All Tutorials

  • Tue Jun 3, 2:30 pm - 3:30 pm
    402
    Walter Library

    This tutorial is a general introduction to the Unix operating system and other basic operations needed to use MSI's resources, including how to set up accounts and submit jobs on the various machines.


  • Tue Jun 3, 1:00 pm - 2:30 pm
    402
    Walter Library

    The Minnesota Supercomputing Institute provides high-performance computing resources, specialized research software, and user support to research groups at the University. This tutorial will give you an introduction to MSI's facilities, personnel and services, including a tour of our machine room and facilities in Walter Library.


  • Thu May 8, 1:00 pm - 3:00 pm
    402
    Walter Library

    Analyst software is used to control Applied Biosystems/MDS SCIEX mass spectrometers and other devices, configure the devices attached to instrument workstations, turn instruments, optimize systems, acquire samples, perform qualitative and quantitative analyses, and print reports. BioAnalyst software analyzes mass spectrometry data obtained from biological samples. You can perform mass reconstruction, sequence peptides, search databases, display sequence information, perform theoretical enzyme digests of protein sequences and consult a data dictionary. This tutorial will cover how to use Analyst QS and BioAnalyst to view and analyze mass spectrometry data.


  • Tue May 6, 1:00 pm - 3:00 pm
    575
    Walter Library

    Calhoun is an SGI Altix XE that offers opportunities to run large chemical simulations using highly scalable computational chemistry programs. Programs that scale to hundreds of processors are vital to take advantage of the Altix XE architecture.


    This tutorial will give an overview of the chemistry packages available and how to run them on Calhoun. We will compare performance between the Calhoun and other MSI machines. We will also address memory usage, application-specific MPI tuning, and local scratch disk.


  • Thu May 1, 1:00 pm - 3:00 pm
    138
    Cargill Building

    The Genome Sequencer (GS) FLX from 454 Life Sciences is the ultra high-throughput instrument for conducting nucleotide sequencing. It can potentially generate one million sequencing readings with an average reading at about 250 bp within a single operation run. This technology has been used for small genome sequencing, mass EST sequencing, and potentially large genome analysis. This tutorial will introduce the principle of 454 sequencing technology, data preparation, and data analysis, especially in sequence assembly and mapping. We will also discuss RNA and protein identification on the assembled genome.


  • Tue Apr 29, 1:00 pm - 3:00 pm
    575
    Walter Library

    MATLAB is a general computational platform for the rapid development of programs. It also has several toolboxes that allow specialized computations. One such toolbox, the Image Processing Toolbox, has functions that can be used to perform various operations on images. These 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 such as 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. Users are also welcome to bring specific questions and problems that they would like to discuss.


  • Thu Apr 24, 1:00 pm - 3:00 pm
    575
    Walter Library

    Single nucleotide polymorphisms (SNP) make individuals different (color, susceptibility to diseases, productivity, etc.). However, there are millions of SNPs in humans. Which SNPs are associated with particular phenotypes? HelixTree is a powerful software tool for studying SNP association with disease or drug response. It also analyzes single marker and haplotype, calculates LD and HWE, identifies tagging SNPs, and more.


    In this tutorial, we will walk through this software using sample data.


  • Tue Apr 22, 1:00 pm - 3:00 pm
    402
    Walter Library

    In this tutorial, we will start with some examples to show how to retrieve and handle genomic data, and how to perform some simple statistical analysis. We will introduce hidden Markov models and demonstrate how to detect change points in the statistical make-up of biological sequences. We will also discuss some applications in whole-genome analysis of multiple species. Techniques and tools for data processing, clustering, and classification for NDA microarray will also be discussed.


  • Thu Apr 17, 1:00 pm - 3:00 pm
    575
    Walter Library

    Mimics is a tool for the visualization and segmentation of CT/MR images and 3D rendering of segmented objects. It also provides an interface to create FEM meshes. In this tutorial, we will first focus on reading and writing images. We will then segment the images using various techniques, improve the quality of segmentation using mask tools, and obtain a 3D object. The 3D object will be stored in various 3D formats and then will be FEM meshed, and the FEM mesh will be refined globally and locally.


  • Tue Apr 15, 1:00 pm - 3:00 pm
    575
    Walter Library

    Image manipulation includes such functions as cropping, rotating, resizing, adding text, photo retouching, color conversion, and much more. Image manipulation can be used when preparing photos for print or the Web or when creating animation. MSI has several programs that can be used for image manipulation; this tutorial will introduce you to three of those programs.


    Adobe Photoshop is the most popular commercial package for image manipulation. ImageMagick is a free collection of programs to display, manipulate and convert images from one format to another. ImageMagick can be used from a GUI or from the command line. GNU Image Manipulation Program (Gimp) is a free general image processing program for editing images.


    The tutorial serves varying interest groups ranging from medicine, biology, chemistry, physics, material sciences, geophysics, astronomy, and engineering.


Pages