All Tutorials

  • Thu Aug 10, 1:00 pm - 3:00 pm
    405
    Walter Library

    Molecular modeling is a general term that covers a wide range of molecular graphics and computational chemistry techniques that are used to build, display, manipulate, simulate, and calculate molecular properties. InsightII is a graphic user interface that acts as a front-end to many of these molecular modeling tools. This tutorial covers the basic biomolecular building and visualization features within InsightII, in addition to demonstrating its interface to some of its molecular modeling modules.


  • Tue Aug 8, 1:00 pm - 3:00 pm
    138
    Cargill Building

    Mascot from Matrix Science is a popular program for proteomics research. It has a powerful search engine that uses mass spectrometry data to identify a protein from a primary sequence database.


    This tutorial will introduce the main functionalities of the Mascot package, including peptide mass fingerprint, sequence query, and MS/MS ion search. We will also discuss how to use Mascot Distiller and Mascot Daemon for batch search job submission.


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

    This tutorial will discuss the general techniques for optimizing computing code and performance tuning on the Altix.


    Users will have a chance to learn through hands-on examples how to use hardware counters and profiling tools 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.


  • Thu Jul 27, 10:00 am - 4:00 pm
    585
    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, the SGI Altix, and the Netfinity Cluster. 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 Jul 25, 1:00 pm - 3:00 pm
    402
    Walter Library

    Do you want to try something user-friendly and closely related to S-PLUS to analyze microarray data? S+ARRAYANALYZER is an S-PLUS module that is a GUI (graphical user interface) driven tool for microarray data analysis. It provides a collection of powerful methods for analyzing Affymetrix MAS 5, CHP, CEL data, and two-channel microarray data.


    This tutorial will demonstrate how to use the GUI to import data and to initiate a statistical analysis through the menu (or the command line).


  • Thu Jul 20, 10:00 am - 4:00 pm
    585
    Walter Library

    OpenMP is a parallel programming interface for shared-memory architectures and is available on the IBM Regatta and the SGI Altix. This one-day workshop will help users to use OpenMP programming more productively for high-performance computing by addressing the different aspects of OpenMP, such as parallel and worksharing constructs, data scope attribute clauses, and synchronization constructs. In addition, the new features in the OpenMP II standard will be covered.


    A hands-on practice will follow the lecture. Examples provided will enable the users to insert OpenMP directives for different parallel tasks and data scope attribute clauses. The users are also encouraged to bring in their serial application codes. The User Support Staff will help you parallelize the code with OpenMP.


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

    Schrödinger, Inc. provides a wide range of computational chemistry and molecule 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. It will also demonstrate its interface with some of its molecular modeling and computational chemistry modules.


  • Thu Jul 13, 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-3D form.


    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 computational geometry, 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.


  • Tue Jul 11, 1:00 pm - 3:00 pm
    402
    Walter Library

    Computational chemistry is a broad area of research that spans from quantum scattering to biomolecular modeling to nanotechnology. This tutorial will give a general overview of some of the major areas of research in computational chemistry. We will give brief explanations of the theory used as a basis for predictive modeling in each area discussed. We will also mention some real-life applications and the more popular programs used to carry out these calculations.


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

    The GeneData Expressionist suite is a computational package from GeneData Inc. used in analyzing gene expression data from one- or two-channel microarrays. It consists of three closely integrated modules (Refiner, CoBi, and Analyst) for data quality control, data management, and statistical data analysis. This tutorial will cover the main features of each module with some practice using sample data. A new feature of Pro 3.0 will also be introduced.


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