All Tutorials

  • Thu Jan 24, 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 an 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 labs’ 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 a hands-on guide to using the UNIX operating environment to navigate around and use MSI resources.


  • Thu Dec 6, 9:00 am - 12:00 pm
    575
    Walter Library

    The workshop provides an overview of COMSOL Multiphysics version 4.3a: its capabilities, new features, enhanced functionality, and revamped graphical user interface. We will examine the model-builder-based interface which, in addition to heightened efficiency, provides new functionality to modify and quickly adapt models. A live example will be shown exemplifying both the speed and ease of the new work flow. New modules will also be looked at.


    The second half of the workshop is a hands-on tutorial in COMSOL Multiphysics Version 4.3a. A hands-on tutorial lets you set up a first model using fast-results application interfaces. Please consider contacting Mia Johansson at miaj@comsol.com with a short description of your application/interests in advance of the workshop.


    Attendees will receive a 2-week free trial to use COMSOL Multiphysics. If you bring your own laptop, you can use this trial for the hands-on session. Alternatively you can use the lab computers provided by MSI.


    Please register on the COMSOL website: http://www.comsol.com/events/cmw/22809/.


  • Wed Dec 5, 1:00 pm - 3:00 pm
    575
    Walter Library

    Kwon "John" Hong from the University of Minnesota College of Pharmacy will present a workshop on using Schrödinger software at MSI. Attendees will learn the basics of structure-based drug design with Schrödinger Suite 2012. Schrödinger provides a complete suite of software solutions with the latest advances in pharmaceutical research and computational chemistry.


  • Wed Nov 28, 1:00 pm - 4:00 pm

    **This is a two-day workshop. Attendance is required on both November 28 and 29 (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.


  • Wed Nov 28, 1:00 pm - 4:00 pm
    575
    Walter Library

    **This is a two-day workshop. Attendance is required on both November 28 and 29 (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.


  • Tue Nov 27, 1:00 pm - 3:00 pm
    575
    Walter Library

    Itasca is an HP Linux cluster with 1,091 HP ProLiant BL280c G6 blade servers and consists of 8,728 compute cores and 24 TiB of main memory. Itasca is a major component of computing resources at MSI. Hence efficient use of Itasca is important both for research groups to better use their service unit allocations and to enhance Itasca's overall performance.


    This tutorial will help MSI researchers profile their parallel (OpenMP and MPI) codes. Attendees will learn through hands-on examples how to use the available tools for code profiling. In addition, we will discuss tips on improving the performance of an application.


  • Tue Nov 13, 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.


    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.


    Webcast url: https://umconnect.umn.edu/riss-plant-rna-seq-2/


  • Tue Nov 13, 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 Nov 6, 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.


    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.


  • Tue Nov 6, 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 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 Human Data Set - WEBINAR.


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