All Tutorials

  • Tue Nov 24, 1:30 pm - 3:30 pm
    585
    Walter Library

    MaxQuant is a suite of algorithms for analysis of high-resolution mass spectrometry (Orbitrap and FT) data. It can be used for protein identification for non-labeled samples and identification and quantification for SILAC-labeled samples. MaxQuant includes all steps needed in a computational proteomic platform except that it uses the Mascot search algorithm for peptide identification.


    In brief, raw data acquired on Orbitrap, is processed using MaxQuant’s “Quant” module. The processed data is further searched with Mascot. Eventually, the Mascot search output files are subjected to statistic analysis and protein grouping using the “Identify” module. Apart from this, information regarding Gene Ontology, Pfam domain and TRANSFAC overrepresentation is also provided.


    In the tutorial we will discuss the algorithm, the recommended experimental setup, and hardware requirements. We will also include a walk-through of how to use MaxQuant.


  • Tue Nov 24, 1:00 pm - 3:00 pm
    575
    Walter Library

    Gaussian is a program that can be used to calculate a variety of chemical properties. Gaussian is primarily used for carrying out electronic structure calculations. This hands-on tutorial will give an overview of the program capabilities, a detailed description of how to run the program at MSI, and tips on how to run jobs efficiently. The tutorial will focus on the new features available in the 09 version.


  • Thu Nov 19, 1:00 pm - 3:00 pm
    402
    Walter Library

    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 on GS de novo Assembler, GS Mapper, and GS Amplicon Variation Analyzer.


  • Tue Nov 17, 1:00 pm - 3:00 pm
    402
    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.


    Using sample data, this tutorial will demonstrate 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.


    This tutorial will be webcast. See https://www.msi.umn.edu/support/materials.html for more information.


  • Thu Nov 12, 1:00 pm - 3:00 pm
    575
    Walter Library

    Avizo is powerful visualization software that enables data manipulation, geometry creation, and viewing in a meaningful format. This tutorial will describe the modular approach in Avizo to build a visualization framework for different scientific data types. The tutorial will also introduce concepts in computational geometry, modeling, and surface and volume rendering in Avizo. The tutorial serves varying interest groups including medicine, biology, chemistry, physics, material sciences, geophysics, astronomy, and engineering.


    Avizo evolved from Amira. Currently the packages are almost identical, but as the programs develop, Amira will be focused on the life sciences and Avizo will be focused on engineering, manufacturing, materials science, geosciences, and other industrial and scientific domains.


    This tutorial is for users who have varying levels of experience with Avizo or Amira. The tutorial will both provide an introduction to Avizo and explore the program in greater depth based on the needs of the audience.


  • Tue Nov 10, 1:00 pm - 3:00 pm
    125
    Walter Library

    VMD is designed for modeling, visualization, and analysis of biological systems such as proteins, nucleic acids, and lipid bilayer assemblies. It supports multicore processors, GPU accelerated computation, and all major operating systems. NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. It scales to hundreds of processors on high-end parallel platforms.


    This tutorial will focus on the simulation, visualization, and analysis of biological macromolecules using VMD and NAMD. Topics covered will include preparing your first NAMD simulation; viewing the trajectory in VMD; a brief introduction to ray tracing and the preparation of high-quality graphics, using the inherent stereoscopic capabilities of VMD with the immersive, active 3D visualization tools in the LMVL; and controlling these software packages with Python and tkl scripting. The support for real-time interactive molecular dynamics will be demonstrated by coupling a locally run VMD with a parallel simulation on MSI’s supercomputers. Interactivity and exploration of biological systems will be further examined with the use of a force feed back capable haptic device available to MSI users.


    This tutorial is geared to any level VMD/NAMD user. It covers advanced topics at an introductory level. Some familiarity with Unix, VMD, NAMD, Python programming, and computational chemistry methods are useful but not required.


  • Thu Nov 5, 1:00 pm - 3:00 pm
    404
    Walter Library

    As the SNP data can be rather easily generated from either next generation sequencing or resequencing arrays, the further comprehensive post processing analyses become more important.


    Helixtree is an unique and leading software application for

    population-based candidate gene, genome-wide association, and family-based SNP and CNV (copy number variation) associations with diseases, drug resistance, or other phenotype properties by using SNP data.

    It also analyzes single marker and haplotype, calculates LD and HWE, identifies tagging SNPs, and more.


    In this webnar, we will use the same projector screen and watch the demonstration. Please bring your own laptop and you can follow the demonstration by playing your own data. This is an interactive tutorial, and is a good chance to have questions and discussion.


    Outline


    Data Import & Preparation


    Importing Affymetrix/Illumina WG SNP & CN Data


    Importing/preparing phenotype data & merging with genotype data


    Merging data from different genotyping platforms or arrays


    Working with annotation files


    Quality Assurance


    Filtering SNP Data


    Principle Component Analysis


    CN Batch Effect Removal


    CN Outlier Removal


    Analysis


    SNP Association Tests


    LD & Haplotype Analysis


    Runs of Homozygosity Analysis


    CNV Detection with Segmentation


    CNV Association Test


    Visualization of Data


    Creating QQ Plots


    Creating Manhattan Plots


    Visualizing CN Data


    Using Genome Browser


    Creating Heat Map from CNV data


    Exporting Images for Publication


    Collaborating


    How To Share Your Analysis Project with Colleagues


  • Tue Nov 3, 1:00 pm - 3:00 pm
    402
    Walter Library

    The SAS system started out in the 1970s as a software package for statistical analysis, but is now a diverse family of integrated products that can be used as building blocks for constructing a complete data analysis system for data sets ranging from small to very large. In this tutorial, we provide an introduction to SAS. Among other skills, we will learn to load, create, and combine data sets in different ways, generate random samples, post results on the Web, and make simple plots. We will also cover writing basic code, using common statements and functions in SAS, and using statistical procedures. This tutorial is appropriate for people who have data that need to be processed and analyzed statistically.


    This tutorial will be webcast. See https://www.msi.umn.edu/support/materials.html for more information.


  • Thu Oct 29, 1:00 pm - 3:00 pm
    575
    Walter Library

    The Parallel Computing Toolbox software extends the MATLAB language with high-level parallel processing constructs such as parallel for-loops, distributed arrays, parallel numerical algorithms, and message-passing functions that let you exploit data and task parallelism in your applications.


    This tutorial aims at teaching MSI’s users how to convert serial MATLAB programs to parallel MATLAB programs and how to use the built-in functions.


    This tutorial consists two parts:


    1) 1-hour lecture to describe the MATLAB functions


    2) An optional 1-hour, hands-on session focusing on the use of the parallel computing toolbox.


  • Wed Oct 28, 1:00 pm - 3:00 pm
    585
    Walter Library

    MaxQuant is a suite of algorithms for analysis of high-resolution mass spectrometry (Orbitrap and FT) data. It can be used for protein identification for non-labeled samples and identification and quantification for SILAC-labeled samples. MaxQuant includes all steps needed in a computational proteomic platform except that it uses the Mascot search algorithm for peptide identification.


    In brief, raw data acquired on Orbitrap, is processed using MaxQuant’s “Quant” module. The processed data is further searched with Mascot. Eventually, the Mascot search output files are subjected to statistic analysis and protein

    grouping using the “Identify” module. Apart from this, information regarding Gene Ontology, Pfam domain and TRANSFAC overrepresentation is also provided.


    In the tutorial we will discuss the algorithm, the recommended experimental setup, and hardware requirements. We will also include a walk-through of how to use MaxQuant.


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