All Tutorials

  • Tue Jun 19, 10:00 am - 5:00 pm
    585
    Walter Library

    Ingenuity Pathways Analysis (IPA) is a software tool/database to model, analyze and understand complex biological systems.


    This training will cover basic and advanced usage of IPA, including the advanced search and reporting features. Example use-cases will be used to highlight functionality. Special topics, Q&A and hands-on sessions will follow the formal presentation. Users are encouraged to bring their own datasets to upload and analyze during this portion of the workshop.


    10:00 am - 11:30 am Introduction to Ingenuity Pathways Analysis


    11:30 am - 12:30 pm Lunch break


    12:30 pm - 1:45 pm Beginning training hands-on session


    1:45 pm - 2:00 pm Break


    2:00 pm - 3:15 pm Intermediate training hands-on session


    3:15 pm - 3:30 pm Break


    3:30 pm - 5:00 pm Advanced training hands-on session


  • Thu Jun 14, 1:00 pm - 3:00 pm
    402
    Walter Library

    This tutorial will introduce hardware, software, database resources and user support for bioinformatics researchers at the Supercomputing Institute. The main focus will be on the more than 100 software tools covering sequence analysis, functional genomics, proteomics, and database development, etc.


  • Thu Jun 14, 10:00 am - 4:00 pm
    585
    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, the SGI Altix, and the Netfinity Cluster. 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.


  • Tue Jun 12, 1:00 pm - 3:00 pm
    402
    Walter Library

    Schrödinger, Inc. provides a wide range of computational chemistry and molecular modeling software packages that are used to build, display, manipulate, simulate, and calculate molecular properties. Maestro is the common graphic user-interface that acts as a front-end to many of these tools. This tutorial covers the basic biomolecular building and visualization features within Maestro. We will also demonstrate its interface with some of its molecular modeling and computational chemistry modules.


  • Thu Jun 7, 1:00 pm - 3:00 pm
    402
    Walter Library

    PERL is a scripting language that can make writing and maintaining scripts for various UNIX tasks considerably easier than using one of the many shell languages. For example, PERL is very useful for retrieving output from files of completed jobs for use in reports, input to subsequent jobs, and so forth. PERL scripts are often very portable, since PERL is supported on virtually all computer platforms. PERL scripts can be extremely simple or complicated and powerful.


  • Wed Jun 6, 1:00 pm - 3:00 pm
    575
    Walter Library

    This workshop is geared to new users and will give detailed descriptions and hands-on examples of how to navigate the UNIX environment, set up accounts and submit jobs on the various machines available at MSI.


  • Tue Jun 5, 1:00 pm - 3:00 pm
    402
    Walter Library

    This tutorial is geared to new users and will provide an introduction to the facilities and computational resources of the Supercomputing Institute. All members of the Technical User Support staff, who assist with all aspects of scientific computing and visualization at the Institute, will be introduced.


  • Thu May 31, 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.


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

    GeneData Expressionist has been widely used for microarray data analysis at the University of Minnesota.


    In this tutorial, we will introduce and go through some of the newly added statistical analysis methods in Expressionist.


  • Thu Apr 26, 1:00 pm - 3:00 pm
    585
    Walter Library

    Molecular modeling is an important tool for understanding structure and function relationships in proteins, with a wide array of software packages that can be used to build and view atomic models of proteins.


    This tutorial is designed to give an overview of the basic use and functionality of some of the software packages (PyMol, Coot, InsightII, etc.) used at MSI to view and build protein models.


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