All Tutorials

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

    MATLAB is an integrated technical computing environment that combines numeric computation, graphics and visualization, and a high-level programming language. MATLAB includes hundreds of functions for data analysis and visualization, numeric and symbolic computation engineering, and scientific graphics modeling and simulation.

    This tutorial consists of two parts:

    1) A 90-minute lecture describing the use of computation and visualization functions and tools.

    2) An optional one-hour, hands-on session focusing on the use of these functions for your application.

  • Thu Sep 18, 10:00 am - 4:00 pm
    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 work sharing 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 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. User Support staff will help you parallelize the code with OpenMP.

  • Tue Sep 16, 1:00 pm - 3:00 pm
    Walter Library

    Perl is a powerful interpreted language that takes very little knowledge to start using. It can be used to automate many research tasks with little effort. This includes tasks such as creating input files, parsing output files, manipulating XML data, or generating Excel documents.

    This tutorial will cover some important properties of Perl and give some examples of simple and useful Perl scripts. We will discuss modules, context, regular expressions, special variables, system calls, and references.

  • Thu Sep 11, 1:00 pm - 3:00 pm
    Walter Library

    The Timelogic DeCypher system implements configurable-computing technology in a unique hardware and software system. It dramatically accelerates computationally intensive bioinformatics algorithms, including BLAST, Smith-Waterman, and HMM analysis.

    This tutorial will first introduce the Web interface to the Timelogic DeCypher system. Then we will focus on the Command Line Interface (CLI) to Timelogic DeCypher, including how to create a target database, submit a search job, and retrieve results.

  • Tue Sep 9, 1:00 pm - 3:00 pm
    Walter Library

    Unix is the base operating system for most systems at MSI. This tutorial is designed to familiarize users with the Unix operating environment and to help them begin to feel comfortable navigating the base functions of the operating system.

    The tutorial is broken up into two parts.

    1) A lecture on the basic functions of the UNIX operating system

    2) A 30- to 45-minute lab designed to give new and current users exercises to practice setting up accounts and trying basic commands

    For users who cannot attend the tutorial or would like a refresher, there is a Unix Web cast in the archives located at:

    (third one down)

    And slides located at:

  • Tue Aug 19, 1:00 pm - 3:00 pm
    Cargill Building

    GenVision from DNASTAR Inc. is a software tool for generating high-quality postscript images for genomic data visualization from annotation data. It can create circular maps or linear maps. These images can be used for visualizing thousands of data points, monitoring project progress, comparing regions of similarity, and identifying areas of interest. This tutorial will introduce the main features of GenVision and go through steps for how to create input data, specify display features, customize image and layout, and generate the postscript image for genomes.

  • Thu Aug 14, 1:00 pm - 2:30 pm
    Walter Library

    FLUENT is an integrated software package for performing computational fluid dynamics. It supports simulation of flow with a wide variety of material properties in complicated geometries on unstructured meshes. Several different fluid solvers are available, which can take advantage of a variety of standard turbulence models. An extremely well developed graphical user interface facilitates initializing, solving, post processing, and visualizing flows.

    In this introductory lecture we will cover the basic operation of FLUENT, including how and where to run FLUENT at MSI. We will cover how to use the graphical user interface. Examples of how to import a mesh, select a fluid solver, set up an initial flow field, run the problem, and examine results will be given. We will discuss solving for both steady state as well as time dependent solutions.

  • Tue Aug 12, 1:00 pm - 3:00 pm
    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
    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
    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.