All Tutorials

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

    Bring your lunch and learn how to effectively search literature databases (e.g., MEDLINE, INSPEC) that are important in bioinformatics and computational biology. We will also explore a number of databases and tools available on the National Center for Biotechnology Information (NCBI) Web site that relate to bioinformatics literature. Finally, the session will include a look at tools for managing personal bibliographies.


  • Thu Apr 12, 10:30 am - 12:00 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. Microarray software tools play an important role in this change.


    The Supercomputing Institute has some of the most powerful microarray analysis tools available. These tools allow for genomics data acquisition, quality assessment, normalization, statistical analysis, functional annotation, pathway, interaction network, and data management.


    This tutorial will overview some of the Institute's microarray and pathway software tools and will compare their different features.


  • Thu Apr 12, 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 to sequence databases and calculate the statistical significance of matches. It can be used to infer functional and evolutionary relationships between sequences as well as to help identify members of gene families.


    During this tutorial, participants will learn the following:


    - The basic principles of BLAST


    - Query and databases


    - Search strategies and result interpretation


    - BLAST searching at NCBI (National Center for Biotechnology Information)

    - NetBLAST and Standalone BLAST


    - BLAST search result parsing


  • Thu Apr 12, 9:00 am - 10:30 am
    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 transcription, translation, sequence retrieval, 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.


  • Wed Apr 4, 10:00 am - Thu Apr 5, 4:00 pm
    585
    Walter Library

    This two-day cell training event provides a comprehensive technical overview of the cell architecture, programming models, and software development environment. It will also cover the cell software development tool kit (SDK) plus hands-on exercise to give participants opportunities to practice cell programming.


    You will learn about the cell multi-core features and components including the Power Processor Element (PPE), Synergistic Processor Element (SPE), Memory Flow Controller (MFC), Element Interconnect Bus (EIB), and I/O and memory interfaces. To develop your application on the 9-core heterogeneous cell, you will be introduced to many cell programming concepts such as the differences between PPE and SPE instruction sets, domains of space, and threading model.


  • Tue Apr 3, 1:00 pm - 3:00 pm
    138
    Cargill Building

    HelixTree software is used for analyzing SNPs (single nucleotide polymorphisms) association with disease or drug response. It also analyzes single marker and haplotypes, calculates LD and HWE, identifies tagging SNPs, and more.


    This tutorial will walk-though the HelixTree software using sample data.


  • Thu Mar 29, 1:00 pm - 3:00 pm
    585
    Walter Library

    Many scientific problems require the optimization of multidimensional functions that have dozens or even thousands of local minima and maxima. Local optimization methods such as the Newton-Raphson method and its many variants can find nearby local extrema but have little or no chance of finding a global minimum or maximum. Using a genetic algorithm (GA) is often a very efficient means to find a global minimum or maximum for complex functions.


    This hands-on tutorial will show how genetic algorithms work and will discuss general optimization strategies with GAs. It will also work through a few GA problems using parallel GA optimization routines.


  • Tue Mar 27, 1:00 pm - 4:30 pm
    585
    Walter Library

    ABAQUS is a suite of powerful engineering simulation programs based on the finite element method. It can solve problems ranging from relatively simple linear analyses to the most challenging nonlinear simulations. ABAQUS contains an extensive library of elements that can model virtually any geometry. It has an equally extensive list of material models that can simulate the behavior of most typical engineering materials including metals, rubber, polymers, composites, reinforced concrete, crushable and resilient foams, and technical materials such as soils and rock.


    This tutorial will discuss the use of ABAQUS CAE for designing engineering models and will consist of two parts:


    (1) A lecture covering the basic equations that ABAQUS uses to solve subject given boundary conditions and material constitutive properties.


    (2) A 2.5-hour hands-on portion focusing on the use of ABAQUS CAE for designing engineering models. A few examples will be demonstrated. Attendees will reproduce one or more of the examples.


  • Thu Mar 22, 1:00 pm - 3:00 pm
    585
    Walter Library

    Microscopic images are mostly collected as stacks (3D) and often with time lapses (the fourth dimension). Huygens is a comprehensive deconvolution package for 3D and 4D microscopy.


    This tutorial will introduce users to image processing algorithms for wide-field and confocal microscopes. It will demonstrate practical applications of Huygens in deconvolution, resolution, and noise reduction for restoring images. Users will also be introduced to batch utilities in Huygens Scripting (available at the Institute) to process large numbers of image datasets automatically.


  • Tue Mar 20, 1:00 pm - 3:00 pm
    585
    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 includes tasks such as creating input files, parsing output files, manipulating XML data, or generating Excel documents.


    This hands-on 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.


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