All Tutorials

  • Tue Apr 10, 1:00 pm - 3:00 pm
    575
    Walter Library

    **This tutorial has been rescheduled for Wednesday, May 23, 10:00-noon, in 402 Walter.**


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

    This tutorial is a walk-through of an RNA-seq analysis pipeline that uses some of the most popular tools: TopHat, Cufflinks and Galaxy. Previous experience with Galaxy is not required; however, attendees are encouraged to attend the RNA-seq tutorial Module 1 first. After this tutorial, attendees will be able to analyze the RNA-seq data using TopHat and Cufflinks in Galaxy.


    The tutorial provides hand-on experience with the RNA-seq analysis programs FastQC, Fastq Groomer, TopHat, and Cufflinks. Attendees will learn how to use the bioinformatics platform Galaxy to upload, download, and analyze their RNA-seq data. Background information on the analytic tools and the working platform will be discussed. Sample data will be used for attendees to familiarize themselves with the analysis pipeline. This tutorial will also provide information on MSI support available to attendees and will encourage collaboration between MSI and local researchers.


  • Wed Mar 28, 1:00 pm - 3:00 pm
    402
    Walter Library

    This tutorial is designed to give experimental scientists a thorough overview of the practical issues involved in designing an RNA-seq experiment and the best practices in analysis of RNA-seq data. After this tutorial, attendees will be aware of the most important factors affecting the successful outcome of an RNA-seq experiment and understand the process for properly analyzing the data.


    This tutorial discusses the main parameters involved in experimental design including read length and depth, and replication required for robust statistical analysis, as well as the main steps of RNA-seq analysis: data quality assessment, data trimming and filtering, read mapping, transcriptome assembly and analysis, transcript abundance estimation, and differential expression analysis. Commonly used software and resources with further information will be identified. Detailed instruction on using individual software packages will be provided in other tutorials.


  • Thu Mar 22, 1:00 pm - 3:00 pm
    575
    Walter Library

    This tutorial will demonstrate how to log in to MSIs computers to get started with R and how to read and manipulate data in the R environment. In addition, attendees will learn how to perform basic statistical analysis in R and produce graphics. R runs on a wide variety of UNIX platforms, Windows and MacOS. It is also available on most of the computers at MSI, including supercomputers, providing an ideal platform for long run-time and/or large memory R applications. This tutorial is a hands-on tutorial intended for those with a very basic knowledge of R acquired either from the preceding tutorial in this series or from other sources.


  • Tue Mar 20, 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.


  • Thu Mar 8, 1:00 pm - 3:00 pm
    585
    Walter Library

    Microscope images are a complex dataset consisting of multiple structures and intensities spread across various channels. Hence, visualizing and analyzing this data becomes paramount.


    Imaris helps in visualizing all standard microscope formats. It can also be used to create iso-surfaces, perform statistical analysis based on the pixel intensities and perform co-localization (identifying pixels and entities that are present in more than one channel.) In addition to these operations, it has other modules to perform specialized functions like movie generation, etc.


  • Thu Mar 1, 1:00 pm - 4:00 pm
    575
    Walter Library

    This tutorial will demonstrate how to log in to MSIs computers to get started with R and how to read and manipulate data in the R environment. In addition, attendees will learn how to perform basic statistical analysis in R and produce graphics. R runs on a wide variety of UNIX platforms, Windows and MacOS. It is also available on most of the computers at MSI, including supercomputers, providing an ideal platform for long run-time and/or large memory R applications. This tutorial is a hands-on tutorial intended for those with a very basic knowledge of R acquired either from the preceding tutorial in this series or from other sources. An additional session of this tutorial will be offered if the first session fills up and there is sufficient demand for a second session.


  • Tue Feb 28, 1:00 pm - 3:00 pm
    575
    Walter Library

    Statistics plays a key role in many scientific research projects, and increasingly, the R statistical platform is being used to perform such analysis. R, an open source version of the S statistical language developed by Bell Laboratories in the 1980s, is a powerful computing environment and language for statistical computing and graphics. More specifically, software packages from R provide capabilities for reading a wide variety of data formats, performing simple and sophisticated data manipulations, applying statistical tests and computations, and plotting the data and results of the statistical analysis. In this tutorial, we will give an overview of the basic concepts and data manipulation techniques in R. In a follow-up tutorial given the coming Thursday (March 1) afternoon, we will offer a hands-on session, where we will practice R step-by-step together.


  • Tue Feb 21, 10:00 am - 4:00 pm
    575
    Walter Library

    OpenMP is a parallel programming interface for shared-memory architectures and is available on all the core clusters. This one-day workshop will help users to use OpenMP programming more productively for high-performance computing by addressing the different aspects of OpenMP, such as parallel and worksharing constructs, data scope attribute clauses, and synchronization constructs. In addition, the new features in the OpenMP II standard will be covered.


    A hands-on practice will follow the lecture. Examples we provide will enable you to insert OpenMP directives for different parallel tasks and data scope attribute clauses. You are also encouraged to bring in your serial application codes. The instructors will help you parallelize the code with OpenMP.


  • Thu Feb 2, 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.


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