All Tutorials

  • Thu Aug 9, 1:00 pm - 3:00 pm
    138
    Cargill Building

    Ensembl is a joint project between EMBL - EBI and the Sanger Institute to develop a software system that produces and maintains automatic annotation on selected eukaryotic genomes.


    This tutorial will introduce the main genome sequence databases, the Ensembl MySQL databases, and the Ensembl Application Programme Interface (API), which are all installed locally at the Supercomputing Institute.


  • Mon Aug 6, 1:00 pm - 3:00 pm
    585
    Walter Library

    The IBM BladeCenter is a new and important component of the computing resources at the Supercomputing Institute. This tutorial will help users quickly port serial and parallel (OpenMP and MPI) codes onto this system.


    Attendees will have a chance to learn through hands-on examples how to use the available tools for code porting and debugging. In addition, we will discuss some tips on how to profile and improve the performance of an application.


  • Thu Aug 2, 1:00 pm - 3:00 pm
    585
    Walter Library

    There are many microarray software tools, both commercially and publicly available. All these tools have the basic analysis methods; however, each also has unique features. Spotfire applies the patented Spotfire DecisionSite visualization technology and DecisionSite Statistics into microarray analysis.


    In this tutorial we will walk through Spotfire for microarray data analysis using demo data.


  • Tue Jul 31, 1:00 pm - 3:00 pm
    402
    Walter Library

    Want to use a tool similar to R/Bioconductor, but with GUI?


    Most researchers conducting microarray analysis are familiar with R/Bioconductor, but many don’t know that the most common features of R/Bioconductor plus a graphical user interface (GUI) are available in S-PLUS ArrayAnalyzer2.1. GUI makes this program more intuitive and easier to use because no coding is necessary.


    S-PLUS ArrayAnalyzer2.1 is an S-PLUS module that is a GUI-driven tool for microarray data analysis. It provides us with a collection of powerful methods for analyzing Affymetrix MAS 5, CHP, and CEL data and two-channel microarray data.


    In this tutorial, I will demonstrate how to use its GUI to import data and to initiate a statistical analysis through the menu (or the command line).


  • Thu Jul 26, 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 Jul 24, 1:00 pm - 3:00 pm
    402
    Walter Library

    Image manipulation includes such functions as cropping, rotating, resizing, adding text, photo retouching, color conversion and much more. Image manipulation can be used when preparing photos for print or the web or when creating animation. There are several programs at the Institute that can be used to do image manipulation and this tutorial will introduce you to three of those programs.


    Adobe Photoshop is the most popular commercial package for image manipulation. ImageMagick is a free collection of programs to display, manipulate and convert images from one format to another. ImageMagick can be used from a GUI or from the command line. GNU Image Manipulation Program (Gimp) is a free general image processing program for editing images.


    This tutorial serves varying interest groups including medicine, biology, chemistry, physics, material sciences, geophysics, astronomy and engineering.


  • Thu Jul 19, 1:00 pm - 3:00 pm
    402
    Walter Library

    In recent years, mass spectrometry has been recognized as one of the most successful techniques in proteomics research, playing a fundamental and indispensable role in current proteomic laboratories. Scaffold software works with SEQUEST or Mascot to identify proteins from mass spectrometry data. Scaffold lets you validate the mass spectrometry results both statistically and visually. This tutorial will cover how to use Scaffold, extracting more detailed and accurate information from SEQUEST or Mascot results for mass spectrometry data analysis.


  • Tue Jul 17, 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, especially its advanced features. 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.


  • Thu Jul 12, 1:00 pm - 3:00 pm
    402
    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 that enables data manipulation, geometry creation and viewing 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.


  • Mon Jul 9, 1:00 pm - 3:00 pm
    575
    Walter Library

    The SAS system is a collection of programs originally designed to

    perform statistical analysis of data. The SAS software started out in

    the 1970s as a package for statistical analysis. By the early 1980s, SAS

    had branched out into graphics and spreadsheets. The SAS system now has

    a diverse family of products, most of which are integrated together and

    can be used as building blocks to construct a seamless system.


    SAS is available on MSI's supercomputers, which have large memory and

    huge disk spaces. By using SAS on MSI's systems, you can free up your

    computer's memory and disk space and speed up your processing time.

    Running SAS on MSI's systems is also a good solution for time-consuming

    applications.


    In this hands-on tutorial, each attendee will have the opportunity to

    use SAS. We will demonstrate how to log into our system and start using

    SAS. Among other skills, we will learn to load, create, and combine data

    sets in different ways in SAS. We will also cover writing basic code in

    SAS and using statistical procedures.


    This tutorial is appropriate for people who have data (not necessarily

    SAS data and not necessarily organized the way you want it to be) that

    need to be processed and analyzed statistically.


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