All Tutorials

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

    TROPIX is set of caGrid web services designed to improve the flow of data from core laboratories. It can be used to share arbitrary data with user-defined groups using the TINT web interface at MSI. TROPIX is also a building block from which one can integrate analytical services, such as ProTIP, to analyze data.


    ProTIP offers an integrated solution for proteomics data analysis by utilizing resources that are available at MSI. ProTIP can be used to extract peaklists from raw data and submit these peaklists for searches to search algorithms like Sequest, X!tandem and OMSSA. The search results from these search algorithms can be further processed by using Scaffold. Moreover, search results from Mascot can also be integrated into the Scaffold workflow.


    This tutorial will introduce you to the basic structure of TROPIX and ProTIP, followed by a tutorial on setting up searches using multiple search algorithms through ProTIP. Results from earlier analyses will also be discussed during the tutorial.


  • Tue Aug 4, 1:00 pm - 3:00 pm
    138
    Cargill Building

    The Genome Sequencer (GS) FLX Titanium from Roche/454 is an ultra high-throughput instrument for conducting nucleotide sequencing. It potentially can generate one million sequencing readings with an average reading at about 400 nucleotides long within a single operation run. This tutorial will introduce the principles of 454 sequencing technology, potential applications, data types, and data analysis. The main focus will be GS de novo Assembler, GS Mapper, and GS Amplicon Variation Analyzer.


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

    The Timelogic DeCypher system implements configurable-computing technology in a unique hardware and software system. It dramatically accelerates computationally intensive bioinformatics algorithms, including BLAST, Smith-Waterman, and HMM analysis.


    This tutorial will first introduce the web interface to the Timelogic DeCypher system. Then we will focus on the Command Line Interface (CLI) to Timelogic Decypher, including how to create a target database, submit a search job, and retrieve results.


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

    MATLAB is a software package for technical computing. Its well-designed user interface, easy-to-use programming language, and wide range of mathematical, statistical, and simulation capabilities have made it a standard in many technical communities. This hands-on tutorial provides an introduction to data mining with MATLAB for users who have a basic familiarity with the program. Topics to be covered include classification, clustering, neural networks, and regression. We will also discuss how to read data into MATLAB, from both text and Excel files, and demonstrate some of MATLAB’s extensive visualization capabilities.


  • Thu Jul 23, 1:00 pm - 3:00 pm
    575
    Walter Library

    Proteomics is emerging as a powerful screening methodology for research in academic institutions and industry. A new generation of mass spectrometers with higher sensitivity and mass accuracy are now able to explore deeper into a proteome. Moreover, various methods are employed for quantitative analysis (such as iTRAQ, ICAT, SILAC, ExacTag, TMT, and spectral counting) that enable a researcher to measure comparative changes in a proteome for two or multiple samples simultaneously. All these developments have resulted in an increase in the data that is generated, which presents potential challenges for data processing of complex datasets.


    This tutorial will offer an overview of proteomics workflow, with a focus on data analysis using various software programs available at MSI.


  • Tue Jul 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 you use OpenMP programming more productively for high-performance computing by addressing the different aspects of OpenMP, such as parallel and work sharing 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. The 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 user support staff will help you parallelize the code with OpenMP.


  • Thu Jul 16, 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.


  • Wed Jul 15, 9:00 am - 11:00 am
    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 Jul 14, 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.


  • Thu Jul 9, 1:00 pm - 3:00 pm
    575
    Walter Library

    GeneSpring is one of the most widely used microarray software programs for both one-channel and two-channel microarray data analysis. Besides the basic statistical methods, it shows strength in various normalizations, gene annotation and gene ontology analysis, and user-friendly visualizations.


    Using test data, we will demonstrate GeneSpring functions including genome installation, data loading, experiment creation, normalization, filtering, clustering, group comparisons, gene list Venn diagram, and gene ontology, class prediction tool, gene ontology, pathway, Scripts, etc.


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