All Tutorials

  • Tue Oct 16, 1:30 pm - 3:00 pm
    575
    Walter Library

    The CCP4 suite is a collection of programs used in most of the computations involved in protein x-ray crystallography. The package includes programs for data processing, molecular replacement, MIR, structure refinement, and validation, as well as a graphical user interface for most of the common programs.


    This tutorial will give an overview of the programs and their use, as well as a detailed description of how to run the program here at MSI.


  • Thu Oct 11, 1:00 pm - 3:00 pm
    402
    Walter Library

    Gaussian is a program that can be used to calculate a variety of chemical properties and is primarily used for carrying out electronic structure calculations. This tutorial will give an overview of the program capabilities, a detailed description of how to run the program at the Institute, and tips on how to run jobs efficiently.


  • Tue Oct 9, 10:00 am - 4:00 pm
    575
    Walter Library

    This one-day workshop on MPI will help researchers write better and portable parallel codes for distributed-memory machines like Linux clusters, such as the Institute's IBM Power4, SGI Altix, BladeCenter and Calhoun. It will focus on basic point-to-point communication and collective communications, which are the most commonly used MPI routines in high-performance scientific computation. In addition, the advantage of using MPI non-blocking communication will be introduced. Each session of the workshop will combine a lecture with hands-on practice. The lecture introduces basic principles, and the hands-on portion focuses on the use of MPI principles via examples.


    Session One: Introduction to basic concepts of "MPI is Small," centering on point-to-point communication.


    Session Two: MPI collective communications including broadcast, gather, scatter, and Alltoall.


    Programming will be done in Fortran and C, so any background in these two languages will be helpful.


  • Thu Oct 4, 1:00 pm - 3:00 pm
    402
    Walter Library

    The Supercomputing Institute has three commercial pathway analysis software packages, Ingenuity Pathways Analysis (Ingenuity Systems), MetaCore (GeneGo) and PathwayStudio (Ariadne). These tools are used to build and examine biological association networks, including canonical pathways, protein-small molecule and protein-protein interaction networks, as well as protein distribution by diseases, for a more complete systems biology network view. This tutorial will explain how to use these software packages to analyze genomics and proteomic data.


  • Tue Oct 2, 1:00 pm - 3:00 pm
    138
    Cargill Building

    The Genome Sequencer (GS) FLX from 454 Life Sciences is the high-throughput instrument for conducting nucleotide sequencing. It can potentially generate one million sequencing readings with an average reading at about 250 bp within a single operation run. This technology has been used for small genome sequencing, mass EST sequencing, and potentially large genome analysis. This tutorial will introduce the principle of 454 sequencing technology, data preparation, and data analysis, especially in sequence assembly and mapping. We will also discuss RNA and protein identification on the assembled genome.


  • Thu Sep 27, 1:00 pm - 3:00 pm
    402
    Walter Library

    Schroedinger, Inc. provides a wide range of computational chemistry and molecular modeling software packages that are used to build, display, manipulate, simulate, and calculate molecular properties. Maestro is the common graphic user-interface that acts as a front-end to many of these tools. This tutorial covers the basic biomolecular building and visualization features within Maestro. We will also demonstrate its interface with some of its molecular modeling and computational chemistry modules.


  • Wed Sep 26, 3:00 pm - 4:00 pm
    575
    Walter Library

    Mimics is a tool for the visualization and segmentation of CT/MR images and 3D rendering of segmented objects. It also provides an interface to create FEM meshes. In this tutorial, we will first focus on reading and writing images. We will then segment the images using the various techniques, improve the quality of segmentation using mask tools, and obtain a 3D object. The 3D object will be stored in various 3D formats and then will be FEM meshed, and the FEM mesh will be refined globally and locally.


  • Tue Sep 25, 1:00 pm - 4:00 pm
    575
    Walter Library

    MATLAB is an integrated technical computing environment that combines numeric computation, graphics and visualization, and a high-level programming language. MATLAB includes hundreds of functions for data analysis and visualization, numeric and symbolic computation engineering, and scientific graphics modeling and simulation. This tutorial consists of two parts: 1. A 90-minute lecture describing the use of computation and visualization functions and tools. 2. An optional one-hour, hands-on session focusing on the use of these functions for your application.


  • Thu Sep 20, 1:00 pm - 3:00 pm
    575
    Walter Library

    PERL is a scripting language that can make writing and maintaining scripts for various UNIX tasks considerably easier than using one of the many shell languages. For example, PERL is very useful for retrieving output from files of completed jobs for use in reports, input to subsequent jobs, and so forth. PERL scripts are often very portable, since PERL is supported on virtually all computer platforms. PERL scripts can be extremely simple or complicated and powerful.


  • Tue Sep 18, 1:00 pm - 3:00 pm
    402
    Walter Library

    Proteomics research includes the characterization of protein mixtures in order to understand complex biological systems and determine relationships between proteins, their function, and protein-protein interactions. Established methods for relative quantitation of proteins involve growth on an isotope-enriched medium or chemical or enzymatic modifications. Recently, an MS/MS-based quantitation method (iTRAQ) has been developed. This tutorial will provide an overview of iTRAQ technology and ProteinPilot, the software for iTRAQ data analysis. Sample iTRAQ data, analysis, and how to work with the results for each of the searches available in ProteinPilot will be described. We will also discuss computation tools to compare multiple iTRAQ experiments and integration of protein annotations into the ProteinPilot protein summary.


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