All Tutorials

  • 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


  • 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.


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