All Tutorials

  • Thu Jan 29, 1:00 pm - 3:00 pm
    575
    Walter Library

    Perl is a scripting language that can make writing and maintaining scripts for various UNIX tasks considerably easier than trying to use one of the many shell languages. Perl is very useful, for example, for retrieving output from files of completed jobs for use in reports, input to subsequent jobs, and so forth. This hands-on tutorial will introduce everyone to the basic syntax, some powerful capabilities, and some tools to keep your code manageable and readable by others.


  • Tue Jan 27, 1:00 pm - 3:00 pm
    575
    Walter Library

    UNIX and UNIX-like systems comprise the majority of MSI computational resources. UNIX-like systems include GNU/Linux distributions, BSD, and even Mac OS X. This tutorial is designed to familiarize participants with the UNIX environment and enable them to comfortably navigate a command-line driven interface. MSI consultants will be available to answer questions related to getting connected to MSI resources or otherwise getting started at the Supercomputing Institute.


    The tutorial consists of two parts.

    1. A lecture on the basic functions of the UNIX operating system

    2. A hands-on session with sample exercises and problems provided


  • Thu Dec 4, 1:00 pm - Tue Dec 2, 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 using dozens or hundreds of processors. This tutorial includes an overview of the program?s capabilities, a detailed description of how to run the program at MSI, and tips on how to run jobs efficiently.


  • Tue Dec 2, 1:00 pm - 3:00 pm
    575
    Walter Library

    Most programs written for distributed memory, parallel computers utilize the Message Passing Interface (MPI) to exchange data or messages among processes.


    MPI derived datatype provides a powerful method to define arbitrary collections of noncontiguous data in memory and to enable the noncontiguous data movement.


    In this tutorial we will describe what the derived datatypes are and when/how to use them.


  • Thu Nov 20, 1:00 pm - 3:00 pm
    138
    Cargill Building

    The Genome Sequencer (GS) FLX from 454 Life Sciences is the ultra high-throughput instrument for conducting next-generation DNA sequencing. It can potentially generate one million sequencing readings with an average reading at about 250 bp within a single operation run.


    This technology has been used for de novo sequencing and assembly of whole genomes, resequencing whole genomes, and amplicon variation analysis.


    This tutorial will introduce the principle of 454 sequencing technology, potential application, data type, and data analysis. The main focus will be GS de novo Assembler, GS Mapper, and GS Amplicon Variation Analyzer.


  • Tue Nov 18, 1:00 pm - 3:00 pm
    575
    Walter Library

    GeneSpring is one of the most widely used microarray software packages for both one-channel and two-channel microarray data analysis. Besides the basic statistical methods, it shows strength in various normalizations, gene annotation and gene ontology analysis, and user-friendly visualizations.


    This tutorial will demonstrate with test data GeneSpring capabilities, including genome installation, data loading, experiment creation, normalization, filtering, clustering, groups comparisons, gene list Venn diagram, class prediction Tool, gene ontology, pathway, Scripts, etc.


  • Thu Nov 13, 1:00 pm - 3:00 pm
    575
    Walter Library

    Image manipulation includes such functions as cropping, rotating, resizing, adding text, photo retouching, color conversion, and much more. Image manipulation can be used when preparing photos for print or the Web or when creating animation. MSI has several programs that can be used for image manipulation; this tutorial will introduce you to three of those programs.


    Adobe Photoshop is the most popular commercial package for image manipulation. ImageMagick is a free collection of programs to display, manipulate and convert images from one format to another. ImageMagick can be used from a GUI or from the command line. GNU Image Manipulation Program (Gimp) is a free, general image-processing program for editing images.


    This tutorial serves varying interest groups ranging from medicine, biology, chemistry, physics, material sciences, geophysics, astronomy, and engineering.


  • Wed Nov 12, 1:00 pm - 3:00 pm
    575
    Walter Library

    The CCP4 suite is a large collection of programs used in most of the computations involved in protein x-ray crystallography. The package includes the programs necessary to solve x-ray crystal structures and includes a convenient GUI interface to do most calculations.


    This tutorial will delve into the CCP4 package and cover some of the more advanced features that the introductory course did not cover, using both a lecture and an open discussion format.


    Please contact Can Ergenekan during the semester if there is a particular topic you would like to discuss.


  • Tue Nov 11, 1:00 pm - 3:00 pm
    575
    Walter Library

    Looking for techniques for prediction and pattern discovery? In Part 2 of this tutorial we present a hands-on overview of SAS Enterprise Miner that will provide you with the practical experience needed to accomplish the different data mining tasks discussed in the first session of this tutorial. The second session will address the same topics as the first session: decision trees for classification tasks, regression for quantitative prediction, K-means clustering for data segmentation and reduction, and evaluation. All techniques will be illustrated with case studies. Part 1 is not a prerequisite for Part 2, but the basic description of data mining will be much more abbreviated in Part 2.


  • Tue Nov 11, 1:00 pm - 3:00 pm
    402
    Walter Library

    Description coming soon.


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