All Tutorials

  • Tue Jun 2, 2:15 pm - 3:15 pm
    402
    Walter Library

    This tutorial is a general introduction to the UNIX operating system and other basic operations needed to use MSI’s resources. We include information on how to set up accounts and submit jobs on the various machines.


  • Tue Jun 2, 1:00 pm - 2:15 pm
    402
    Walter Library

    The Minnesota Supercomputing Institute provides high-performance computing resources, specialized research software, and user support to research groups at the University. This tutorial will give you an introduction to MSI’s facilities, personnel, and services, including a tour of our machine room and facilities in Walter Library.


  • Tue May 5, 1:00 pm - 3:00 pm
    138
    Cargill Building

    The Genome Sequencer (GS) FLX Titanium from Roche/454 is an ultra high-throughput instrument for conducting nucleotide sequencing. It potentially can generate one million sequencing readings with an average reading at about 400 nucleotides long within a single operation run. This tutorial will introduce the principles of 454 sequencing technology, potential applications, data types, and data analysis. The main focus will be GS de novo Assembler, GS Mapper, and GS Amplicon Variation Analyzer.


  • Thu Apr 23, 1:00 pm - 3:00 pm
    402
    Walter Library

    Web applications written with Perl, PHP, or other scripting languages offer an easy method for researchers to collect and share data through a web interface. They also can offer intruders the opportunity to destroy data, intercept and collect passwords, or use the hosting machine for other nefarious purposes.


    This tutorial will introduce developers to basic rules for developing secure web applications. It will mention some of the online references for developers available at the University. Topics discussed will include file permissions and ownership, database interactions, passwords, https, as well as common problems in Perl and PHP applications.


  • Tue Apr 21, 1:00 pm - 3:00 pm
    575
    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 tutorial, we will explore topics suggested by users of Fluent. If you have a topic or problem you would like covered in this tutorial, please contact David Porter at porter@msi.umn.edu. Because of time, only a few topics can be covered in depth. The number of people interested and availability of time to research and develop a presentation will determine which topics are chosen for this first special topics tutorial, so get your suggestions in early. A few seed ideas that could be covered, if there is interest, are: 1) running FLUENT on multiple processors; and 2) user defined functions. This site will be updated as soon a set of topics is determined.


  • Thu Apr 16, 1:30 pm - 3:00 pm
    402
    Walter Library

    Proteomics using mass spectrometry is emerging as a powerful screening methodology. The newer generation of mass spectrometers can now generate a large amount of raw data. Analysis of this complex and huge amount of data is becoming a bottleneck in proteomics workflow. Most of the analysis is handled by commercial software programs that work optimally and sometimes exclusively with raw data generated from the associated vendor’s mass spectrometer. However, open-source software (search algorithms, conversion and data-sharing tools) is becoming available now. Although most of these tools require further testing, they offer an alternative approach to commercial software.


    This tutorial will offer an overview of proteomics workflow, with special emphasis on post-mass spectrometry data analysis. It will also introduce several software programs available in the public domain.


  • Thu Apr 16, 1:30 pm - 3:00 pm
    575
    Walter Library

    Statistics plays a key role in many scientific research projects. Increasingly, the R statistical platform is being used to perform such analysis. R, an open source version of the S statistical language developed by Bell Laboratories in the 1980s, together with its commercial offshoot, S-PLUS, are powerful computing environments and languages for statistical computing and graphics. More specifically, these software packages provide capabilities for reading a wide variety of data formats, performing simple and sophisticated data manipulations, applying statistical tests and computations, and graphing the data and the results of the statistical analysis.


    This tutorial will demonstrate how to log in to MSIs computers to get started with R and S-PLUS and how to read and manipulate data in the R and S-PLUS environments. In addition, attendees will learn to perform basic statistical analysis in R and to produce graphics. Both R and S-PLUS run on a wide variety of UNIX platforms, Windows and MacOS. They are available on the computers at MSI, including the supercomputers, providing an ideal platform for long run-time and/or large memory R or S-Plus applications.


  • Thu Apr 16, 12:00 pm - 1:30 pm
    402
    Walter Library

    This session introduces effective search strategies for research literature databases (PubMed, Web of Science), the use of citation analysis databases, and current awareness tools (RSS feeds and filters). In addition, the session will also describe the use of some personal information management tools (Connotea, Zotero).


  • Thu Apr 16, 10:30 am - 12:00 pm
    405
    Walter Library

    BLAST (Basic Local Alignment Search Tool) is a set of similarity search programs designed to compare nucleotide or protein sequences to sequence databases and calculate the statistical significance of matches. It can be used to infer functional and evolutionary relationships between sequences as well as to help identify members of gene families.


    During this tutorial, participants will learn the following:


    * The basic principles of BLAST


    * Query and databases


    * Search strategies and result intepretation


    * How to perform BLAST searches at NCBI (National Center for Biotechnology Information)


    * NetBLAST and Standalone BLAST


    * Batch BLAST search and result parsing


  • Thu Apr 16, 10:30 am - 12:00 pm
    402
    Walter Library

    Microarray is a powerful technology for biological exploration that enables researchers to simultaneously measure the level of activity of thousands of genes. It is becoming a routine experimental technique in life science research.


    This tutorial provides an overview of this technology. Topics include different microarray platforms, array design, data acquisition, data normalization, data analysis, and gene list interpretation. We will also introduce and compare several microarray software tools available at MSI.


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