All Tutorials

  • Tue Nov 27, 1:30 pm - 3:00 pm
    575
    Walter Library

    The CCP4 suite is a large collection of programs used in most of the computations involved in protein x-ray crystallography. The package includes the programs necessary to solve x-ray crystal structures and includes a convenient GUI interface to do most calculations.


    This tutorial will delve into the CCP4 package and cover some of the more advanced features that the introductory course did not cover, using both a lecture and an open discussion format.


    Please contact Can Ergenekan during the semester if there is a particular topic you would like discussed.


  • Thu Nov 15, 1:00 pm - 3:00 pm
    575
    Walter Library

    The Expressionist version Pro4.0 is a comprehensive microarray data analysis system. It provides many analysis methods. In this tutorial we will demonstrate some of these complicated methods including raw data inspection, N-Way ANOVA, volcano plot, Fisher's Exact test for annotation, profile shift analysis and periodogram, Ranking, Maximal Order Preserving set (MOPS), regression, Operon identification, and analysis workflow.


  • Tue Nov 13, 1:00 pm - 3:00 pm
    575
    Walter Library

    Expressionist is a powerful microarray data analysis software system for Affymetrix data analysis. It provides a workflow for data loading and quality control. It offers comprehensive statistical methods for data analysis, as well as a database for data management.


    This hands-on tutorial will introduce the basic features of Expressionist including data loading, data quality assurance, data normalization, experiment grouping, fold changes, T test, scatter plot and bar chart view, and data export. We will practice these features using demo data.


  • Thu Nov 8, 1:00 pm - 3:00 pm
    575
    Walter Library

    Tecplot is a software package for 2D or 3D visualization of technical data obtained from analysis, experiments, and simulations. The objective of this tutorial is to teach users how to use Tecplot. This tutorial consists of three parts:


    1. A lecture describing the capabilities of Tecplot.

    2. An introduction to different graphing capabilities.

    3. A hands-on session focusing on the use of this tool for your practical applications.


  • Tue Nov 6, 1:00 pm - 3:00 pm
    402
    Walter Library

    The GCG Wisconsin Package is an integrated collection of tools for molecular biology. It includes more than 130 programs/applications for sequence analysis, database searching, DNA/RNA secondary structure, fragment assembly, gene identification, pattern analysis, and many others.


    This tutorial will cover: UNIX basic for using GCG, overview of GCG, how to get started, command line with GCG, and seqLab GUI interface for GCG.


  • Thu Nov 1, 10:00 am - 4:00 pm
    575
    Walter Library

    OpenMP is a parallel programming interface for shared-memory architectures and is available on the IBM Regatta, the Blade Center, the SGI Altix and Calhoun. This 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. Provided examples will enable users to insert OpenMP directives for different parallel tasks and data scope attribute clauses. Users are also encouraged to bring in their serial application codes. The User Support staff will help you parallelize the code with OpenMP.


  • Tue Oct 30, 1:30 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 free energy calculations. This tutorial will cover the basic 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 simple command files for doing a simple MD simulation and how to carry out a typical analysis in CHARMM.


  • Thu Oct 25, 1:00 pm - 3:00 pm
    402
    Walter Library

    R and S-PLUS are powerful computing environments and languages for statistical computing and graphics that run on a wide variety of UNIX platforms, Windows and Mac OS. Both R and S-PLUS are available on the computers, including the supercomputers, at MSI.


    Bell Laboratories developed the S language and the environment in the 1980s for data analysis. S was further developed into a commercial product called S-PLUS. R, a dialect of the S language, is free. R is available on MSI's supercomputers, which are ideal for long run-time and/or large memory R applications.


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


  • Tue Oct 23, 1:00 pm - 3:00 pm
    575
    Walter Library

    MATLAB is a general computational platform for rapid development of programs. It also has several toolboxes that allow specialized computations. One such toolbox, the Image Processing Toolbox, has functions that can be used to perform various operations on images.


    These operations can be classified into reading, processing, and writing images. We will begin the tutorial by performing simple image reading operations on jpeg, gif, etc. We will also discuss reading complex image formats like DICOM. We will then perform various image processing operations such as filtering, visualization, and analysis. We will output these images to different formats to be read by other applications.


    Finally we will conclude with hands-on practice using various example images. Users are also welcome to bring specific questions and problems that they would like to discuss.


  • Thu Oct 18, 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.


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