All Tutorials

  • Thu May 31, 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.


  • Tue May 1, 1:00 pm - 3:00 pm
    585
    Walter Library

    GeneData Expressionist has been widely used for microarray data analysis at the University of Minnesota.


    In this tutorial, we will introduce and go through some of the newly added statistical analysis methods in Expressionist.


  • Thu Apr 26, 1:00 pm - 3:00 pm
    585
    Walter Library

    Molecular modeling is an important tool for understanding structure and function relationships in proteins, with a wide array of software packages that can be used to build and view atomic models of proteins.


    This tutorial is designed to give an overview of the basic use and functionality of some of the software packages (PyMol, Coot, InsightII, etc.) used at MSI to view and build protein models.


  • Tue Apr 24, 1:00 pm - 3:00 pm
    585
    Walter Library

    The purpose of visualization is to analyze, understand, and communicate information contained within computed data. There are various tools and techniques in computer graphics that enable raw data to be visualized in 2D and 3D.


    Amira is a powerful visualization software package that enables data manipulation, geometry creation, and viewing the data in a meaningful format.


    This tutorial will introduce concepts in modeling, surfaces, volume rendering, and measurements in Amira. It will also describe the modular approach in Amira to build a visualization framework for different scientific data types. The tutorial serves varying interest groups ranging from medicine, biology, chemistry, physics, material sciences, geophysics, astronomy, and engineering.


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

    The Institute’s IBM BladeCenter 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 BladeCenter architecture.


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


  • Tue Apr 17, 1:00 pm - 3:00 pm
    585
    Walter Library

    This is an introductory tutorial for protein sequence analysis. The tutorial will show how to use bioinformatics and computational software tools for multiple protein sequence alignments, phylogenetic analysis, pattern identification, and prediction of functional domains from primary protein sequences. ClustalW, MUSCLE, T-COFFEE, Readseq, PFAAT, Phylip, Hidden Markov Models, HMMER, Pfam and Smart will be covered. Some public online databases and resources for protein sequence analysis will also be introduced.


  • Thu Apr 12, 1:30 pm - 3:30 pm
    585
    Walter Library

    Databases play a very important role in bioinformatics. Customized Web-based databases help you to better organize your own research data and provide a more convenient way for you to view and enter your data. This tutorial will introduce you to basic skills in building a Web-based database using MSI utilities including, Perl, CGI with Oracle, and PHP with mysql.


  • Thu Apr 12, 1:30 pm - 3:30 pm
    405
    Walter Library

    Schrödinger, Inc. provides a wide range of computational chemistry and molecular modeling software tools that are used to build, display, manipulate, simulate and calculate molecular properties. One of its applications is called Glide. It is used to provide a reliable means of automatically docking small ligands into the protein active site. In addition, it also has the high throughput virtual screening (HTVS) feature that allows researchers to search through large chemical databases to identify alternative lead compounds in drug design. This tutorial will demonstrate the common graphical user interface and the basic procedure for performing a ligand docking and HTVS using Glide.


  • Thu Apr 12, 12:00 pm - 1:30 pm
    402
    Walter Library

    Bring your lunch and learn how to effectively search literature databases (e.g., MEDLINE, INSPEC) that are important in bioinformatics and computational biology. We will also explore a number of databases and tools available on the National Center for Biotechnology Information (NCBI) Web site that relate to bioinformatics literature. Finally, the session will include a look at tools for managing personal bibliographies.


  • Thu Apr 12, 10:30 am - 12:00 pm
    402
    Walter Library

    Genomics has changed the face of life sciences since the first draft of the human genome sequence was released in 2000. Microarray software tools play an important role in this change.


    The Supercomputing Institute has some of the most powerful microarray analysis tools available. These tools allow for genomics data acquisition, quality assessment, normalization, statistical analysis, functional annotation, pathway, interaction network, and data management.


    This tutorial will overview some of the Institute's microarray and pathway software tools and will compare their different features.


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