All Tutorials

  • Thu Oct 5, 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 to 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 carry out a typical analysis in CHARMM.


  • Tue Oct 3, 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 describing the capabilities of Tecplot


    2. A hands-on portion 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. Datasets will be available to use if you want to learn Tecplot, but do not have a dataset ready.


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

    GAMESS is a program that can be used to calculate a variety of chemical properties. GAMESS is primarily used for carrying out electronic structure calculations. This tutorial includes 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.


  • Tue Sep 26, 1:00 pm - 3:00 pm
    138
    Cargill Building

    The GCG Wisconsin Package is an integrated collection of tools for comprehensive sequence analysis. The package includes tools for comparison, database searching and retrieval, DNA/RNA secondary structure, fragment assembly, gene finding, pattern recognition, and many others.


    This tutorial will cover an introduction to GCG, databases and data files, comparison of SeqLab and SeqWeb, mapping, sequence comparison, protein analysis, and other aspects of this versatile software.


  • Thu Sep 21, 1:00 pm - 3:00 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.


  • Thu Sep 14, 10:00 am - 4:00 pm
    585
    Walter Library

    Numerical simulation of fluid flow (CFD) is generally computationally expensive and very time consuming. Recently, various commercial codes have been developed to simplify the geometry construction, meshing, solving, and processing of results. The ANSYS package allows users to integrate the above-listed steps in a single program. The tutorial will introduce novice users to the ANSYS/CFX software packages and will be structured around a combination of lectures and hands-on workshops. It is expected that attendees will become very familiar with the software by the end of the course and will be able to adapt it for problems of their own interest.


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

    Numerical simulation of fluid flow (CFD) is generally computationally expensive and very time consuming. Recently, various commercial codes have been developed to simplify the geometry construction, meshing, solving, and processing of results. The ANSYS package allows users to integrate the above-listed steps in a single program. The tutorial will introduce novice users to the ANSYS/CFX software packages and will be structured around a combination of lectures and hands-on workshops. It is expected that attendees will become very familiar with the software by the end of the course and will be able to adapt it for problems of their own interest.


  • Thu Aug 24, 1:00 pm - 3:00 pm
    402
    Walter Library

    The Supercomputing Institute hosts several proteomic software tools to meet the growing needs of proteomics research at the university. ClinProTools is a mass spectra data post-processing software package used for visualization, data reduction, and data mining, and for building predictive models. It combines intuitive visualization features and multiple mathematical algorithms to generate pattern recognition models from mass spectrometry-based profiling data. This can be used, for example, to classify and predict disease.


    In this tutorial, we use sera protein mass spectra sample data to demonstrate the use of the ClinProTools software package.


  • Thu Aug 17, 1:00 pm - 3:00 pm
    402
    Walter Library

    Statistics are very important to many scientific research projects. R and S-PLUS are powerful statistical computing languages and environments available at the Supercomputing Institute. 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 is a dialect of the S language.


    This tutorial will demonstrate how to read and manipulate data in the R and S-PLUS environments. In addition, attendees will learn how to perform basic statistical analysis in R and how to produce graphics with the software packages.


  • Tue Aug 15, 1:00 pm - 3:00 pm
    585
    Walter Library

    In the technical computing environment MATLAB is a powerful, high-level programming language. This tutorial is designed to help researchers solve some of their computational problems without spending a lot of time dealing with programming details through Matlab functions. This tutorial starts with a quick review of Matlab's syntax and I/O handlers. In addition, the tutorial will cover the use of some computational functions and toolboxes.


    To enhance the tutorial, users are encouraged to contact the User Support Staff (help@msi.umn.edu or 612-626-0802) with any current Matlab-specific issues. This valuable input will be used in the tutorial.


    This tutorial will consist of two parts:

    1) A 50-minute lecture describing the MATLAB functions

    2) An optional 1-hour hands-on session focusing on the use of these functions for your application.


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