All Tutorials

  • Thu Oct 2, 2:00 pm - 5:00 pm
    Walter Library
    This is a practical, hands-on tutorial designed to give participants experience with RNA-Seq

    data analysis using Tophat, Cufflinks, and CummRbund in Galaxy. The analysis in this

    tutorial is typical of experiments in eukaryotic species with high-quality genomes and

    genome annotation available. Participants are expected to be familiar with next-generation

    sequence data, basic theory of RNA-Seq, and Galaxy. Participants do not need previous

    experience with Tophat, Cufflinks, or CummeRbund.

  • Tue Sep 30, 1:00 pm - 3:00 pm
    Walter Library

    This tutorial is for new MSI users and interested individuals, and it provides an introduction to the facilities and computational resources at MSI. The quick start portion of the tutorial consists of instructions for setting up accounts, and accessing the various machines and resources. The second portion consists of a brief introduction to the MSI Linux environment, including hands-on examples. The UNIX operating system is a fundamental part of the MSI experience for people using the MSI Linux workstations and core systems. Many of MSI's scientific codes require that the user understand basic UNIX operating commands and functionality. This latter part of the tutorial will give a novice user an introduction to using the UNIX operating environment to navigate and use MSI resources.

  • Thu Sep 25, 1:00 pm - 3:00 pm
    Cargill Building

    This lecture will go over more advanced RNA-Seq topics and complements Basics of RNA-seq. 

    Lecture Topics:

    • Non-mammal specific RNA-Seq issues

    • Transcriptome assembly and other uses of RNA-Seq data

    • Sample replicate and pooling decisions

    • Advanced mapping statistics and troubleshooting 

    • Exploring the data and results from a DGE experiment

  • 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.