All Tutorials

  • Tue Apr 26, 1:00 pm - 3:00 pm
    585
    Walter Library

    The SGI Altix has been a major component of computing resources at the Supercomputing Institute. With the objective of helping researchers better use this system, this tutorial will introduce some tools available on the Altix for code performance evaluation, tuning, memory usage, and application I/O characteristics. These tools include pfmon, profile.pl, histx, strace, dlook and dplace. In addition, we will discuss some tips/tricks to improve the performance of applications.


  • Thu Apr 21, 1:00 pm - 3:00 pm
    138
    Cargill Building

    There are many proteins that have similar functional and structural features but share a very low sequence similarity. For these proteins, it is not possible to apply homology modeling to predict their protein structures.


    Instead, one may examine the structure motifs. Structure motifs are individual structural features including secondary structure, sulfide bridges, turns, etc. They are essential in how a protein folds and assembles into the overall tertiary structure. In this tutorial, we will give an overview of the various types of protein structure motifs and demonstrate one of the software packages for performing structure motifs analysis, called Promotif.


  • Tue Apr 19, 1:00 pm - 3:00 pm
    1-280
    Nils Hasselmo Hall (NHH)

    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 microscopic images.


    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 the tool, Huygens Scripting, available at the Institute to process large number of image datasets automatically.


  • Thu Apr 14, 1:30 pm - 3:00 pm
    402
    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 other homologous reference proteins whose atomic structures are known.


    When the sequence region 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 14, 1:30 pm - 3:00 pm
    405
    Walter Library

    This is an introductory workshop covering the basic principles of biology. It includes DNA structure and protein synthesis, basic gene structure, and regulation. There will also be an introduction to DNA and protein sequencing.


    This workshop is designed for students and staff with limited knowledge of Biology.


  • Thu Apr 14, 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. We will also explore a number of databases and tools available on the National Center for Biotechnology Information (NCBI) web site which relate to the literature. Finally, this tutorial will include a look at tools for managing personal bibliographies.


  • Thu Apr 14, 10:30 am - 12:00 pm
    402
    Walter Library

    Microarray technology is a new high-throughput system for gene expression detections. It is becoming a routine experimental technique for life science research.


    This tutorial will overview the microarray technology including gene chip design, data acquisition, data normalization, data analysis, and gene list interpretation.


    We will also introduce and compare several microarray software tools that the Institute hosts including: GeneSpring, Expressionist, and GeneTraffic.


  • Thu Apr 14, 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 novel sequences with previously characterized genes. It provides a method for rapid searching of nucleotide or protein databases. The results of similarity may provide important clues to the characterization and functionality of protein and nucleotide sequences.


    During this tutorial, participants will learn the following:


    - The basic principle of BLAST


    - Query and databases


    - Search strategies and result interpretation


    - Perform BLAST search at NCBI (National Center for Biotechnology Information)


    - NetBLAST and Standalone BLAST


    - BLAST search result parsing


  • Thu Apr 14, 9:00 am - 10:30 am
    402
    Walter Library

    With the development of genomics and proteomics, biologists will need to handle more and more data in 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 examples such as: extraction of text files, manipulation of sequence data, parsing BLAST results, and so forth, to demonstrate how bioinformatics programming can make your work more efficient.


  • Tue Apr 12, 1:00 pm - 3:00 pm
    402
    Walter Library

    SPSS is a powerful statistical analysis and data management system in a user-friendly graphical environment. The menus and simple dialog boxes are descriptive and easy to use. Most tasks can be accomplished by clicking the mouse and the software writes the syntax for us. SPSS is useful for many applications including those in biology and medicine related fields.


    In this tutorial, topics such as loading and exploring data, t-test, one-way ANOVA, paired sample t-test, nonparametric tests, and some regression analysis will be covered.


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