All Tutorials

  • 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.


  • Thu Apr 6, 1:00 pm - 3:00 pm
    402
    Walter Library

    This tutorial focuses on the study of ligands that exhibit optimal interactions with a known biochemical receptor. Participants will gain experience with graphical manipulations in SYBYL; building, minimizing, and aligning molecules; importing and viewing a receptor structure.


  • Tue Mar 28, 1:00 pm - 3:00 pm
    585
    Walter Library

    Writing a code with no compiling errors is the first step in completing a programming project. The second important step is to run a code efficiently on a given computer platform. This workshop will discuss general techniques for optimization of computer programs and present the code optimization and performance tuning tools that are available at the Institute.


    Users will have a chance to learn through hands-on examples how to use hardware counters and profiler tools such as pfmon and XPROFILER, for code performance evaluation, tuning, memory usage and I/O characteristics. In addition, we will discuss some tips on how to improve the performance of an application by using tuned libraries and compiler options.


  • Tue Mar 21, 1:00 pm - 3:00 pm
    402
    Walter Library

    Molpro is a program that can be used to calculate a variety of chemical properties. Molpro is primarily used for carrying out electronic structure calculations. Molpro is often the program of choice for calculating CCSD(T) energies.


    This tutorial will give an overview of the program capabilities, a detailed description of how to run the program here at the Institute, and tips on how to run jobs efficiently.


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