All Tutorials

  • Tue Sep 23, 10:00 am - 12:00 pm
    Walter Library

    This lecture will provide a basic overview of DGE analysis from RNA-Seq data.

    Lecture Topics:

    • - RNA-Seq vs Microarray

    • - Experimental Design 

    • - Sequencing Technology 

    • - Data Quality Assessments

    • - Mapping to a genome

    • - Differential Gene Expression (DGE)  Analysis 

  • Thu Sep 18, 2:00 pm - 5:00 pm
    Walter Library

    This tutorial is paired with Quality Control of Illumina Data using Galaxy and will take the user though the same steps but using the command line versions of the tools used in the Galaxy environment. 

    This tutorial will:

    1. Provide a brief introduction to MSI systems.
    2. Provide a very brief introduction to UNIX.
    3. Take users step-by-step though the process needed to run quality control and trimming on Illumina data at the command line.
    4. Provide users with a basic PBS script to automate the quality control and trimming process.
    5. Teach users how to edit and run the script to be used in the future. 

    Students will need to bring their own laptops to this tutorial and have some software preinstalled. Once you sign up for the tutorial, instructions for which software to have installed will be given to you.

  • Tue Sep 16, 2:00 pm - 5:00 pm
    Walter Library

    This hands-on tutorial will help a new user understand how to use the Galaxy platform to analyze NGS data by working though the quality control steps needed for Illumina sequencing data. 

    This tutorial will:

    1. Introduce the Galaxy platform to new users

    2. Explain the features of the Galaxy platform including:
          a. Data libraries
          b. Histories
          c. Workflows
          d. Getting Help

    3. Take users through the specific quality control and trimming steps needed to work with Illumina sequenceing data

  • Wed Aug 13, 1:30 pm - 4:30 pm
    Walter Library


    ANSYS Presentation: What's new in ANSYS/FLUENT 15
    Time: Wednesday, August 13th, 1:30pm - 4:30pm
    Place: MSI, Walter room 575
    Presenter: Seyed Hosseini, PhD (ANSYS Technical Services Engineer)

    Dr. Hosseini will  present what's new in Fluent 15.  He can cover  meshing techniques, multiphase models including DPM & DEM, and much more depending on audience interest.  There will be plenty of opportunity for questions and hands-on demonstrations.  Please join us to learn from an ANSYS technical services expert.

  • Thu Aug 7, 1:00 pm - 4:00 pm
    Cargill Building

    IPA staff will be on hand to introduce novice users to IPA. This workshop is geared to new IPA users and will cover uploading a dataset, normalizing the data, setting up a Core analysis, and waking through and interpreting the results. You need a email address to access IPA, please register for your IPA account here before attending class:


  • Thu Aug 7, 10:00 am - 12:00 pm
    105 Cargill Building

    IPA staff will be on campus providing an in-depth look at what IPA can do to enhance your scientific discovery. Both novice and advanced users of IPA are recommended to attend. 


  • Thu Jun 19, 9:30 am - 12:30 pm
    Walter Library

    The workshop is presented by Aditya Kalavagunta from COMSOL.

    The first portion of the workshop provides an overview of COMSOL Multiphysics:
    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. A hands-on tutorial lets you set up a first model using fast-results application interfaces. Please consider contacting Aditya Kalavagunta 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.

  • Thu May 22, 1:00 pm - 4:00 pm
    Walter Library

    Instructors: Partek Training Staff and RISS

    This hands-on tutorial will complement complement the morning lecture allowing attendees to gain experience with the workflow and analysis discussed. This session will also be webcast via UMconnect.

    Partek Genomics Suite website:

    Webcast via UMconnect:

  • Thu May 22, 9:30 am - 12:00 pm
    Walter Library

    Instructors: Partek Training Staff and RISS

    Partek Genomics Suite (PGS) allows users to analyze all manner of microarray data, from gene expression to ChIP-chip and DNA methylation. PGS includes powerful statistics and interactive visualizations to explore your data and built in workflows geared towards common analyses. This morning session will be an overview of PGS as well as a demonstration of the gene expression workflow. This session will also be webcast via UMconnect.

    MSI will no longer support Genedata or the OmicOffice suit of tools in within Spotfire. If you currently use Genedata or Spotfire to analyze your microarray data you will want to attend this session to learn how to use PGS to analyze your microarray data.

    Partek Genomics Suite website:

    Webcast via UMconnect:

  • Tue May 13, 11:00 am - 12:00 pm
    Walter Library

    This webinar will provide an overview of the AMBER Molecular Dynamics Software package with focus on what is new with regards to GPU acceleration in the recently released version 14. This includes details of peer-to-peer support and optimizations, which have resulted in version 14 being the fastest MD software package on commodity hardware. Benchmarks will be provided, along with recommended hardware choices. In addition, an overview of the new GPU centric features in AMBER 14 will be covered, including support for multi-dimensional replica exchange MD, hydrogen mass repartitioning, accelerated MD, Scaled MD, and support-as-a-service on Amazon Web Services. This is a joint webinar by Ross C. Walker, University of California San Diego, Scott Le Grand, Amazon Web Services, and Adrian Roitberg, University of Florida.