All Tutorials

  • Thu Apr 6, 1:00 pm - 3:00 pm
    402
    Walter Library

    This tutorial focuses on the study of ligands that exhibit optimal interactions with a known biochemical receptor. Participants will gain experience with graphical manipulations in SYBYL; building, minimizing, and aligning molecules; importing and viewing a receptor structure.


  • Tue Mar 28, 1:00 pm - 3:00 pm
    585
    Walter Library

    Writing a code with no compiling errors is the first step in completing a programming project. The second important step is to run a code efficiently on a given computer platform. This workshop will discuss general techniques for optimization of computer programs and present the code optimization and performance tuning tools that are available at the Institute.


    Users will have a chance to learn through hands-on examples how to use hardware counters and profiler tools such as pfmon and XPROFILER, for code performance evaluation, tuning, memory usage and I/O characteristics. In addition, we will discuss some tips on how to improve the performance of an application by using tuned libraries and compiler options.


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

    Molpro is a program that can be used to calculate a variety of chemical properties. Molpro is primarily used for carrying out electronic structure calculations. Molpro is often the program of choice for calculating CCSD(T) energies.


    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 Mar 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. Hands-on part focusing on the use of this tool for your practical applications.


    Users are encouraged to bring practice data and to contact Seema (seemaj@msi.umn.edu) to format their practice data (or real data, if available) 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.


  • Thu Mar 2, 1:00 pm - 3:00 pm
    402
    Walter Library

    From the Web to PowerPoint presentations, animations and graphics are powerful collaboration and research tools. This tutorial will introduce some powerful tools for generating high-quality molecular images and animations for both the biologist and the chemist. We will focus on using Amira and PyMol for producing and manipulating molecular pictures and various tools for generating animations from the created images.


  • Thu Feb 23, 1:00 pm - 3:00 pm
    402
    Walter Library

    Many scientific problems require the optimization of multidimensional functions that have dozens or even thousands of local minima and maxima. Local optimization methods such as the Newton-Raphson method and its many variants can find nearby local extrema but have little or no chance of finding a global minimum or maximum. Using a genetic algorithm (GA) is often a very efficient means to find a global minimum or maximum for complex functions.


    This tutorial will describe how genetic algorithms work and we will discuss general optimization strategies with GAs. We will also discuss a few GA programs available and how one might parallelize a GA optimization.


  • Tue Feb 21, 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, the IBM SP, and the SGI Altix. 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 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 will help you parallelize the code with OpenMP.


  • Thu Feb 16, 1:00 pm - 3:00 pm
    585
    Walter Library

    GeneData Expressionist is widely used for microarray data analysis at the University of Minnesota. It offers many statistical analysis methods for microarray data analysis. Understanding these methods is very important when using this software.


    In this tutorial, we will go through some basic statistical methods used in Expressionist, including those used in data display, summary statistics, sample comparison, similarity search, and clustering.


  • Tue Feb 7, 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, such as the Institute’s IBM Power4, the IBM SP, the SGI Altix, and the Netfinity Cluster. 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 Feb 2, 1:00 pm - 3:00 pm
    585
    Walter Library

    The GeneData Expressionist suite is a computational system from GeneData Inc. for analyzing gene expression data from one or two-channel microarrays. It consists of three closely integrated modules (Refiner, CoBi, and Analyst) for data quality control, data management, and statistical data analysis. This tutorial will cover the main features of each module with some practice using sample data


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