All Tutorials

  • Tue Oct 16, 1:00 pm - 4:00 pm
    575
    Walter Library

    RNA-seq is rapidly supplanting microarray analysis as a means of comprehensively profiling gene expression due to rapidly decreasing costs and unparalleled gene isoform resolution capabilities. In the last two years, the Tuxedo Suite Tools (i.e., Bowtie, TopHat, Cufflinks and CummeRbund) have become standardized software packages to analyze this rich and complex data. The Galaxy bioinformatics framework provides an invaluable front end to these and many other analysis packages, enabling researchers without in-depth programming knowledge and command-line familiarity to carry out their own data analysis.


    In this hands-on tutorial, participants will perform standard best-practices analysis with sample Human RNA-seq data from the Human BodyMap project to illustrate from start to finish the use of RNA-seq to replace microarrays. This will include sample QA/QC, mapping via TopHat, assessing mapping statistics, visualizing data in Trackster and IGV, computing differential expression via Cuffdiff, and doing some sample comparisons via PCA analysis and clustering.


    Familiarity with using Galaxy is strongly recommended (http://usegalaxy.org/).


    Seating is limited. Please note however that this tutorial will be presented online. See details below in RNA-Seq Applied Tutorial - Analysis of Human Data Set - WEBINAR.


  • Tue Oct 16, 1:00 pm - 3:00 pm
    402
    Walter Library

    The new MSI SandyBridge addition to Itasca is now available. This informational tutorial will cover the following topics:

    1. Description of the new nodes, scheduling information and how to access them

    2. Performance of the SB nodes

    3. Code compilation examples

    4. Examples of tuning applications for the best performance.

    5. Question and answer


  • Tue Sep 18, 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 Sep 13, 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 Sep 11, 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.


    Basic knowledge of UNIX is a prerequisite for this tutorial. The following links provide an introduction to UNIX and Linux.


    http://www.tuxfiles.org/


    http://www.ee.surrey.ac.uk/Teaching/Unix/unixintro.html


  • Tue Aug 14, 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 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


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