfmon, profile.pl, histx, strace, dlook and dplace. In addition, we will discuss some tips/tricks to improve the performance of applications.


  • Thu Apr 21, 1:00 pm - 3:00 pm
    138
    Cargill Building

    There are many proteins that have similar functional and structural features but share a very low sequence similarity. For these proteins, it is not possible to apply homology modeling to predict their protein structures.


    Instead, one may examine the structure motifs. Structure motifs are individual structural features including secondary structure, sulfide bridges, turns, etc. They are essential in how a protein folds and assembles into the overall tertiary structure. In this tutorial, we will give an overview of the various types of protein structure motifs and demonstrate one of the software packages for performing structure motifs analysis, called Promotif.


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