All Tutorials

  • Thu Apr 10, 1:00 pm - 3:00 pm
    402
    Walter Library

    In this tutorial, we will introduce some common approaches to the extraction of data in relational databases.


    The SAS/ACCESS interface provides methods to access relational database data. We will discuss how we can use these methods to interact with data residing on a remote server, say in an Oracle database.


    We will also introduce the SAS SQL procedure and learn how to complete many tasks with a single SQL statement while a more traditional SAS approach may involve several SAS procedures and DATA steps.


  • Tue Apr 8, 1:00 pm - 3:00 pm
    575
    Walter Library

    The majority of MPI codes use point-to-point and collective communication routines from the original MPI standard (MPI 1.1). MPI-2 implementations are being undertaken now by all vendors and provide a rich functionality to MPI. MPI-2 features include all MPI-1 features, dynamic process creation and management, one-sided communications, extended collective communications, parallel I/O, C++ and Fortran 90 binding, and other miscellaneous features.


    This tutorial will go over MPI-2 features and will cover in detail MPI-derived data types and parallel I/O. The I/O part will include data file partitioning among processes, transfer global data between memory and files (collective I/O), and asynchronous transfers. This tutorial will also provide examples on how to use these new features.


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

    Pymol is a free-for-academic-use modeling software program useful for viewing and creating figures and animation of protein models. This tutorial is designed to help users learn how to navigate and view protein models in Pymol with the goal of making figures and animations for presentations and publications.


  • Tue Apr 1, 1:00 pm - 3:00 pm
    575
    Walter Library

    This tutorial will show how to call MATLAB routines from FORTRAN and C codes. Calling MATLAB from within a FORTRAN or C code provides a convenient method for interactive visualization of computational results. The tutorial will include the description of the MATLAB communication functions, which start and end the MATLAB process, how to send data to and from MATLAB, and how to send commands to be processed in MATLAB. The presentation will be followed by a hands-on exercise to practice the mixed programming of FORTRAN or C with MATLAB with an emphasis on interactive visualization.


  • Thu Mar 27, 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 isotope-enriched medium or chemical or enzymatic modifications. Recently, an MS/MS-based quantitation method (iTRAQ) has been developed. This tutorial will cover overview of iTRAQ technology and the software for iTRAQ data analysis, ProteinPilot. Sample iTRAQ data, analysis and how to work with the results for each of the searches available in ProteinPilot software will be described. Some other computational tools to compare multiple iTRAQ experiments and the integration of protein annotations into a ProteinPilot protein summary will also be discussed.


  • Tue Mar 25, 1:00 pm - 3:00 pm
    575
    Walter Library

    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 microscopy. 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 Huygens Scripting to process large numbers of image datasets automatically


  • Thu Mar 13, 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.


  • Tue Mar 11, 1:30 pm - 3:00 pm
    575
    Walter Library

    The Crystallographic Object-Oriented Toolkit (Coot) is a free academic software package mainly used by crystallographers to build, manipulate, and validate protein structures. Coot is similar to programs like O and Insight II in functionality, with the advantage of having many of the building and validation features automated. Coot also has the added benefit of being able to read the main binary files of CCP4 (.mtz files) directly to allow for easy map creation and refinement of the structure.


    This hands-on tutorial will bring the user up to speed using the Coot software for model building, manipulation, and validation.


  • Tue Mar 4, 1:00 pm - 3:00 pm
    575
    Walter Library

    This is a hands-on workshop introducing relational databases and structural query language (SQL). Attendees will practice creating and querying databases in an Oracle environment. Topics include a brief overview of relational database design concepts and principals, and conceptual data models and constraints.


  • Thu Feb 28, 1:00 pm - 3:00 pm
    138
    Cargill Building

    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 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 results, etc., to demonstrate how bioinformatics programming can make your work easier and more efficient.


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