All Tutorials

  • Tue Aug 12, 1:00 pm - 3:00 pm
    575
    Walter Library

    GeneSpring is one of the most widely used microarray software packages for both one-channel and two-channel microarray data analysis. Besides the basically statistical methods, it shows strength in various normalizations, gene annotation and gene ontology analysis, and user friendly visualizations.


    The newest version 9.0 is fundamentally different from the previous version. Using test data, this tutorial will demonstrate GeneSpring v9.0, including technology creation, data loading, experiment creation, normalization, filtering, clustering, groups comparisons, gene list Venn diagram, gene ontology, class prediction Tool, pathway, Scripts, etc.


  • Thu Aug 7, 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.


  • Tue Aug 5, 1:00 pm - 3:00 pm
    585
    Walter Library

    Microscope images are a complex dataset consisting of multiple structures and intensities spread across various channels. Hence, visualizing and analyzing this data becomes paramount.


    Imaris and Volocity are two separate packages available at MSI that provide similar tools that can help read and visualize all standard microscope formats. They can also be used to create iso-surfaces, perform statistical analysis based on the pixel intensities and perform colocalization (identifying pixels and entities that are present in more than one channel.) In addition to these operations, the two software packages also have other modules to perform specialized functions like filament tracking, movie generation, etc.


  • Thu Jul 31, 1:00 pm - 3:00 pm
    138
    Cargill Building

    The Genome Sequencer (GS) FLX from 454 Life Sciences is the ultra high-throughput instrument for conducting the next generation of DNA sequencing. It potentially can generate one million sequencing readings with an average reading at about 250 bp within a single operation run. This technology has been used for de novo sequencing and assembly of whole genomes, re-sequencing whole genomes, and amplicon variation analysis. This tutorial will introduce the principle of 454 sequencing technology, potential applications, data type, and data analysis. The main focus will be on GS de novo Assembler, GS Mapper, and GS Amplicon Variation Analyzer.


  • Tue Jul 29, 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.


  • Thu Jul 24, 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, generate random samples, post results on the Web, and make simple plots in SAS. We will also cover writing basic code, using common statements and functions 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.


  • Tue Jul 22, 1:00 pm - 3:00 pm
    575
    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. MSI has several programs that can be used for image manipulation; 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.


    The tutorial serves varying interest groups ranging from medicine, biology, chemistry, physics, material sciences, geophysics, astronomy, and engineering.


  • Thu Jul 17, 1:00 pm - 3:00 pm
    575
    Walter Library

    Amira is a powerful visualization software package that enables data manipulation, geometry creation, and viewing in a meaningful format. This tutorial will describe the modular approach in Amira to build a visualization framework for different scientific data types. We will introduce concepts in computational geometry, modeling, and surfaces and volume rendering in Amira. This tutorial serves varying interest groups including medicine, biology, chemistry, physics, material sciences, geophysics, astronomy, and engineering.


  • Tue Jul 15, 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.


  • Thu Jul 10, 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. Examples will enable the 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. MSI’s user support staff will help you parallelize the code with OpenMP.


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