All Tutorials

  • 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.


  • Thu Jul 24, 1:00 pm - 3:00 pm
    575
    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 branched out into graphics and spreadsheets. The SAS system now has a diverse family of products, most of which are integrated together and can be used as building blocks to construct a seamless system.


    SAS is available on MSI’s supercomputers, which have large memory and huge disk spaces. By using SAS on MSI’s systems, you can free up your computer’s memory and disk space and speed up your processing time. Running SAS on MSI’s systems is also a good solution for time-consuming applications.


    In this hands-on tutorial, each attendee will have the opportunity to use SAS. We will demonstrate how to log into our system and start using SAS. Among other skills, we will learn to load, create, and combine data sets in different ways, generate random samples, post results on the Web, and make simple plots in SAS. We will also cover writing basic code, using common statements and functions in SAS, and using statistical procedures.


    This tutorial is appropriate for people who have data (not necessarily SAS data and not necessarily organized the way you want it to be) that need to be processed and analyzed statistically.


  • Tue Jul 22, 1:00 pm - 3:00 pm
    575
    Walter Library

    Image manipulation includes such functions as cropping, rotating, resizing, adding text, photo retouching, color conversion, and much more. Image manipulation can be used when preparing photos for print or the Web or when creating animation. MSI has several programs that can be used for image manipulation; this tutorial will introduce you to three of those programs.


    Adobe Photoshop is the most popular commercial package for image manipulation. ImageMagick is a free collection of programs to display, manipulate and convert images from one format to another. ImageMagick can be used from a GUI or from the command line. GNU Image Manipulation Program (Gimp) is a free general image processing program for editing images.


    The tutorial serves varying interest groups ranging from medicine, biology, chemistry, physics, material sciences, geophysics, astronomy, and engineering.


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