All Tutorials

  • Tue Apr 24, 1:00 pm - 3:00 pm
    585
    Walter Library

    The purpose of visualization is to analyze, understand, and communicate information contained within computed data. There are various tools and techniques in computer graphics that enable raw data to be visualized in 2D and 3D.


    Amira is a powerful visualization software package that enables data manipulation, geometry creation, and viewing the data in a meaningful format.


    This tutorial will introduce concepts in modeling, surfaces, volume rendering, and measurements in Amira. It will also describe the modular approach in Amira to build a visualization framework for different scientific data types. The tutorial serves varying interest groups ranging from medicine, biology, chemistry, physics, material sciences, geophysics, astronomy, and engineering.


  • Thu Apr 19, 1:00 pm - 3:00 pm
    402
    Walter Library

    The Institute’s IBM BladeCenter offers opportunities to run large chemical simulations using highly scalable computational chemistry programs. Programs that scale to hundreds of processors are vital to take advantage of the BladeCenter architecture.


    This tutorial will give an overview of the chemistry packages available and how to run them on the BladeCenter. It will give performance comparisons between the BladeCenter and other MSI machines. It will address memory usage, application-specific MPI tuning, and local scratch disk.


  • Tue Apr 17, 1:00 pm - 3:00 pm
    585
    Walter Library

    This is an introductory tutorial for protein sequence analysis. The tutorial will show how to use bioinformatics and computational software tools for multiple protein sequence alignments, phylogenetic analysis, pattern identification, and prediction of functional domains from primary protein sequences. ClustalW, MUSCLE, T-COFFEE, Readseq, PFAAT, Phylip, Hidden Markov Models, HMMER, Pfam and Smart will be covered. Some public online databases and resources for protein sequence analysis will also be introduced.


  • Thu Apr 12, 1:30 pm - 3:30 pm
    585
    Walter Library

    Databases play a very important role in bioinformatics. Customized Web-based databases help you to better organize your own research data and provide a more convenient way for you to view and enter your data. This tutorial will introduce you to basic skills in building a Web-based database using MSI utilities including, Perl, CGI with Oracle, and PHP with mysql.


  • Thu Apr 12, 1:30 pm - 3:30 pm
    405
    Walter Library

    Schrödinger, Inc. provides a wide range of computational chemistry and molecular modeling software tools that are used to build, display, manipulate, simulate and calculate molecular properties. One of its applications is called Glide. It is used to provide a reliable means of automatically docking small ligands into the protein active site. In addition, it also has the high throughput virtual screening (HTVS) feature that allows researchers to search through large chemical databases to identify alternative lead compounds in drug design. This tutorial will demonstrate the common graphical user interface and the basic procedure for performing a ligand docking and HTVS using Glide.


  • 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.


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