All Tutorials

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

    The Supercomputing Institute hosts several proteomic software tools to meet the growing needs of proteomics research at the university. ClinProTools is a mass spectra data post-processing software package used for visualization, data reduction, and data mining, and for building predictive models. It combines intuitive visualization features and multiple mathematical algorithms to generate pattern recognition models from mass spectrometry-based profiling data. This can be used, for example, to classify and predict disease.


    In this tutorial, we use sera protein mass spectra sample data to demonstrate the use of the ClinProTools software package.


  • Thu Aug 17, 1:00 pm - 3:00 pm
    402
    Walter Library

    Statistics are very important to many scientific research projects. R and S-PLUS are powerful statistical computing languages and environments available at the Supercomputing Institute. Bell Laboratories developed the S language and the environment in the 1980s for data analysis. S was further developed into a commercial product called S-PLUS. R is a dialect of the S language.


    This tutorial will demonstrate how to read and manipulate data in the R and S-PLUS environments. In addition, attendees will learn how to perform basic statistical analysis in R and how to produce graphics with the software packages.


  • Tue Aug 15, 1:00 pm - 3:00 pm
    585
    Walter Library

    In the technical computing environment MATLAB is a powerful, high-level programming language. This tutorial is designed to help researchers solve some of their computational problems without spending a lot of time dealing with programming details through Matlab functions. This tutorial starts with a quick review of Matlab's syntax and I/O handlers. In addition, the tutorial will cover the use of some computational functions and toolboxes.


    To enhance the tutorial, users are encouraged to contact the User Support Staff (help@msi.umn.edu or 612-626-0802) with any current Matlab-specific issues. This valuable input will be used in the tutorial.


    This tutorial will consist of two parts:

    1) A 50-minute lecture describing the MATLAB functions

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


  • Thu Aug 10, 1:00 pm - 3:00 pm
    405
    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 tutorial covers the basic biomolecular building and visualization features within InsightII, in addition to demonstrating its interface to some of its molecular modeling modules.


  • Tue Aug 8, 1:00 pm - 3:00 pm
    138
    Cargill Building

    Mascot from Matrix Science is a popular program for proteomics research. It has a powerful search engine that uses mass spectrometry data to identify a protein from a primary sequence database.


    This tutorial will introduce the main functionalities of the Mascot package, including peptide mass fingerprint, sequence query, and MS/MS ion search. We will also discuss how to use Mascot Distiller and Mascot Daemon for batch search job submission.


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

    This tutorial will discuss the general techniques for optimizing computing code and performance tuning on the Altix.


    Users will have a chance to learn through hands-on examples how to use hardware counters and profiling tools for code performance evaluation, tuning, memory usage, and I/O characteristics. In addition, we will discuss some tips on how to improve the performance of an application by using tuned libraries and compiler options.


  • Thu Jul 27, 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.


  • Tue Jul 25, 1:00 pm - 3:00 pm
    402
    Walter Library

    Do you want to try something user-friendly and closely related to S-PLUS to analyze microarray data? S+ARRAYANALYZER is an S-PLUS module that is a GUI (graphical user interface) driven tool for microarray data analysis. It provides a collection of powerful methods for analyzing Affymetrix MAS 5, CHP, CEL data, and two-channel microarray data.


    This tutorial will demonstrate how to use the GUI to import data and to initiate a statistical analysis through the menu (or the command line).


  • Thu Jul 20, 10:00 am - 4:00 pm
    585
    Walter Library

    OpenMP is a parallel programming interface for shared-memory architectures and is available on the IBM Regatta and the SGI Altix. This one-day workshop will help users to use OpenMP programming more productively for high-performance computing by addressing the different aspects of OpenMP, such as parallel and worksharing constructs, data scope attribute clauses, and synchronization constructs. In addition, the new features in the OpenMP II standard will be covered.


    A hands-on practice will follow the lecture. Examples provided will enable the users to insert OpenMP directives for different parallel tasks and data scope attribute clauses. The users are also encouraged to bring in their serial application codes. The User Support Staff will help you parallelize the code with OpenMP.


  • Tue Jul 18, 1:00 pm - 3:00 pm
    402
    Walter Library

    Schrödinger, Inc. provides a wide range of computational chemistry and molecule modeling software packages that are used to build, display, manipulate, simulate, and calculate molecular properties. Maestro is the common graphic user-interface that acts as a front-end to many of these tools. This tutorial covers the basic biomolecular building and visualization features within Maestro. It will also demonstrate its interface with some of its molecular modeling and computational chemistry modules.


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