All Tutorials

  • Wed May 21, 1:00 pm - 4:00 pm
    575
    Walter Library

    Instructors: Partek Training Staff and RISS


    This hands-on tutorial will complement complement the morning lecture allowing attendees to gain experience with the workflow and analysis discussed. This session will also be webcast via UMconnect.


    Partek Genomics Suite website: http://www.partek.com/?q=partekgs

    Webcast via UMconnect: https://umconnect.umn.edu/pgs-tutorial/


  • Wed May 21, 9:30 am - 12:00 pm
    402
    Walter Library

    Instructors: Partek Training Staff and RISS


    Partek Genomics Suite (PGS) allows users to analyze all manner of microarray data, from gene expression to ChIP-chip and DNA methylation. PGS includes powerful statistics and interactive visualizations to explore your data and built in workflows geared towards common analyses. This morning session will be an overview of PGS as well as a demonstration of the gene expression workflow. This session will also be webcast via UMconnect.


    MSI will no longer support Genedata or the OmicOffice suit of tools in within Spotfire. If you currently use Genedata or Spotfire to analyze your microarray data you will want to attend this session to learn how to use PGS to analyze your microarray data.


    Partek Genomics Suite website: http://www.partek.com/?q=partekgs

    Webcast via UMconnect: https://umconnect.umn.edu/pgs-lecture/


  • Tue Apr 22, 9:00 am - 4:00 pm
    575
    Walter Library

    Python is a general purpose programming language with a rich syntax and structure. You can learn to use Python and see almost immediate gains in productivity relative to programming with other languages. Python has many modules specializing in various topics of interest to the scientific community and is used as an interface for numerous scientific packages.


    The morning section will provide an introduction to Python. Simple and advanced data types, variable assignment, control structures, mathematical and logical operators, program input and output, and functional programming will be discussed.


    The afternoon section will cover advanced features of Python relevant to high performance computing. Topics will include efficient data processing with NumPy and Scipy, data visualization, and techniques for using python to drive parallel supercomputing tasks.


  • Wed Apr 16, 1:00 pm - 4:00 pm
    575
    Walter Library

    This is a practical, hands-on tutorial designed to give participants experience analyzing next-generation sequence (NGS) data in Galaxy. Attendees will learn how to access their UMGC sequence datasets in Galaxy using Data Libraries, how to evaluate sequence quality using FastQC, and how to correct quality issues using trimming and filtering tools. These are the initial steps required for any NGS experiment, including RNA-Seq analysis or variant discovery. Attendees will also learn about data sharing and workflow building in Galaxy.


  • Thu Mar 27, 1:00 pm - 3:00 pm
    575
    Walter Library

    This tutorial will help users learn the basics of parallel computation methods, including strategies for collecting calculations together for parallel execution. A brief description of parallel programming using MPI message passing will be given. This will be a fast crash course on the most basic parallel computation and programming methods. Examples of how to compile and execute simple parallel programs will be given.


  • Tue Mar 25, 1:00 pm - 4:00 pm
    575
    Walter Library

    This half-day tutorial provides an introduction on how to write an accelerator program using OpenACC and will help researchers write better and portable parallel codes for accelerator (nVidia GPGPU) nodes using the PGI compiler. The tutorial will focus on basic OpenACC directives for loop parallelization, and OpenACC routines.


  • Mon Mar 24, 10:00 am - 4:00 pm
    575
    Walter Library

    This one-day, hands-on workshop provides an introduction on how to write a parallel program using MPI and will help researchers write better and portable parallel codes for distributed-memory Linux clusters. The tutorial 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 will introduce basic principles, and the hands-on portion will focus on the use of MPI principles via examples.


    Session 1: Introduction to basic concepts of MPI, centering on point-to-point communication.


    Session 2: MPI collective communications including broadcast, gather, scatter, and All-to-All. Programming will be done in Fortran and C, so any background in these two languages will be helpful.


  • Thu Mar 13, 1:00 pm - 3:00 pm
    575
    Walter Library

    This tutorial is geared to new MSI users and will provide an introduction to the facilities and computational resources at MSI. The quick start portion of the tutorial will provide instructions for accessing these resources such as setting up accounts, accessing the various machines, etc. We will conclude with a brief introduction of the MSI Unix environment, including hands-on examples. The UNIX operating system is a fundamental part of the MSI experience for people using the MSI 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 an introduction to using the UNIX operating environment to navigate around and use MSI resources.


  • Tue Mar 11, 1:00 pm - 3:00 pm
    575
    Walter Library

    This tutorial will introduce users to MSI systems, outlining the hardware available, and introducing the module and queuing systems, as well as methods for remote access and file transfer. Users will be shown how to construct queue scripts and submit their calculation jobson MSI's high-performance systems. The features of different systems will be compared so that users may determine which might best suit their research needs. Software options and availability will be discussed.


  • Fri Mar 7, 1:00 pm - 3:00 pm
    575
    Walter Library

    In the second workshop on GPU computing, more attention will be on the use of multi-GPUs for accelarating Matlab applications under the parallel computing toolbox (PCT). We will teach attendees how to distribute different (independent) portions of an application onto different GPU devices on a compute node and how to use MATLAB/CUDA interface to run some existing CUDA/C++ code.


    A hands-on practice will follow the lecture. Provided examples will enable the attendees to get direct experience of executing tests on GPU and CPU, and appreciating the performance enhancement.


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