All Tutorials

  • Tue Mar 22, 1:00 pm - 3:00 am
    585
    Walter Library

    The GeneData Expressionist suite is a computational system from GeneData Inc. for analyzing gene expression data from any 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 walk-though practice using sample data.


  • Tue Mar 8, 1:00 pm - 3:00 pm
    402
    Walter Library

    Insight II is a common user interface for many of the Accelrys modeling, simulation and analysis tools. It can be used graphically or non-graphically. This tutorial covers Insight II as a non-graphical interface and how it can be scripted for modeling and simulation tasks. In addition, participants will learn about Insight II Base Class Library (BCL) programming to develop interfaces within Insight II for other applications.


  • Mon Mar 7, 1:00 pm - 3:00 pm
    405
    Walter Library

    Many scientific problems require the optimization of complex functions that have dozens or even thousands of local minima and maxima. Local optimization methods such as Newton-Raphson and its many variants can find nearby local extrema but have little or no chance of finding a global minimum or maximum. Using a genetic algorithm (GA) is often a very efficient means to find a global minimum or maximum for complex functions.


    This tutorial will describe how genetic algorithms work and we will discuss general optimization strategies with GAs. We will also discuss a few GA programs available and how one might parallelize a GA optimization


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

    Statistics are very important to many scientific research projects. R and S-PLUS are powerful statistical computing environments available at the Supercomputing Institute. Bell Laboratories developed the S language and environment in the 1980s for data analysis. S was further developed into a commercial product called S-PLUS. R is a dialect of the S language.


    This tutorial will demonstrate how to read and manipulate data in the R and S-PLUS environments. In addition, attendees will learn how to perform basic statistical analysis and how to produce graphics with the software packages.


  • Tue Mar 1, 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. 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.


    The workshop will combine 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 Feb 24, 1:00 pm - 3:00 pm
    402
    Walter Library

    CHARMM (Chemistry at HARvard Macromolecular Mechanics) is an academically and commercially distributed software for molecular dynamics (MD) simulations. It is used extensively to simulate the dynamic behavior of molecular and biomolecular systems as well as for free energy calculations. This tutorial will cover the fundamental theory of MD simulation and how an MD simulation can be used to study the conformational dynamics of a biomolecular system. This tutorial will also show you how to write command files for doing a simple MD simulation and how to carry out a typical analysis in CHARMM.


  • Tue Feb 22, 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, IBM SP, and the SGI Altix. For better use of OpenMP programming in high performance computing, the Supercomputing Institute will organize a one-day workshop addressing the different aspects of OpenMP, such as parallel and worksharing constructs, data scope attribute clauses, and synchronization constructs.


    A hands-on practice will follow the lecture. Provided examples 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 members will help you parallelize the code with OpenMP.


  • Thu Feb 17, 1:00 pm - 3:00 pm
    402
    Walter Library

    This tutorial will introduce the principles of a relational database system. Topics will include database modeling, database management system, SQL query, as well as schema refinement and normal forms.


  • Tue Feb 15, 1:00 pm - 3:00 pm
    402
    Walter Library

    Graphical user interfaces are a quick and easy way to get started using and learning a new software package, to tame an old complex one, or to produce some descriptive visual aids. GaussView is a handy, flexible graphical interface to the Gaussian electronic structure package. Other interfaces include Maestro for Schrödinger products and Ecce for NWChem.


    This tutorial will focus on the features of GaussView that will help you easily create input files for Gaussian, submit calculations on the various platforms, and visualize the generated output. The Maestro and Ecce interfaces will also be discussed in general.


  • Tue Feb 8, 9:00 am - Wed Feb 9, 5:00 pm
    585
    Walter Library

    This course focuses on the study of ligands that exhibit optimal interactions with a known receptor. Participants will gain experience with graphical manipulations in SYBYL; building, minimizing, and aligning molecules; importing and viewing a receptor structure; and searching databases for compounds which can bind at a given receptor site. Additionally, users will dock ligands into a receptor site.


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