All Tutorials

  • Thu Mar 8, 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 helps in visualizing all standard microscope formats. It can also be used to create iso-surfaces, perform statistical analysis based on the pixel intensities and perform co-localization (identifying pixels and entities that are present in more than one channel.) In addition to these operations, it has other modules to perform specialized functions like movie generation, etc.


  • Thu Mar 1, 1:00 pm - 4:00 pm
    575
    Walter Library

    This tutorial will demonstrate how to log in to MSIs computers to get started with R and how to read and manipulate data in the R environment. In addition, attendees will learn how to perform basic statistical analysis in R and produce graphics. R runs on a wide variety of UNIX platforms, Windows and MacOS. It is also available on most of the computers at MSI, including supercomputers, providing an ideal platform for long run-time and/or large memory R applications. This tutorial is a hands-on tutorial intended for those with a very basic knowledge of R acquired either from the preceding tutorial in this series or from other sources. An additional session of this tutorial will be offered if the first session fills up and there is sufficient demand for a second session.


  • Tue Feb 28, 1:00 pm - 3:00 pm
    575
    Walter Library

    Statistics plays a key role in many scientific research projects, and increasingly, the R statistical platform is being used to perform such analysis. R, an open source version of the S statistical language developed by Bell Laboratories in the 1980s, is a powerful computing environment and language for statistical computing and graphics. More specifically, software packages from R provide capabilities for reading a wide variety of data formats, performing simple and sophisticated data manipulations, applying statistical tests and computations, and plotting the data and results of the statistical analysis. In this tutorial, we will give an overview of the basic concepts and data manipulation techniques in R. In a follow-up tutorial given the coming Thursday (March 1) afternoon, we will offer a hands-on session, where we will practice R step-by-step together.


  • Tue Feb 21, 10:00 am - 4:00 pm
    575
    Walter Library

    OpenMP is a parallel programming interface for shared-memory architectures and is available on all the core clusters. 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 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 we provide will enable you to insert OpenMP directives for different parallel tasks and data scope attribute clauses. You are also encouraged to bring in your serial application codes. The instructors will help you parallelize the code with OpenMP.


  • Thu Feb 2, 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 computation on images. One such toolbox, the Image Processing Toolbox, has hundreds of functions that can be used to perform operations on images.


    The various image processing 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 like 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. You are also welcome to bring specific questions and problems that you would like to discuss.


  • Thu Jan 26, 9:30 am - 4:00 pm
    575
    Walter Library

    This one-day work shop on general purpose GPU computing (GPGPU) is hosted jointly by the Supercomputing Institute and the Department of Electrical and Computer Engineering. The workshop will consist of a lecture and hands-on exercises covering the following topics: MSI’s GPGPU resources, basic CUDA programing, use of acceleration tools, and memory hierarchy for performance enhancement.


  • Tue Jan 24, 1:00 pm - 3:00 pm
    575
    Walter Library

    The UNIX operating system is a fundamental part of the MSI experience for people using the labs’ Linux workstations and core systems. Many of MSI’s scientific codes require that the user understand basic UNIX operating commands and functionality. This tutorial will give the novice user a hands-on guide to using the UNIX operating environment to navigate around and use MSI resources.


  • Wed Dec 14, 1:00 pm - 3:30 pm
    419
    University Square

    Galaxy (http://usegalaxy.org; http://galaxy.msi.umn.edu) is a bioinformatics workflow framework designed to provide a web interface to bioinformatics tools that are routinely used though generally accessed by command line. The ease with which users can share data and results, review analytical logs and create analytical pipelines contributes to the user-friendliness of the Galaxy tool. Within this framework, biologists can carry out a variety of computational analyses including meta-genomics, gene expression profiling (RNA-seq), selective re-sequencing (ChIP-seq), and Next Generation Sequencing (NGS) sequence data manipulations, without needing any programming skills. Statistical tools are also available through Galaxy. Initially developed at Pennsylvania State University, this international open source platform was adopted by the University of Minnesota as the informatics component of the Minnesota partnership HAITI (High throughput sequence Analysis Infrastructure Technology Investigation) project and implemented at MSI. Galaxy has become a key informatics resource for University of Minnesota researchers. In this tutorial, participants will become familiar with the layout of Galaxy, the scope of the tools provided, getting data into and out of Galaxy, the execution of selected tasks, the creation and manipulation of workflows, the modification of histories and their attributes, the sharing of data, workflows and histories with other users, and visualizing genomic tracks of information. For more information about Galaxy, visit http://galaxy.msi.umn.edu/home or view a Galaxy video tour at http://www.openhelix.com/galaxy.


    Access to galaxy.msi.umn.edu requires an active MSI account.


  • Thu Dec 8, 1:00 pm - 3:15 pm
    402
    Walter Library

    OpenFOAM is an open source software package which is designed to scale well on large distributed memory systems. While originally written for CFD, with its open source strategy and a large user base OpenFOAM has grown to be a general purpose finite element toolbox. This tutorial will cover the basics of using OpenFOAM to set up, solve, and view results for a variety of physical models. Techniques for running OpenFOAM on thousands of cores will be discussed. A hands-on session in 575 Walter will immediately follow this one-hour presentation.


    Presentation: 1:00-2:00 in 402 Walter


    Optional hands-on session: 2:15-3:15 in 575 Walter


  • Wed Dec 7, 1:00 pm - 3:00 pm
    575
    Walter Library

    ProTIP is a package of services that integrates analysis tools into the TROPIX framework. As part of the ProTIP project, standard analysis tools such as Sequest, X!Tandem, and Scaffold are executable from within the TINT graphical interface.


    The tutorial will include a walk-through on using ProTIP and new features included in ProTIP.


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