All Tutorials

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

    In this two-hour WebEx workshop, attendees will learn the basics of structure-based drug design with Schrödinger Suite 2012. The workshop will begin with a short presentation on best practices for structure-based drug design, followed by a hands-on training session designed to help attendees gain competence and confidence with Maestro, Schrödinger's graphical interface to Schrödinger's modeling software. Workshop attendees will also learn how to use Glide to set up and analyze the results of a docking calculation.


    Although we recommend that tutorial participants attend the tutorial in Walter Library, users may log in from remote sites. Please note that we will not be able to provide the same level of support to remote users and that the software may run more slowly when logging in remotely. Users may bring a laptop to Walter Library or they may use the lab workstations. Please register as usual. Registered users will receive meeting information by email within 24 hours of the workshop start date. Remote participants either need to have speakers on their machine or access to a telephone for the audio portion of the conference.


  • Wed Oct 31, 9:30 am - 4:00 pm
    575
    Walter Library

    MSI will host a one-day workshop on general purpose GPU computing (GPGPU). The workshop will consist of a lecture and hands-on exercises covering the following topics: MSI’s GPGPU resources, basic CUDA and OpenACC programing, use of acceleration tools, and memory hierarchy for performance enhancement.


  • Tue Oct 23, 1:00 pm - 4:00 pm

    ONLINE PARTICIPATION:

    People unable to attend the tutorial RNA-Seq Applied Tutorial - Analysis of Plant Data Set 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.


  • Tue Oct 23, 1:00 pm - 4:00 pm
    138
    Cargill Building

    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 RNA-seq data from pathogen-infected and mock-infected potato tubers to illustrate from start to finish the use of RNA-seq to replace microarrays. This will include sample QA/QC, mapping with TopHat, assessing mapping statistics, visualizing data in IGV, computing differential expression with Cuffdiff, and sample clustering with MDS plots.


    Participants are expected to be familiar with next-generation sequence data and basic theory of RNA-Seq. Participants do not need previous experience with Tophat, Cufflinks, or Galaxy.


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


  • Tue Oct 16, 1:00 pm - 4:00 pm

    ONLINE PARTICIPATION:

    People unable to attend the tutorial RNA-Seq Applied Tutorial - Analysis of Human Data Set 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.


  • 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


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