All Tutorials

  • Thu Jun 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 May 4, 1:00 pm - 3:00 pm
    402
    Walter Library

    In this tutorial, we will introduce some common approaches to the extraction of data in relational databases.


    The SAS/ACCESS interface provides methods to access relational database data. In this tutorial we will discuss how we can use these methods to interact with data residing on a remote server (for example, in an Oracle database).


    We will also introduce the SAS SQL procedure and learn how to complete many tasks with a single SQL statement, while a more traditional SAS approach may involve several SAS procedure and DATA steps.


    Any researchers interested in using databases and SAS to enhance data mining and analysis procedures will find this tutorial helpful.


  • Tue May 2, 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.


  • Thu Apr 27, 1:00 pm - 3:00 pm
    402
    Walter Library

    Perl is a powerful interpreted language that takes very little knowledge to get started. It can be used to automate many research tasks with little effort. This might include tasks such as creating input files, parsing output files, manipulating XML data, or generating Excel documents.


    This tutorial will cover some important properties of Perl and give some examples of simple and useful Perl scripts. We will discuss modules, context, regular expressions, special variables, system calls, and references.


  • Thu Apr 20, 1:00 pm - 3:00 pm
    585
    Walter Library

    MATLAB, FORTRAN, and C are the languages commonly used in scientific computations. Each one has its own strength and weakness. A combination of MATLAB with FORTRAN or C can greatly increase the computational flexibility of your application.


    This tutorial will show how to call MATLAB routines from FORTRAN and C codes, which provides a convenient method for interactive visualization of computational results. It 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 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.


  • Tue Apr 18, 1:00 pm - 3:00 pm
    585
    Walter Library

    VOLOCITY is an interactive volume visualization system for 3D and 4D biomedical data, such as those collected from fluorescence microscopy. This tutorial will introduce users to several features of VOLOCITY modules. It will demonstrate practical applications for image analysis, segmentation, object classification, quantitation, and tracking of biological structures in 2D, 3D and 4D. The Movie Sequencer authoring tool that enables creation of volume animation templates will also be shown.


  • Thu Apr 13, 1:30 pm - 3:00 pm
    405
    Walter Library

    HOMOLOGY is a module within a commercially available software package called Insight II. It is used to help build the structure of a protein by comparing its amino acid sequence with homologous reference proteins whose atomic structures are known.


    When the sequence regions of two proteins share a high level of sequence similarity, the conformations of these two regions are assumed to be conserved, and the structure of the unknown protein is generated based on this reference protein structure.


    This tutorial will cover the basic fundamental theory of HOMOLOGY, as well as the basic procedure to generate protein structures from sequences using HOMOLOGY.


  • Thu Apr 13, 1:30 pm - 3:00 pm
    402
    Walter Library

    The Integrated Microbial Genomes (IMG) system (http://img.jgi.doe.gov) provides a framework for comparative analysis of genomes sequenced by the Joint Genome Institute. Its goal is to facilitate the visualization and exploration of genomes from a functional and evolutionary perspective. IMG aims at providing high levels of data diversity in terms of integrated genomes, data coherence in terms of gene annotation quality, data completeness in terms of breadth of functional annotations, and system comprehensibility in terms of documenting its structural and operational semantics. IMG was released in March 2005 and is updated on a quarterly basis.


  • Thu Apr 13, 12:00 pm - 1:30 pm
    402
    Walter Library

    This tutorial will provide attendees with an introduction to effectively searching literature databases (e.g., MEDLINE, INSPEC), which are well suited to bioinformatics and computational biology. It will also explore a number of databases and tools available on the National Center for Biotechnology Information (NCBI) web site, which relates to the literature. Finally, this tutorial will include a look at tools for managing personal bibliographies.


  • Thu Apr 13, 10:30 am - 12:00 pm
    405
    Walter Library

    BLAST (Basic Local Alignment Search Tool) is a set of similarity search programs designed to compare nucleotide or protein sequences with previously characterized genes. It provides a method for rapid searching of nucleotide or protein databases. The similarity results may provide important clues to the characterization and functionality of protein and nucleotide sequences.


    During this tutorial the following will be covered:

    The basic principle of BLAST

    Queries and databases

    Search strategies and result interpretation

    BLAST searches at the NCBI (National Center for Biotechnology Information)

    NetBLAST and Standalone BLAST

    BLAST search result parsing


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