All Tutorials

  • Thu Feb 26, 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 and Volocity are two separate packages available at MSI that provide similar tools to help read and visualize all standard microscope formats. They can also be used to create iso-surfaces, perform statistical analysis based on the pixel intensities, and perform colocalization (identifying pixels and entities that are present in more than one channel.) In addition to these operations, the two software programs also have other modules that perform specialized functions like filament tracking, movie generation, etc.


  • Tue Feb 24, 1:00 pm - 3:00 pm
    575
    Walter Library

    Avizo is powerful visualization software that enables data manipulation, geometry creation, and viewing in a meaningful format. This tutorial will describe the modular approach in Avizo to build a visualization framework for different scientific data types. The tutorial will also introduce concepts in computational geometry, modeling, and surface and volume rendering in Avizo. The tutorial serves varying interest groups including medicine, biology, chemistry, physics, material sciences, geophysics, astronomy, and engineering.


    Avizo evolved from Amira. Currently the packages are almost identical, but as the programs develop, Amira will be focused on the life sciences and Avizo will be focused on engineering, manufacturing, materials science, geosciences, and other industrial and scientific domains.


    This tutorial is for users who have varying levels of experience with Avizo or Amira. The tutorial will both provide an introduction to Avizo and explore the program in greater depth based on the needs of the audience.


    Mike Marsh is from Mercury Computing, vendor of Avizo. If there is a particular feature of Avizo you would like addressed, please contact Nancy Rowe at rowe@msi.umn.edu before February 14, so that the tutorial can be structured appropriately. You can also bring your questions to the tutorial and they will be addressed as time permits.


  • Thu Feb 19, 1:00 pm - 3:00 pm
    402
    Walter Library

    Computational chemistry is a broad area of research that spans from quantum scattering to biomolecular modeling and nanotechnology. This tutorial will give a general overview of some of the methods and areas of research in computational chemistry. We will briefly explain the theory used as a basis for predictive modeling in each area discussed. We will also mention some real-life applications and the more popular programs used to carry out these calculations. Tutorials focusing on many of these programs will follow later in the semester.


  • Wed Feb 18, 10:00 am - 12:00 pm
    575
    Walter Library

    GeneGo's unique bioinformatics technology for systems biology enables complete reconstruction of mammalian cellular functionality from interactions data at the level of ligand-receptor interactions, cell signaling and regulation and core metabolism. Whether you are working with one gene or an extensive list from high throughput data, learn how to tweak out the associated cellular functionality with Basic Training using MetaCore.


    In this training you will learn how to upload your gene list or build the list using MetaCore search tools, exploit the functional enrichment of a data set and build a network to depict these functional interactions. You will also learn how MetaCore allows for the comparison (1-2-3 step workflow) of several data sets to determine what biology is shared or unique to each. In addition, we will cover how to overlay and visualize expression levels of objects from the same data to help you formulate more applicable hypotheses.


  • Tue Feb 17, 1:00 pm - 3:00 pm
    575
    Walter Library

    PEAKS is a software program for analysis of peptide mass spectrometry data. The PEAKS suite includes algorithms for protein/peptide identification, de novo sequencing, post-translational modification analysis, peak detection, and preprocessing of RAW, profile data and quantitation. PEAKS can be used in four product versions – Client, Online, Studio and Viewer. The suite of algorithms and their use in above-mentioned product versions will be introduced.


  • Thu Feb 12, 1:00 pm - 3:00 pm
    125
    Walter Library

    The LMVL is a large-screen visualization system capable of immersive visualization with 3D stereo projection and motion tracking. The system can be run as a large desktop enabling users to easily view their data in 3D stereo with software they already use on their desktop systems. The system can also be used to display high-resolution images. The screen is 28 feet wide by 7.5 feet high and can display a resolution of 7680 x 2048 in high resolution.


    This tutorial will teach users how to access the system and how to use the system in both stereo mode and high-definition mode. We will cover the software programs currently being used in the lab, the control system, motion tracking, etc.


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

    Elmo is a Sun Fire X4600 Linux cluster consisting of six computing nodes, each of which has 32 cores (AMD Opteron Model 8356) sharing memory of 128 GB, and one interactive node, which has 8 AMD Opteron (Model 8222) cores sharing memory of 32 GB. This tutorial will help users port serial and parallel (OpenMP and MPI) codes. The emphasis will be on shared memory computing.


    Attendees will have a chance to learn through hands-on examples how to use the available tools for code porting and debugging. In addition, we will discuss some tips on how to profile and improve the performance of an application.


  • Thu Feb 5, 1:00 pm - 3:00 pm
    402
    Walter Library

    PyMOL is a free-for-academic-use modeling software program useful for viewing and creating figures and animation of protein models. This tutorial is designed to help users learn how to navigate and view protein models in PyMOL with the goal of making simple figures and animations for presentations and publications. It will also prepare users for the PyMOL workshop later on in the semester, which focuses on some of the incentive programs available in the licensed version.


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

    Python is a general purpose programming language with a rich syntax and structure. It also has many modules specializing in various topics of interest to the scientific community, like mathematical and textual processing. It is also used as an interface for numerous scientific packages.


    This tutorial is divided into two parts. The first will focus on an introduction to programming with Python. Topics covered will include control structures, data types, functions, mathematical and logical operators, and program input and output. The second part of the tutorial will cover advanced topics in Python, such as issuing commands to the UNIX shell, reading and writing spreadsheet files, creating XML documents, and performing mathematical operations like a Pythonista.


  • Thu Jan 29, 1:00 pm - 3:00 pm
    575
    Walter Library

    Perl is a scripting language that can make writing and maintaining scripts for various UNIX tasks considerably easier than trying to use one of the many shell languages. Perl is very useful, for example, for retrieving output from files of completed jobs for use in reports, input to subsequent jobs, and so forth. This hands-on tutorial will introduce everyone to the basic syntax, some powerful capabilities, and some tools to keep your code manageable and readable by others.


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