All Tutorials

  • 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


  • Thu Apr 13, 10:30 am - 12:00 pm
    402
    Walter Library

    Gene Ontology (GO) is becoming standard terminology to describe gene products in terms of their associated biological processes, cellular components, and molecular functions in a species-independent manner. It is now widely used by biologists for describing gene products and annotating genome sequences. It is especially useful to microarray researchers for classifying and interpreting gene lists that result from expression analysis. There are many software tools for GO annotation available now. In this tutorial, we will overview Gene Ontology and some GO annotation tools.


  • Thu Apr 13, 9:00 am - 10:30 am
    405
    Walter Library

    This is an introductory workshop covering the basic principles of biology. It will begin with an introduction to genome structure and composition.

    Basic biological processes such as DNA and protein synthesis, gene structure, and regulation will be discussed. Techniques such as DNA sequencing and PCR will be covered.


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


  • Thu Apr 13, 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 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 RNA transcription, promoter sequence extraction from genomic DNA, motif scanning, parse BLAST result etc to demo how bioinformatics programming can make you work easier and more efficient.


  • Thu Apr 13, 8:00 am - 8:00 am
    138
    Cargill Building

    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.


  • Tue Apr 11, 1:00 pm - 3:00 pm
    138
    Cargill Building

    Sequence evolutionary analysis is an important solution in exploring the relatedness of species or proteins. There are many programs employing a variety of algorithms. MrBayes is a program for the Bayesian estimation of phylogeny. It uses a Markov Chain Monte Carlo (MCMC) method to approximate the posterior probability distribution of trees, which is the probability of a tree conditioned on the observations.


    In this tutorial, we will discuss the Bayesian estimation theory and demonstrate the MrBayes program using test sequence data.


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