All Tutorials

  • Tue Feb 26, 2:00 pm - 3:15 pm
    138
    Cargill Building

    Supercomputing in Plain English: A High Performance Computing Workshop Series

    Session 6: Distributed Multiprocessing


    This is a videoconference of a workshop being presented by OSCER.


    The OU Supercomputing Center for Education & Research (OSCER) is presenting a workshop series on Supercomputing in Plain English (SiPE). MSI is videoconferencing these sessions live. While attendance at all sessions is not required, the sessions build on each other, so we recommend that you attend as many as possible to get the most value from them. Information about the complete series can be found here: http://www.oscer.ou.edu/education.php.


    Please register with MSI for each session you plan to attend. We also encourage you to register with OSCER by sending an email to hneeman@ou.edu. Knowing how many people are participating may enable them to present more workshops in the future.


  • Tue Feb 19, 2:00 pm - 3:15 pm
    138
    Cargill Building

    Supercomputing in Plain English: A High Performance Computing Workshop Series

    Session 5: Shared Memory Multithreading


    This is a videoconference of a workshop being presented by OSCER.


    The OU Supercomputing Center for Education & Research (OSCER) is presenting a workshop series on Supercomputing in Plain English (SiPE). MSI is videoconferencing these sessions live. While attendance at all sessions is not required, the sessions build on each other, so we recommend that you attend as many as possible to get the most value from them. Information about the complete series can be found here: http://www.oscer.ou.edu/education.php.


    Please register with MSI for each session you plan to attend. We also encourage you to register with OSCER by sending an email to hneeman@ou.edu. Knowing how many people are participating may enable them to present more workshops in the future.


  • Tue Feb 19, 1:00 pm - 4:00 pm
    575
    Walter Library

    The tutorial will consist of lectures and hands-on exercises covering the following topics: MSI’s GPGPU resources, basics of GPU Computing with CUDA, and better use of memory hierarchy for performance enhancement.


  • Tue Feb 12, 2:00 pm - 3:15 pm
    138
    Cargill Building

    Supercomputing in Plain English: A High Performance Computing Workshop Series

    Session 4: Stupid Compiler Tricks


    This is a videoconference of a workshop being presented by OSCER.


    The OU Supercomputing Center for Education & Research (OSCER) is presenting a workshop series on Supercomputing in Plain English (SiPE). MSI is videoconferencing these sessions live. While attendance at all sessions is not required, the sessions build on each other, so we recommend that you attend as many as possible to get the most value from them. Information about the complete series can be found here: http://www.oscer.ou.edu/education.php.


    Please register with MSI for each session you plan to attend. We also encourage you to register with OSCER by sending an email to hneeman@ou.edu. Knowing how many people are participating may enable them to present more workshops in the future.


  • Tue Feb 12, 1:00 pm - 4:00 pm

    This is a two-day workshop. Attendance is required on both February 12 and 13 (1:00 to 4:00 both days).


    ONLINE PARTICIPATION:

    People unable to attend the tutorial SNP Variant Detection Applied Tutorial in person in 575 Walter will be able to view the tutorial online through UMConnect. Please register for the tutorial as usual.


    Registered users will receive an email with the meeting information within 24 hours of the workshop start date. Please visit http://www.oit.umn.edu/umconnect/ to ensure that your system meets the minimum requirements necessary to participate in this webinar.


    IMPORTANT NOTE: To ensure completion of the computational exercises that are part of the tutorial only in-person attendees will be able to participate in the hands-on activities.


    VIRTUAL ATTENDEES WILL ONLY BE ABLE TO VIEW THE TUTORIAL.


    For our virtual attendees who may have existing MSI and Galaxy accounts, we ask them to observe the presenters’ request to not run the hands-on portion of the tutorial. Systems will be monitored and non-complying processes will be terminated.


    The tutorial will be recorded with high-definition video and audio for later viewing along with the stepwise tutorial instructions (PDF file). Please refer to our website to download the materials (https://www.msi.umn.edu/tutorial-materials). We encourage researchers who are on the waiting list or not able to attend to review this material and go through the tutorial at their leisure. RISS analysts will be able to answer questions from users with MSI research accounts; please send questions to help@msi.umn.edu (subject line: RISS tutorial).


    All registered participants will be notified before the tutorial of any changes.


    Participants are expected to be familiar with next-generation sequence data. Participants do not need previous experience with the GATK or Galaxy.


  • Tue Feb 12, 1:00 pm - 4:00 pm
    575
    Walter Library

    This is a two-day workshop. Attendance is required on both February 12 and 13 (1:00 to 4:00 both days).


    DNA resequencing with the intent to identify single nucleotide polymorphisms in individual samples is emerging as a frequent core task to identify genotypic differences in a population that may contribute to important phenotypic effects. The computational field has converged on a standardized best practices suite of tools for analyzing this type of data centered around the Genome Analysis Toolkit (GATK).


    In this hands-on tutorial, participants will perform analyses from start to finish with the goal of identifying SNP variants using data from de-identified human DNA samples. This will include (1) sample QA/QC, (2) mapping via BWA, post-processing of alignment files to remove PCR duplicates, re-calibrate basecalls and cleanup regions near indels, (3) genotype calling, (4) SNP annotation, and (5) SNP filtering and quality re-calibration.


    The first half hour of the first session will cover the basics of the Galaxy interface, so those already familiar with Galaxy can safely arrive one half-hour late for the first session.


  • Thu Feb 7, 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.


  • Tue Feb 5, 2:00 pm - 3:15 pm
    138
    Cargill Building

    Supercomputing in Plain English: A High Performance Computing Workshop Series

    Session 3: Instruction Level Parallelism


    This is a videoconference of a workshop being presented by OSCER.


    The OU Supercomputing Center for Education & Research (OSCER) is presenting a workshop series on Supercomputing in Plain English (SiPE). MSI is videoconferencing these sessions live. While attendance at all sessions is not required, the sessions build on each other, so we recommend that you attend as many as possible to get the most value from them. Information about the complete series can be found here: http://www.oscer.ou.edu/education.php.


    Please register with MSI for each session you plan to attend. We also encourage you to register with OSCER by sending an email to hneeman@ou.edu. Knowing how many people are participating may enable them to present more workshops in the future.


  • Tue Jan 29, 2:00 pm - 3:15 pm
    138
    Cargill Building

    Supercomputing in Plain English: A High Performance Computing Workshop Series

    Session 2: The Tyranny of the Storage Hierarchy


    **This is a videoconference of a workshop being presented by OSCER.**


    The OU Supercomputing Center for Education & Research (OSCER) is presenting a workshop series on Supercomputing in Plain English (SiPE). MSI is videoconferencing these sessions live. While attendance at all sessions is not required, the sessions build on each other, so we recommend that you attend as many as possible to get the most value from them. Information about the complete series can be found here: http://www.oscer.ou.edu/education.php.


    Please register with MSI for each session you plan to attend. We also encourage you to register with OSCER by sending an email to hneeman@ou.edu. Knowing how many people are participating may enable them to present more workshops in the future.


  • Tue Jan 29, 1:15 pm - 2:45 pm
    402
    Walter Library

    DNA resequencing with the intent to identify single nucleotide polymorphisms in individual samples is emerging as a frequent core task to identify genotypic differences in a population that may contribute to important phenotypic effects. The computational field has converged on a standardized best practices suite of tools for analyzing this type of data centered around the Genome Analysis Toolkit (GATK). This lecture-style tutorial will cover the background material necessary for investigators who are just entering the field, and will serve as a good introduction to the more in-depth hands-on tutorial that follows.


    General topics covered will include: Basic background on Next-Generation Sequencing (NGS) DNA-Seq experimental protocols and data formats (e.g., fastq, SAM, BAM, VCF), overview of high-level project strategies (e.g., whole genome resequencing, hybridization capture, amplicon sequencing approaches, and pooling strategies), fundamental steps in analysis, design concerns and recommendations for different organism characteristics (e.g., diploid bi-allelic, polyploid, aneuploid, multi-allelic) and internal and external resources for subsequent consultation.


    Tutorial slides are largely based on The Broad’s BroadE Workshop 2012 Dec 4-5 posted at http://www.broadinstitute.org/gatk/guide/events?id=2038#materials.


Pages