All Tutorials

  • Thu Feb 24, 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 for free energy calculations. This tutorial will cover the 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 how to carry out a typical analysis in CHARMM.


  • Tue Feb 22, 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 organize 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 Feb 17, 1:00 pm - 3:00 pm
    402
    Walter Library

    This tutorial will introduce the principles of a relational database system. Topics will include database modeling, database management system, SQL query, as well as schema refinement and normal forms.


  • Tue Feb 15, 1:00 pm - 3:00 pm
    402
    Walter Library

    Graphical user interfaces are a quick and easy way to get started using and learning a new software package, to tame an old complex one, or to produce some descriptive visual aids. GaussView is a handy, flexible graphical interface to the Gaussian electronic structure package. Other interfaces include Maestro for Schrödinger products and Ecce for NWChem.


    This tutorial will focus on the features of GaussView that will help you easily create input files for Gaussian, submit calculations on the various platforms, and visualize the generated output. The Maestro and Ecce interfaces will also be discussed in general.


  • Tue Feb 8, 9:00 am - Wed Feb 9, 5:00 pm
    585
    Walter Library

    This course focuses on the study of ligands that exhibit optimal interactions with a known receptor. Participants will gain experience with graphical manipulations in SYBYL; building, minimizing, and aligning molecules; importing and viewing a receptor structure; and searching databases for compounds which can bind at a given receptor site. Additionally, users will dock ligands into a receptor site.


  • Thu Feb 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 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.


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

    This tutorial will explain how to submit jobs on the core resource computing machines including the Netfinity Cluster, the SGI, and IBM Supercomputers. The PBS and LoadLeveler queuing systems along with the Maui Scheduler will be discussed, and tips for better turnaround times will be provided.


  • Thu Jan 27, 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.


  • Wed Jan 26, 1:00 pm - 3:00 pm
    145
    Peters Hall

    Genomics has changed the face of life sciences since the first draft of the human genome sequence was released in 2000. Computational tools play an important role in this change.

    The Supercomputing Institute has some of the most powerful computational genomics software tools available. These tools allow for genomics data acquisition, quality assessment, normalization, statistical analysis, functional annotation, pathway, interaction network, structural genomics, and data management.


    This tutorial will overview around 15 of the Institute/.s microarray and pathway genomics software tools and will guide users in accessing these resources.


  • Tue Dec 7, 1:00 pm - 3:00 pm
    585
    Walter Library

    MatlabMPI is a Matlab implementation of the Message Passing Interface (MPI) standard made by Lincoln Laboratory at MIT. It allows any Matlab program to exploit multiple processors. MatlabMPI currently implements the basic functions that are the core of the MPI point-to-point communications standard.


    This tutorial focuses on the use of MatlabMPI as a tool of parallel computing under the Matlab environment. A one-hour hands-on segment will follow the lecture to help the users get familiar with the concepts and syntax, as well as develop simple application codes.


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