All Tutorials

  • 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.


  • 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.


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