All Tutorials

  • Wed Aug 10, 9:30 am - 11:30 am
    575
    Walter Library

    Genedata provides a suite of powerful tools for the analysis, integration, visualization, and interpretation of experimental data in life science R&D. Genedata will conduct a demonstration of the Refiner MS module for processing mass spectrometry data, including workflows for both proteomics and metabolomics.


    Genedata Refiner MS allows users to process and visualize mass spectrometry data from all major technology platforms (i.e., LC-MS, LC-MS/MS, MSn, GC-MS, labeled and label-free MS, MRM, and Infusion MS). In this session, both a proteomics and metabolomics workflow will be demonstrated in the live software.


  • Tue Aug 9, 1:00 pm - 4:00 pm
    402
    Walter Library

    Genedata provides a suite of powerful tools for the analysis, integration, visualization, and interpretation of experimental data in life science R&D. Genedata will conduct a 3-session, on-site training for the Genedata Analyst module with a focus on expression data, as well as integrating across data types (e.g., microarray, mass spectrometry, qPCR and associated metadata). The training will also provide an overview of the Genedata Refiner Genome module for next-generation sequencing data.


    Genedata Refiner Genome allows users to process, analyze, and visualize massive amounts of data in the context of genomic positions. All major technologies are supported, such as next-generation sequencing and high-density microarrays (e.g., RNA expression, gene regulation, DNA methylation, SNP analysis, copy number variation, etc.), and data are visualized with a genomic browser capable of displaying terabytes of data. Genedata will train users on genomic data processing in Refiner Genome, including data pre-processing; combining data from different technology platforms; performing genomic position dependent analyses; creating new genomic or sequence annotations; and condensing data to selected genomic features.


  • Tue Aug 9, 11:30 am - 12:30 pm
    402
    Walter Library

    Genedata provides a suite of powerful tools for the analysis, integration, visualization, and interpretation of experimental data in life science R&D. Genedata will conduct a 3-session, on-site training for the Genedata Analyst module with a focus on expression data, as well as integrating across data types (e.g., microarray, mass spectrometry, qPCR and associated metadata). The training will also provide an overview of the Genedata Refiner Genome module for next-generation sequencing data.


    Genedata Analyst allows scientists of all levels to run in-depth statistical analyses for many purposes, including data normalization, marker identification, clustering, classification, survival curve analysis, and biological pathway analysis. In this session, we will demonstrate integration of data analysis from different technology platforms, as well as QPCR data processing, linking to outside resources and data management.


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

    Genedata provides a suite of powerful tools for the analysis, integration, visualization, and interpretation of experimental data in life science R&D. Genedata will conduct a 3-session, on-site training for the Genedata Analyst module with a focus on expression data, as well as integrating across data types (e.g., microarray, mass spectrometry, qPCR and associated metadata). The training will also provide an overview of the Genedata Refiner Genome module for next-generation sequencing data.


    Genedata Analyst allows scientists of all levels to run in-depth statistical analyses for many purposes, including data normalization, marker identification, clustering, classification, survival curve analysis, and biological pathway analysis. An overview for processing Agilent, Affymetrix, Illumina and other expression data in Analyst, as well as methods for standardizing data processing and sharing results will be provided.


  • Thu Aug 4, 1:00 pm - 3:00 pm
    575
    Walter Library

    Nowadays, almost all desktops and laptops are equipped with multi-core facilities. Collectively, efficient use of this type of machine can have a valuable economic impact. This tutorial will help MSI users who are running sequential codes on either their desktops or MSI’s lab machines improve computing performance by taking advantage of computing power provided by the multi-core systems. It will teach the attendees a series of tactics, which can be used for speeding up their calculations, including C, FORTRAN and Matlab jobs.


  • Tue Aug 2, 1:00 pm - 3:00 pm

    This introductory level webinar combines elements from both the Introduction to MSI and Introduction to UNIX workshops to provide general assistance to new users getting started at MSI. It includes an introduction to MSI resources and a technical demonstration of commonly used UNIX tools and features.


    This tutorial utilizes UMConnect and takes place entirely online. Please register as usual. Registered users will receive meeting information by email within 24 hours of the workshop start date. To participate in the hands-on portion of the workshop, users must have access to an ssh command line tool (Putty on Windows, Terminal on Mac). Please visit http://www.oit.umn.edu/umconnect/ to ensure that your system meets the minimum requirements necessary to participate in this webinar.


  • Thu Jul 28, 1:00 pm - 3:00 pm
    575
    Walter Library
    http://tinyurl.com/orbitalk2011

    Proteomics is emerging as a powerful screening methodology for research in academic institutions and industry. LTQ Orbitrap is a popular mass spectrometer with high mass accuracy, sensitivity, and speed to generate high-quality datasets.


    This tutorial will offer an overview of proteomics workflow using an LTQ Orbitrap instrument and will go through various data analysis workflows using software programs available at MSI.


  • Tue Jul 26, 1:00 pm - 3:00 pm
    575
    Walter Library

    Python is a general purpose programming language with a rich syntax and structure. Easily extensible, Python has been adopted as the language of choice by molecular scientists to search, convert, analyze, and store data from molecular modeling, chemistry, biochemistry, solid-state materials, and other related areas. BioPython, an analog of BioPerl, additionally provides excellent support for biological computing. This tutorial will provide an introduction to reading and writing chemical formats, programmatically generating new chemical structures, and automating common computational tasks such as energy calculations and geometry optimizations.


  • Tue Jul 19, 10:00 am - 4:00 pm
    575
    Walter Library

    This one-day, hands-on workshop provides an introduction on how to write a parallel program using MPI and will help researchers write better and portable parallel codes for distributed-memory Linux clusters. The tutorial 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 will introduce basic principles, and the hands-on portion will focus on the use of MPI principles via examples.


    Session One: Introduction to basic concepts of MPI, centering on point-to-point communication.


    Session Two: MPI collective communications including broadcast, gather, scatter, and All-to-All. Programming will be done in Fortran and C, so any background in these two languages will be helpful.


  • Tue Jul 12, 1:00 pm - 3:00 pm
    575
    Walter Library

    Microscopic images are mostly collected as stacks (3D) and often with time lapses (the fourth dimension). Huygens is a comprehensive deconvolution package for 3D and 4D microscopy.


    This tutorial will introduce users to image processing algorithms for wide-field and confocal microscopes. It will demonstrate practical applications of Huygens in deconvolution, resolution, and noise reduction for restoring images. Users will also be introduced to batch utilities in Huygens Scripting to process large numbers of image datasets automatically.


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