All Tutorials

  • Tue Mar 25, 1:00 pm - 3:00 pm
    575
    Walter Library

    Microscopic images are mostly collected as stacks (3D) and often with time lapses (the fourth dimension). Huygens is a comprehensive deconvolution package for 3D and 4D microscopy. This tutorial will introduce users to image processing algorithms for wide-field and confocal microscopes. It will demonstrate practical applications of Huygens in deconvolution, resolution, and noise reduction for restoring images. Users will also be introduced to batch utilities in Huygens Scripting to process large numbers of image datasets automatically


  • Thu Mar 13, 10:00 am - 4:00 pm
    575
    Walter Library

    This one-day workshop on MPI will help researchers write better and portable parallel codes for distributed-memory machines like Linux clusters, such as the Institute's IBM Power4, SGI Altix, BladeCenter and Calhoun. It 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 introduces basic principles, and the hands-on portion focuses on the use of MPI principles via examples.


    Session One: Introduction to basic concepts of "MPI is Small," centering on point-to-point communication.


    Session Two: MPI collective communications including broadcast, gather, scatter, and Alltoall. Programming will be done in Fortran and C, so any background in these two languages will be helpful.


  • Tue Mar 11, 1:30 pm - 3:00 pm
    575
    Walter Library

    The Crystallographic Object-Oriented Toolkit (Coot) is a free academic software package mainly used by crystallographers to build, manipulate, 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 using the Coot software for model building, manipulation, and validation.


  • Tue Mar 4, 1:00 pm - 3:00 pm
    575
    Walter Library

    This is a hands-on workshop introducing relational databases and structural query language (SQL). Attendees will practice creating and querying databases in an Oracle environment. Topics include a brief overview of relational database design concepts and principals, and conceptual data models and constraints.


  • Thu Feb 28, 1:00 pm - 3:00 pm
    138
    Cargill Building

    With the development of genomics and proteomics, many biologists now need to handle large amounts of data for their research. Bioinformatics programming, especially Perl programming, is well-suited for biological data manipulation and analysis.


    This tutorial will introduce the fundamental concepts and mechanisms of computer programs, using Perl language as an example. We will use practical program examples such as transcription, translation, sequence retrieval, promoter sequence extraction from genomic DNA, motif scanning, parse BLAST results, etc., to demonstrate how bioinformatics programming can make your work easier and more efficient.


  • Tue Feb 26, 1:00 pm - 3:00 pm
    402
    Walter Library

    GAMESS is a program that can be used to calculate a variety of chemical properties. GAMESS 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 Feb 21, 1:00 pm - 3:00 pm
    575
    Walter Library

    GeneSpring is one of the most widely used microarray software package 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.


    This tutorial will demonstrate various capabilities of GeneSpring including genome installation, data loading, experiment creation, normalization, filtering, clustering, group comparisons, gene list Venn diagrams, and gene ontology, class prediction tool, gene ontology, pathway, Scripts, etc.


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

    Microarray is a powerful technology for biological exploration which enables researchers to simultaneously measure the level of activity of thousands of genes. It is becoming a routine experimental technique for life science research.


    This tutorial will present an overview of this technology including different microarray platforms, array design, data acquisition, data normalization, data analysis, and gene list interpretation. We will also introduce and compare several microarray software tools that MSI hosts.


  • Thu Feb 14, 1:00 pm - 3:00 pm
    575
    Walter Library

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


  • Tue Feb 12, 1:00 pm - 3:00 pm
    402
    Walter Library

    In recent years, mass spectrometry has been recognized as one of the most successful techniques in proteomics research, playing a fundamental and indispensable role in current proteomic laboratories. This tutorial will review current computational tools in mass spectrometry data analysis and show a detailed MS data analysis workflow, including spectrum reconstruction, peptide and protein identification, protein function annotation, function prediction for hypothetical proteins, data mining of quantitation MS data, and downstream bioinformatics analysis. All the corresponding computation tools will be discussed.


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