All Tutorials

  • Thu Nov 2, 1:00 pm - 3:00 pm
    585
    Walter Library

    This tutorial will show how to call MATLAB routines from FORTRAN and C codes. Calling MATLAB from within a FORTRAN or C code provides a convenient method for interactive visualization

    of computational results. The tutorial will include the description of the MATLAB communication functions, which start

    and end the MATLAB process, how to send data to and from MATLAB, and how to send commands to be processed in MATLAB. The presentation will be followed by a hands-on exercise to practice the mixed programming of FORTRAN or C with MATLAB with an emphasis on the interactive visualization.


  • Tue Oct 31, 1:00 pm - 3:00 pm
    402
    Walter Library

    Schrodinger's, Inc. provides a wide range of computational chemistry and molecule modeling software tools that are used to build, display, manipulate, simulate, and calculate molecular properties. The common graphic user interface, Maestro, acts as a front-end to many of these tools. This tutorial covers the basic biomolecular building and visualization features within Maestro, in addition to demonstrating its interface to some of its molecular modeling and computational chemistry modules.


  • Thu Oct 26, 1:00 pm - 3:00 pm
    402
    Walter Library

    NWChem is a program that can be used to calculate a variety of chemical properties. NWChem is primarily used for carrying out electronic structure calculations. In particular, it is used for problems that can scale to hundreds of processors. 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.


  • Tue Oct 24, 1:00 pm - 3:00 pm
    402
    Walter Library

    With the development of genomics and proteomics, many biologists now need to handle large amounts of data for their research. Bioinformatics programming, especially Perl programming, is a well-suited tool for biological data manipulation and analysis.


    This tutorial will introduce the fundamental concepts and mechanisms of computer programs, using Perl language as an example. We will use practical program examples such as RNA transcription, promoter sequence extraction from genomic DNA, motif scanning, parse BLAST result, etc. to demonstrate how bioinformatics programming can make you work easier and more efficient.


  • Thu Oct 19, 1:00 pm - 3:00 pm
    585
    Walter Library

    Expressionist is a powerful microarray data analysis software system that is especially useful when working with affymetrix chip data. It provides a workflow for data loading and quality control. It offers comprehensive statistical methods for data analysis, as well as a database for data management. In this hands-on tutorial we will walk through this software system using sample data.


  • Tue Oct 17, 1:00 pm - 3:00 pm
    585
    Walter Library

    This is a hands-on workshop focusing on an introduction to relational databases and structural query language (SQL). People will have an opportunity to practice creating and querying databases in an Oracle environment. Topics will include a brief overview of relational database design concepts and principals, and conceptual data models and constraints.


  • Tue Oct 10, 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, such as the Institute's IBM Power4, IBM BladeCenter, Netfinity Cluster, and the SGI Altix. 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 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.


Pages