All Tutorials

  • Thu Mar 22, 1:00 pm - 3:00 pm
    585
    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 (available at the Institute) to process large numbers of image datasets automatically.


  • Tue Mar 20, 1:00 pm - 3:00 pm
    585
    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 includes tasks such as creating input files, parsing output files, manipulating XML data, or generating Excel documents.


    This hands-on 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.


  • Thu Mar 8, 1:00 pm - 3:00 pm
    585
    Walter Library

    Expressionist is a powerful microarray data analysis software system for Affymetrix data analysis. It provides a workflow for data loading and quality control. It offers comprehensive statistical methods for data analysis, as well as a database for data management. The new version, 3.1, added a few new features and enhancements.


    In this hands-on tutorial, we will walk through the data loading workflow and some data analysis using sample data


  • Thu Mar 1, 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 to working with graphics and spreadsheets. The SAS system now has a diverse family of products. Most of its products are integrated together and can be used as building blocks to construct a seamless system.


    In this tutorial, we will discuss a few techniques to improve SAS programming. We will go through a few examples on how to access observations and combine data efficiently, how to use lookup tables to match data, and how to measure efficiencies


  • Tue Feb 20, 1:00 pm - 3:00 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 graphics user interface that acts as a front end to many of these molecular modeling tools. This tutorial covers the basic biomolecular molecular building and visualization features within InsightII in addition to demonstrating its interface to some of its molecular modeling modules.


  • Tue Feb 13, 10:00 am - 4:00 pm
    585
    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, the SGI Altix, and the Netfinity Cluster. 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.


  • Thu Feb 8, 1:00 pm - 3:00 pm
    402
    Walter Library

    The Institute’s addition of an IBM BladeCenter significantly increased the computing power available, and introduces a unique architecture to the Institute. The 1,140 processor cores on this system are connected by an Infiniband switch for large parallel calculations.


    This tutorial will give an overview of the queuing system and compiling tools available. It will show some examples of parallel performance, as well as examples of programs that can take advantage of this computer


  • Tue Feb 6, 1:00 pm - 3:00 pm
    585
    Walter Library

    The CCP4 Suite is a collection of programs used in most computations involved in protein x-ray crystallography. The package includes programs for data processing, molecular replacement, MIR, structure refinement, and validation, as well as a graphical user interface for most of the common programs.


    This tutorial will give an overview of the programs and their use, as well as a detailed description of how to run the program here at MSI


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

    The Genome Sequencer 20 (GS20) from the 454 Life Sciences Company is a high-throughput instrument for rapid and comprehensible nucleotide sequencing. The targeted application is the sequencing of whole genomes and ultra-deep sequencing of target genes. The Rig program contains multiple applications for GS20 sequence data analysis including assembly and mapping.


    This tutorial will introduce the principle of 454 Life Sciences’ sequencing technology, data preparation, and data analysis, especially in sequence assembly and mapping


  • Tue Jan 30, 1:00 pm - 3:00 pm
    585
    Walter Library

    Tecplot is a plotting software package with extensive 2- and 3-D capabilities for visualizing technical data from analyses, simulations and experiments. It combines general engineering plotting with high-end, 3-D scientific data visualization. Tecplot is an easy software package to learn and use.


    The objective of this tutorial is to teach users how to use this tool. The tutorial consists of two parts:


    (1) A 45-minute lecture describing the capabilities of the Tecplot package.


    (2) A 1.5 hours hands-on portion focusing on the use of this tool for your application.br>

    Users are encouraged to contact the technical support staff (help@msi.umn.edu) to format your data so that the hands-on workshop can be effective. Datasets will be available to use if you want to learn Tecplot, but do not have a dataset ready


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