All Tutorials

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

    Molecular Dynamics (MD) Simulation is used extensively to simulate the dynamic behavior of molecular and biomolecular systems by a classical mechanical treatment of nuclear motion. There are a variety of MD software packages available at MSI. This tutorial will cover the basic fundamental theory of MD simulation and an overview of some of these software packages.


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

    The majority of the most powerful scientific research computers in the world use UNIX or Linux (which is a type of UNIX) for their operating systems. Learning the basics of Linux/UNIX is the first step to effectively utilizing these powerful resources 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


  • Sun Jan 1, 1:00 pm - 3:00 pm
    402
    Walter Library

    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.


  • Thu Dec 8, 1:00 pm - Sat Oct 8, 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 point-to-point communications standard.


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


  • Tue Dec 6, 1:00 pm - 3:00 pm
    402
    Walter Library

    The Supercomputing Institute maintains a wide range of software packages dedicated to structural biology. This tutorial offers an overview of those packages, focusing on how to start using them. In particular, we will look at Auremol, CCP4, CNS/Xplor, NMRPipe, etc.


  • Tue Nov 29, 1:00 pm - 3:00 pm
    402
    Walter Library

    Schrödinger, LLC provides a wide range of computational chemistry and molecule modeling software used to build, display, manipulate, simulate, and calculate molecular properties. The common interface, Maestro, is the graphic user interface that 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 Nov 17, 1:00 pm - 3:00 pm
    585
    Walter Library

    Building a web interface for your database will expand the use of the database. A web-based database is more convenient for viewing and sharing data, especially in the field of bioinformatics. This tutorial will introduce you to building a web database using CGI/PERL and PHP in the Unix environment. We will cover the dynamic web page development using CGI or PHP, as well as how to connect databases such as Oracle and mySQL using DBI. SQL will also be introduced in the tutorial.


    This is a hands-on workshop. Attendees will have the opportunity to create a simple web database during the workshop.


  • Tue Nov 15, 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. 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 Nov 10, 12:00 pm - 4:00 pm
    585
    Walter Library

    Molecular modeling is a general term that covers a wide range of molecular graphics and computational chemistry techniques that are used to build, display, manipulate, simulate and calculate molecular properties. InsightII is a graphic user interface that acts as a front end to many of these molecular modeling tools. This workshop covers the basic biomolecular building and visualization features within InsightII, in addition to demonstrating its interface to some of its molecular modeling modules.


  • Tue Nov 8, 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.


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