All Tutorials

  • Wed Oct 1, 1:00 pm - 3:00 pm
    575
    Walter Library

    The CCP4 suite is a collection of programs used in most of the 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 suite and its use, as well as a detailed description of how to run the program here at MSI, including how to run some of the basic programs initially used in refining protein structures like Molrep and Refmac.


  • Tue Sep 30, 1:00 pm - 3:00 pm
    402
    Walter Library

    EMBOSS (European Molecular Biology Open Software Suite) is a free open-source package designed for the needs of the molecular biology community. Currently, EMBOSS has approximately 100 applications that cover several areas of molecular biology: sequence alignment, database searching, protein motif identification, and many others.


    This tutorial will cover an overview of software, file and database for EMBOSS, DNA sequence analysis and protein sequence analysis, protein primary and secondary structure, etc.


  • Thu Sep 25, 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 MSI?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.


  • Tue Sep 23, 1:00 pm - 3:00 pm
    402
    Walter Library

    MATLAB is an integrated technical computing environment that combines numeric computation, graphics and visualization, and a high-level programming language. MATLAB includes hundreds of functions for data analysis and visualization, numeric and symbolic computation engineering, and scientific graphics modeling and simulation.


    This tutorial consists of two parts:

    1) A 90-minute lecture describing the use of computation and visualization functions and tools.


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


  • Thu Sep 18, 10:00 am - 4:00 pm
    575
    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 work sharing 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. Provided examples 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. User Support staff will help you parallelize the code with OpenMP.


  • 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.


Pages