All Tutorials

  • Tue Sep 16, 1:00 pm - 3:00 pm
    402
    Walter Library

    Perl is a powerful interpreted language that takes very little knowledge to start using. 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 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 Sep 11, 1:00 pm - 3:00 pm
    575
    Walter Library

    The Timelogic DeCypher system implements configurable-computing technology in a unique hardware and software system. It dramatically accelerates computationally intensive bioinformatics algorithms, including BLAST, Smith-Waterman, and HMM analysis.


    This tutorial will first introduce the Web interface to the Timelogic DeCypher system. Then we will focus on the Command Line Interface (CLI) to Timelogic DeCypher, including how to create a target database, submit a search job, and retrieve results.


  • Tue Sep 9, 1:00 pm - 3:00 pm
    575
    Walter Library

    Unix is the base operating system for most systems at MSI. This tutorial is designed to familiarize users with the Unix operating environment and to help them begin to feel comfortable navigating the base functions of the operating system.


    The tutorial is broken up into two parts.

    1) A lecture on the basic functions of the UNIX operating system

    2) A 30- to 45-minute lab designed to give new and current users exercises to practice setting up accounts and trying basic commands


    For users who cannot attend the tutorial or would like a refresher, there is a Unix Web cast in the archives located at:
    http://www.msi.umn.edu/webcast/archive.html

    (third one down)


    And slides located at:
    http://static.msi.umn.edu/tutorial/hardwareprogramming/intro_to_unix_06_...


  • Tue Aug 19, 1:00 pm - 3:00 pm
    138
    Cargill Building

    GenVision from DNASTAR Inc. is a software tool for generating high-quality postscript images for genomic data visualization from annotation data. It can create circular maps or linear maps. These images can be used for visualizing thousands of data points, monitoring project progress, comparing regions of similarity, and identifying areas of interest. This tutorial will introduce the main features of GenVision and go through steps for how to create input data, specify display features, customize image and layout, and generate the postscript image for genomes.


  • Thu Aug 14, 1:00 pm - 2:30 pm
    402
    Walter Library

    FLUENT is an integrated software package for performing computational fluid dynamics. It supports simulation of flow with a wide variety of material properties in complicated geometries on unstructured meshes. Several different fluid solvers are available, which can take advantage of a variety of standard turbulence models. An extremely well developed graphical user interface facilitates initializing, solving, post processing, and visualizing flows.


    In this introductory lecture we will cover the basic operation of FLUENT, including how and where to run FLUENT at MSI. We will cover how to use the graphical user interface. Examples of how to import a mesh, select a fluid solver, set up an initial flow field, run the problem, and examine results will be given. We will discuss solving for both steady state as well as time dependent solutions.


  • Tue Aug 12, 1:00 pm - 3:00 pm
    575
    Walter Library

    GeneSpring is one of the most widely used microarray software packages for both one-channel and two-channel microarray data analysis. Besides the basically statistical methods, it shows strength in various normalizations, gene annotation and gene ontology analysis, and user friendly visualizations.


    The newest version 9.0 is fundamentally different from the previous version. Using test data, this tutorial will demonstrate GeneSpring v9.0, including technology creation, data loading, experiment creation, normalization, filtering, clustering, groups comparisons, gene list Venn diagram, gene ontology, class prediction Tool, pathway, Scripts, etc.


  • Thu Aug 7, 1:00 pm - 3:00 pm
    575
    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.


    This hands-on tutorial will introduce the basic features of Expressionist including data loading, data quality assurance, data normalization, experiment grouping, fold changes, T test, scatter plot and bar chart view, and data export. We will practice these features using demo data.


  • Tue Aug 5, 1:00 pm - 3:00 pm
    585
    Walter Library

    Microscope images are a complex dataset consisting of multiple structures and intensities spread across various channels. Hence, visualizing and analyzing this data becomes paramount.


    Imaris and Volocity are two separate packages available at MSI that provide similar tools that can help read and visualize all standard microscope formats. They can also be used to create iso-surfaces, perform statistical analysis based on the pixel intensities and perform colocalization (identifying pixels and entities that are present in more than one channel.) In addition to these operations, the two software packages also have other modules to perform specialized functions like filament tracking, movie generation, etc.


  • Thu Jul 31, 1:00 pm - 3:00 pm
    138
    Cargill Building

    The Genome Sequencer (GS) FLX from 454 Life Sciences is the ultra high-throughput instrument for conducting the next generation of DNA sequencing. It potentially can generate one million sequencing readings with an average reading at about 250 bp within a single operation run. This technology has been used for de novo sequencing and assembly of whole genomes, re-sequencing whole genomes, and amplicon variation analysis. This tutorial will introduce the principle of 454 sequencing technology, potential applications, data type, and data analysis. The main focus will be on GS de novo Assembler, GS Mapper, and GS Amplicon Variation Analyzer.


  • Tue Jul 29, 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.


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