All Tutorials

  • Tue Nov 11, 10:00 am - 11:30 am
    402
    Walter Library

    Looking for techniques for prediction and pattern discovery? In Part 1 of this tutorial, we discuss some of the data mining capabilities provided by SAS Enterprise Miner that are applicable to a wide variety of application areas. After a brief introduction to data mining, we will cover decision trees for classification tasks, regression for quantitative prediction, and K-means clustering for data segmentation and reduction. We will also discuss ways to evaluate different approaches to a data mining problem.


    This session of the tutorial, which will be webcast, will be followed by a hands-on session at the MSI SDVL lab in the afternoon.


  • Mon Nov 10, 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 interaction 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 dataset, and build a network to depict these functional interactions. Also learn how MetaCore allows for the comparison (1-2-3 step workflow) of several datasets to determine what biology is shared or unique to each. In this session you will also learn how to overlay and visualize expression levels of objects from the same data to help you formulate more applicable hypotheses.


  • Thu Nov 6, 1:00 pm - 3:00 pm
    575
    Walter Library

    QChem is a program that can be used to calculate a variety of chemical

    properties. QChem is primarily used for carrying out electronic structure

    calculations. This tutorial includes an overview of the program?s

    capabilities, a detailed description of how to run the program at MSI, and

    tips on how to run jobs efficiently.


  • Thu Oct 30, 1:00 pm - 3:00 pm
    575
    Walter Library

    This tutorial will describe the history, evolution, and current state of molecular docking. Conformation generation and scoring will be discussed along with strengths and weaknesses of various methods. Emphasis is placed on the problems addressed with several docking algorithms and what questions can reasonably be approached with a molecular docking study.


    Note: This is not a workshop that focuses on a specific program or the technical aspects of running calculations.


  • Wed Oct 29, 1:30 pm - 4:00 pm
    402
    Walter Library

    The MathWorks, Inc. is presenting a free technical seminar demonstrating the use of MATLAB in bioinformatics research. Brian Madsen, M.S., Application Engineer Manager with The MathWorks, Inc. Will present the seminar. Check-in is from 1:00 to 1:30 and walk-ins are welcome. The seminar will include the following topics: covering sequence analysis and genotyping, access to proteomics data, analyzing microarray data, and pre-processing and analyzing MS data.


    Please register at www.mathworks.com/seminars/umn1029


  • Tue Oct 28, 1:30 pm - 3:30 pm
    575
    Walter Library

    The Crystallographic Object-Oriented Toolkit (Coot) is a free, academic software package mainly used by crystallographers to build, manipulate, refine and validate protein structures. Coot is similar to programs like O and Insight II in functionality, with the advantage of having many of the building and validation features automated. Coot also has the added benefit of being able to read the main binary files of CCP4 (.mtz files) directly to allow for easy map creation and refinement of the structure.


    This hands-on tutorial will bring the user up to speed on using Coot for the modeling portion of protein crystal structure refinement.


  • Mon Oct 27, 1:00 pm - 5:00 pm
    575
    Walter Library

    SIMULIA is the Dassault Systemes brand that delivers a scalable portfolio of Realistic Simulation solutions including Abaqus. The Abaqus Unified FEA product suite offers powerful and complete solutions for both routine and sophisticated engineering problems covering a vast spectrum of industrial applications. For example, in the automotive industry, engineering work groups are able to consider full vehicle loads, dynamic vibration, multibody systems, impact/crash, nonlinear static, thermal coupling, and acoustic-structural coupling using a common model data structure and integrated solver technology. Best-in-class companies are taking advantage of Abaqus Unified FEA to consolidate their processes and tools, reduce costs and inefficiencies, and gain a competitive advantage.


    The workshop will demonstrate how to do FEA of simple problems using Abaqus. The workshop will give students hands-on experience. The following topics may be covered: building models using Abaqus CAE; native geometry, geometry import, assemblies; finite element analysis using beam elements, shell elements, 3D solid elements; dynamic analysis using Abaqus Explicit; post-processing using Abaqus Viewer; incorporating contact in your model (if time allows).


  • Thu Oct 23, 1:00 pm - 4:00 pm
    575
    Walter Library

    Effectively using the large number of processors (1,000-100,000 and more) available on today?s (c. 2008) MPPs often requires careful structuring of the flow of information and computation for many computational tasks. Data output from thousands of processors can also present issues of efficiency and usable data format. We will discuss which MPI constructs kill scalability and techniques for producing scalable codes. Strategies and MPI constructs for overlapping interprocessor communication with computation will be discussed. We will also cover issues of weak and strong scaling, as well as efficient strategies for parallel IO.


  • Tue Oct 21, 1:00 pm - 3:00 pm
    402
    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 then output these images to different formats to be read by other applications.


    We will conclude with a hands-on session using various example images. You are also welcome to bring specific questions and problems that you would like to discuss.


  • Thu Oct 16, 1:00 pm - 3:00 pm
    575
    Walter Library

    The Schrodinger software suite is a full-featured molecular modeling package designed to solve real world problems in pharmaceutical, biotechnology, and materials science research. One major advantage over other computational chemistry packages is that little to no text editing, scripting, or otherwise manual preparation of files is necessary to get started with the suite. This introduction to molecular modeling will focus on developing input and setting up calculations with the front-end GUI Maestro, various molecular mechanics and dynamics calculations, and the technical aspects of docking, quantum mechanics, and QM/MM studies.


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