All Tutorials

  • Wed Sep 28, 1:00 pm - 3:00 pm
    Online

    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.


    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. Please visit http://www.oit.umn.edu/umconnect/ to ensure that your system meets the minimum requirements necessary to participate in this webinar.


  • Tue Sep 27, 4:00 pm - 6:00 pm
    575
    Walter Library

    The UNIX operating system is a fundamental part of the MSI experience for people using the labs’ Linux workstations and core systems. Many of MSI’s scientific codes require that the user understand basic UNIX operating commands and functionality. This tutorial will give the novice user a hands-on guide to using the UNIX operating environment to navigate around and use MSI resources.


  • Tue Sep 27, 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.


  • Thu Sep 22, 1:00 pm - 3:00 pm
    402 and 575
    Walter Library

    The UNIX operating system is a fundamental part of the MSI experience for people using the labs’ Linux workstations and core systems. Many of MSI’s scientific codes require that the user understand basic UNIX operating commands and functionality.


    This tutorial will give the novice user a hands-on guide to using the UNIX operating environment to navigate around and use MSI resources.


  • Tue Sep 20, 10:00 am - 3:00 pm
    402
    Walter Library

    This workshop, presented by Partek, will provide an overview of all the features and capabilities of the next generations sequencing and microarray data analysis in the Partek Genomics Suite software package. It will also introduce Partek® Flow™, a new software package from Partek for web-based analysis and alignment of Next Generation Sequencing data.


    The morning session will run from 10am to 12pm, and will focus on microarray data analysis. The following workflows will be discussed:


    - Gene Expression


    - MicroRNA


    - Copy Number


    - Exon


    - ChIP-on-Chip


    The afternoon session will run from 1pm to 3pm, and will focus on next generation sequencing data analysis. The following workflows will be discussed:


    - RNA-Seq Data Analysis


    - ChIP-Seq Data Analysis


    - DNA Methylation


    *Pizza will be provided during lunch.


  • Thu Sep 15, 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 users to use OpenMP programming more productively for high-performance computing by addressing the different aspects of OpenMP, such as parallel and worksharing 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. Examples we provide will enable you to insert OpenMP directives for different parallel tasks and data scope attribute clauses. You are also encouraged to bring in your serial application codes. The instructors will help you parallelize the

    code with OpenMP


  • Tue Sep 13, 1:00 pm - 3:00 pm
    575
    Walter Library

    The UNIX operating system is a fundamental part of the MSI experience for people using the labs’ Linux workstations and core systems. Many of MSI’s scientific codes require that the user understand basic UNIX operating commands and functionality. This tutorial will give the novice user a hands-on guide to using the UNIX operating environment to navigate around and use MSI resources.


  • Fri Aug 19, 1:00 pm - 3:00 pm
    585
    Walter Library

    ProTIP is a package of services that integrates analysis tools into the TROPIX framework. As part of the ProTIP project, standard analysis tools such as Sequest, X!Tandem, and Scaffold are executable from within the TINT graphical interface.


    The tutorial will also include a walk-through on using ProTIP and new features included in ProTIP.


  • 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.


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