All Tutorials

  • Thu Apr 14, 10:30 am - 12:00 pm
    405
    Walter Library

    BLAST (Basic Local Alignment Search Tool) is a set of similarity search programs designed to compare novel sequences with previously characterized genes. It provides a method for rapid searching of nucleotide or protein databases. The results of similarity may provide important clues to the characterization and functionality of protein and nucleotide sequences.


    During this tutorial, participants will learn the following:


    - The basic principle of BLAST


    - Query and databases


    - Search strategies and result interpretation


    - Perform BLAST search at NCBI (National Center for Biotechnology Information)


    - NetBLAST and Standalone BLAST


    - BLAST search result parsing


  • Thu Apr 14, 9:00 am - 10:30 am
    402
    Walter Library

    With the development of genomics and proteomics, biologists will need to handle more and more data in their research. Bioinformatics programming, especially PERL programming, is a well-suited tool 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 examples such as: extraction of text files, manipulation of sequence data, parsing BLAST results, and so forth, to demonstrate how bioinformatics programming can make your work more efficient.


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

    SPSS is a powerful statistical analysis and data management system in a user-friendly graphical environment. The menus and simple dialog boxes are descriptive and easy to use. Most tasks can be accomplished by clicking the mouse and the software writes the syntax for us. SPSS is useful for many applications including those in biology and medicine related fields.


    In this tutorial, topics such as loading and exploring data, t-test, one-way ANOVA, paired sample t-test, nonparametric tests, and some regression analysis will be covered.


  • Thu Apr 7, 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 computational problems using MATLAB functions, without spending much time dealing with programming details. This tutorial starts with a quick review on MATLAB's syntax and I/O handlers. There will be a focus on the use of 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. This kind of input will be used within the tutorial whenever possible.


    This tutorial consists of two parts:


    1) A 50-minute lecture to describe the MATLAB functions

    2) An optional 1-hour, hands-on session focusing on the use of these functions for your application.


  • Tue Apr 5, 1:00 pm - 3:00 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. 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.


  • Thu Mar 31, 1:00 pm - 3:00 pm
    402
    Walter Library

    Perl is a powerful interpreted language that takes very little knowledge to get started. It can be used to automate many research tasks with little effort.


    This tutorial will cover some important properties of Perl and give some examples of simple and useful Perl scripts. We will discuss modules, context, regular expressions, special variables, system calls, and references.


  • Tue Mar 29, 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- ImarisTime, Imaris MeasurementPro, and ImarisColoc. It will demonstrate practical applications for image analysis, segmentation, object classification, quantitation, analyze co-localization, and tracking of biological structures in 2D, 3D, and 4D.


  • Thu Mar 24, 1:00 pm - 3:00 pm
    402
    Walter Library

    The SAS system is a collection of programs originally designed to perform statistical analysis of data. The SAS software started out in the 1970s as a package for statistical analysis. By the early 1980s SAS had already branched out into graphics and spreadsheets. The SAS system now has a diverse family of products. For example, it includes tools for building interfaces to the World Wide Web and compilers for the C programming language. Most of its products are integrated together and can be used as building blocks to construct a seamless system.


    In this tutorial, we will cover topics such as getting data into the SAS system, summarizing the data, getting started with some basic macro concepts, and using basic statistical procedures.


  • Tue Mar 22, 1:00 pm - 3:00 am
    585
    Walter Library

    The GeneData Expressionist suite is a computational system from GeneData Inc. for analyzing gene expression data from any one- or two-channel microarrays. It consists of three closely integrated modules: Refiner, CoBi, and Analyst (for data quality control, data management, and statistical data analysis).


    This tutorial will cover the main features of each module with some walk-though practice using sample data.


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

    Insight II is a common user interface for many of the Accelrys modeling, simulation and analysis tools. It can be used graphically or non-graphically. This tutorial covers Insight II as a non-graphical interface and how it can be scripted for modeling and simulation tasks. In addition, participants will learn about Insight II Base Class Library (BCL) programming to develop interfaces within Insight II for other applications.


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