All Tutorials

  • Wed Jul 25, 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.


  • Tue Jul 24, 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 Jun 21, 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, submitting jobs on the various machines, etc. We will conclude with a brief introduction of the MSI Unix environment, including hands-on examples.


  • Wed Jun 13, 9:00 am - 2:00 pm
    402
    Walter Library

    This tutorial is presented by Mark Ebersole, NVIDIA CUDA Developer.


    9:00-10:00 Introduction to GPU Computing; CUDA 101 - An introduction to what GPU Computing is about and a brief tutorial on programming with CUDA C.


    10:30-11:30 CUDA 5 and Beyond - Come learn what's new and exciting with CUDA 5 and the Kepler architecture, and how it can further accelerate your science. Finally, where do we see CUDA going?


    12:00-1:00 Solving Sparse & Irregular Problems on GPUs


    Modern GPUs are widely recognized to excel at dense, regular computations rich with floating point arithmetic. Their throughput-oriented architecture provides tremendous raw potential, and dense computations typically achieve high percentages of peak performance. What is less widely recognized is that GPUs also perform very well on sparse, irregular computations. In fact, their high memory bandwidth coupled with massive multithreading for latency tolerance makes them well suited to these kinds of computations as well.


    Event info: http://www.facebook.com/events/323183474424250


  • Thu May 24, 1:30 pm - 3:30 pm
    402
    Walter Library

    This tutorial is designed to provide advanced information on RNA-seq analysis, including visualization tools, alternative analysis packages, other applications of RNA-seq, and trouble-shooting of common analysis problems. After this tutorial attendees will be able to analyze RNA-seq data independently or in collaboration with MSI.


    This tutorial discusses the broad impact of RNA-seq technology and outlines advanced tools to be used in the RNA-seq analysis pipeline with a focus on the visualization and effective presentation of the data and results. It also discusses “real world” issues in RNA-seq analysis, so that attendees will learn about the common errors and misunderstandings in the analysis and feel more comfortable running the analysis.


    More details can be found here:
    https://sites.google.com/a/umn.edu/galaxy-umn/home/RNASeqMod3


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

    PyMOL is a molecular viewing software used to make stunning pictures and movies for presentations and manuscripts. It is easy to pick up, because of its GUI interface, but has a lot of flexibility because of its myriad scripting options. PyMOL has the ability to export MPEG movies. A timeline feature makes the storyboarding of complex movies a snap. There is a small molecule builder and there are advanced electrostatic calculation options.


    This tutorial will take beginning users unfamiliar with molecular modeling and/or PyMOL through the basics, including how to load, draw, and manipulate molecular models; make simple scripts; and create simple pictures and movies.


  • Wed Apr 25, 1:00 pm - 4:00 pm
    575
    Walter Library

    Checkpointing HPC applications has been a challenging, but highly desired functionality for saving the state of long-running applications. This functionality hedges against failure modes from unexpected events that can cause premature failure of an application.


    This workshop will teach MSI users the available checkpointing tools that MSI supports and how to use them for checkpointing your application without modifying the code. A hands-on session of 1.5 hours will be provided, allowing attendees to implement the procedures for checkpointing your jobs.


  • Tue Apr 24, 1:00 pm - 3:00 pm
    402
    Walter Library

    This tutorial is a walk-through of an RNA-seq analysis pipeline that uses some of the most popular tools: TopHat, Cufflinks and Galaxy. Previous experience with Galaxy is not required; however, attendees are encouraged to attend the RNA-seq tutorial Module 1 first. After this tutorial, attendees will be able to analyze the RNA-seq data using TopHat and Cufflinks in Galaxy.


    The tutorial provides hand-on experience with the RNA-seq analysis programs FastQC, Fastq Groomer, TopHat, and Cufflinks. Attendees will learn how to use the bioinformatics platform Galaxy to upload, download, and analyze their RNA-seq data. Background information on the analytic tools and the working platform will be discussed. Sample data will be used for attendees to familiarize themselves with the analysis pipeline. This tutorial will also provide information on MSI support available to attendees and will encourage collaboration between MSI and local researchers.


  • Thu Apr 19, 1:00 pm - 3:00 pm
    402
    Walter Library

    This tutorial is designed to give experimental scientists a thorough overview of the practical issues involved in designing an RNA-seq experiment and the best practices in analysis of RNA-seq data. After this tutorial, attendees will be aware of the most important factors affecting the successful outcome of an RNA-seq experiment and understand the process for properly analyzing the data.


    This tutorial discusses the main parameters involved in experimental design including read length and depth, and replication required for robust statistical analysis, as well as the main steps of RNA-seq analysis: data quality assessment, data trimming and filtering, read mapping, transcriptome assembly and analysis, transcript abundance estimation, and differential expression analysis. Commonly used software and resources with further information will be identified. Detailed instruction on using individual software packages will be provided in other tutorials.


  • Tue Apr 10, 1:00 pm - 3:00 pm
    575
    Walter Library

    **This tutorial has been rescheduled for Wednesday, May 23, 10:00-noon, in 402 Walter.**


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