All Tutorials

  • Thu Nov 17, 1:00 pm - 3:00 pm
    585
    Walter Library

    Building a web interface for your database will expand the use of the database. A web-based database is more convenient for viewing and sharing data, especially in the field of bioinformatics. This tutorial will introduce you to building a web database using CGI/PERL and PHP in the Unix environment. We will cover the dynamic web page development using CGI or PHP, as well as how to connect databases such as Oracle and mySQL using DBI. SQL will also be introduced in the tutorial.


    This is a hands-on workshop. Attendees will have the opportunity to create a simple web database during the workshop.


  • Tue Nov 15, 1:00 pm - 3:00 pm
    402
    Walter Library

    NWChem is a program that can be used to calculate a variety of chemical properties. NWChem is primarily used for carrying out electronic structure calculations. This tutorial will give an overview of the program capabilities, a detailed description of how to run the program here at the Institute, and tips on how to run jobs efficiently.


  • Thu Nov 10, 12:00 pm - 4:00 pm
    585
    Walter Library

    Molecular modeling is a general term that covers a wide range of molecular graphics and computational chemistry techniques that are used to build, display, manipulate, simulate and calculate molecular properties. InsightII is a graphic user interface that acts as a front end to many of these molecular modeling tools. This workshop covers the basic biomolecular building and visualization features within InsightII, in addition to demonstrating its interface to some of its molecular modeling modules.


  • Tue Nov 8, 1:00 pm - 3:00 pm
    402
    Walter Library

    From the Web to PowerPoint presentations, animations and graphics are powerful collaboration and research tools. This tutorial will introduce some powerful tools for generating high-quality molecular images and animations for both the biologist and the chemist. We will focus on using Amira and PyMol for producing and manipulating molecular pictures and various tools for generating animations from the created images.


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

    Affymetrix GeneChip is the most widely used microarray technology in medical microarray research. The GeneChip Operating Software (GCOS) is Affymetrix freeware specific to the GeneChip instrument control, first-level data analysis, and desktop data management.


    In this tutorial, we will focus on the first level of data analysis and data quality control using GCOS.


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

    In the technical computing environment, MATLAB is a powerful high-level programming language. This tutorial will help researchers solve some computational problems using MATLAB functions without spending much time dealing with programming details. We will start with a quick review of MATLAB’s syntax and I/O handlers. More attention will be focused on the use of some computational functions and toolboxes.


    Users are encouraged to contact the User Support Staff (help@msi.umn.edu or (612) 626-0802) about the computation problems you need to solve and/or some specific issues that you meet in solving them. We will use this information to make the tutorial more productive.


    This tutorial consists of two parts:


    1. A 50-minute lecture describing the MATLAB functions


    2. An optional one-hour, hands-on session focusing on the use of these functions for your application.


  • Thu Oct 27, 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 capabilities, a detailed description of how to run the program here at the Institute, and tips on how to run jobs efficiently.


  • Tue Oct 25, 1:00 pm - 3:00 pm
    138
    Cargill Building

    Sequences evolutionary analysis is an important method for exploring the relatedness of species or proteins. There are many software tools that use different algorithms. PAUP (Phylogenetic Analysis Using Parsimony) is a widely used package for the inference of evolutionary trees. The new version 4.0 includes maximum likelihood, parsimony, and distance methods.


    In this tutorial, we will demonstrate the parsimony, maximum likelihood, and distance methods of PAUP using test sequence data.


  • Thu Oct 20, 1:00 pm - 3:00 pm
    585
    Walter Library

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

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


    This tutorial will overview around 15 of the Institute/.s microarray and pathway genomics software tools and will guide users in accessing these resources.


  • Tue Oct 18, 1:00 pm - 3:00 pm
    585
    Walter Library

    More and more biological studies involve collection and analysis of three-dimensional images varying over time, often called 4D images. IMARIS is an interactive volume visualization system for 3D and 4D biomedical data.


    This tutorial will introduce users to several features of the IMARIS modules Imaris Time, Imaris MeasurementPro, and ImarisColoc. It will demonstrate practical applications for image analysis, segmentation, object classification, quantitation, colocalization analysis, and tracking of biological structures in 2D, 3D, and 4D.


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