All Tutorials

  • Thu Apr 16, 9:00 am - 10:30 am
    575
    Walter Library

    With the development of genomics and proteomics, many biologists now need to handle large amounts of data for their research. Bioinformatics programming, especially Perl programming, is a tool well-suited for biological data manipulation and analysis.


    This tutorial will introduce the fundamental concepts and mechanisms of computer programming. We will use practical examples to demonstrate how to write the Perl codes to do transcription, translation, batch sequence retrieval, promoter sequence extraction from genomic DNA, motif scanning, query gene ontology database, etc. Through these examples, you will learn how bioinformatics programming can make your work easier and more efficient.


  • Tue Apr 14, 9:00 am - 11:00 am
    402
    Walter Library

    This seminar will present the power of COMSOL Multiphysics for finite element modeling of various phenomena. A step-by-step introduction to the finite element modeling process will be shown on a model that combines electro-thermal heating and structural mechanics.


    The capabilities of COMSOL in other areas will be presented, specifically in electromagnetics, structural mechanics, heat transfer, fluid flow, and chemical engineering. Time-permitting, more advanced topics will be covered, including acoustics, piezoelectric modeling, multiphase flow modeling, and using COMSOL on supercomputers, as well as the new features of COMSOL Multiphysics 3.5a.


    For more information, see http://www.comsol.com/events/cmms/6990/.


  • Thu Apr 9, 1:00 pm - 3:00 pm
    575
    Walter Library

    This is a hands-on workshop introducing relational databases and structural query language (SQL). Attendees will practice creating and querying databases in an Oracle environment. Topics include a brief overview of relational database design concepts and principals, and conceptual data models and constraints.


  • Tue Apr 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.


  • Mon Apr 6, 10:00 am - 2:00 pm
    402
    Walter Library

    Join us for an overview of GPU Computing, the CUDA parallel programming model, and Tesla GPU computing products for computational scientists and researchers.


    Experts from NVIDIA and University of Minnesota Fellow David Lilja will talk about their experience using CUDA and ongoing work with GPU computing. In addition, NVIDIA will be present to offer a demonstration of the Tesla Personal Supercomputer. There will also be an introduction and demo of the software Jacket. The Jacket software allows for Matlab code to be run on GP/GPUs. Lunch will be served.


    Who should attend?


    Professors and researchers working in the life sciences, engineering, finance or medicine who are interested in learning more about high-performance computing using GPU technology from NVIDIA.


    Agenda:


    10:00 Registration/check in (room 402)


    10:10 NVIDIA Tesla Hardware Overview (room 402)


    10:30 CUDA Tesla Research Topics - Life Sciences Focus


    11:00 NVIDIA Research's Michael Garland - Introduction to using CUDA (room 402)


    12:00 Lunch and demos


    12:30 UMN's David Lilja's Experience with CUDA and GP/GPU Computing (room 575)


    1:00 Jacket Software Overview and Demo (room 575)


    1:45 Velocity Micro - Visual Supercomputer Overview (room 575)


    1:50 Q&A and hands-on demos (room 575)


    NOTE: You must register by Friday, April 3.


  • Thu Apr 2, 1:00 pm - 3:00 pm
    575
    Walter Library

    Analyzing the differential expression of genes, the annotation of groups of genes, or the significance of SNPs requires careful analysis in order to ensure that the resulting conclusions represent real biological phenomena and are not an artifact of random chance or a superficial statistical analysis. In this tutorial, we provide an introduction and extensive discussion of how to use the recently developed approach of Gene Set Enrichment Analysis (GSEA) and related techniques, which can be used to find functionally important groups of genes. An important part of this approach is a careful consideration of multiple hypothesis testing, so we also discuss statistical techniques for this task, including the Bonferroni correction and false discovery rate (FDR). In addition to giving a basic conceptual introduction to these topics, we will identify the appropriate software, including MATLAB and R routines, to use to perform this type of analysis for real applications.


    Prerequisites: This course requires some knowledge of SNP and microarray analysis, as well as a good understanding of basic statistical concepts. However, since the goal of the course is to give users a practical introduction in how to apply these techniques, an advanced statistical background is not necessary. Some knowledge of either MATLAB or R would be helpful.


  • Thu Mar 26, 1:00 pm - 3:00 pm
    575
    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


  • Tue Mar 24, 1:00 pm - 3:00 pm
    125
    Walter Library

    The Schrodinger software suite is a full-featured molecular modeling package designed to solve real world problems in pharmaceutical, biotechnology, and materials science research. One major advantage over other computational chemistry packages is that little to no text editing, scripting, or other manual preparation of files is necessary to get started with the suite. This introduction to molecular modeling will focus on developing input and setting up calculations with the front-end GUI Maestro, various molecular mechanics and dynamics calculations, and the technical aspects of docking, quantum mechanics, and QM/MM studies.


  • Thu Mar 12, 10:00 am - 4:00 pm
    575
    Walter Library

    OpenMP is a parallel programming interface for shared-memory architectures and is available on all the core clusters. This one-day workshop will help you 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, we will cover the new features in the OpenMP II standard.


    Hands-on practice will follow the lecture. Users will learn to insert OpenMP directives for different parallel tasks and data scope attribute clauses. You are also encouraged to bring in their serial application codes. MSI user support staff will help you parallelize the code with OpenMP.


  • Tue Mar 10, 1:00 pm - 3:00 pm
    575
    Walter Library

    MSI has recently purchased the incentive version of PyMOL (iPyMOL), which includes many new features and options for viewing and creating figures and movies for manuscripts and presentations.


    This hands-on tutorial will give users already familiar with PyMOL or other modeling software a working knowledge of the new features of iPyMOL.


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