All Tutorials

  • Wed Dec 2, 1:00 pm - 3:00 pm
    Walter Library

    eMolecules is a chemical database that aggregates purchasable compounds from hundreds of chemical vendors. The database is useful for computational lead discovery tasks such as virtual screening and combinatorial library building. This tutorial will introduce the attendee to the 9-million-compound database and computational tools useful for viewing and analyzing the library.

  • Tue Dec 1, 1:00 pm - 3:00 pm
    Walter Library

    ProteinPilot™ is a proteomics software program used for analysis of peptide tandem mass spectrometry data and for relative quantification of proteins using the iTRAQ® technology and other modes of stable isotope labeling. Raw data acquired on Applied Biosystems instruments such as MALDI-TOF/TOF 4800 or QSTAR systems is searched against protein sequence databases; the Paragon scoring algorithm provides confidence levels for protein hits, and the ProGroup algorithm tool (PMID: 17533153) groups related and homologous proteins. The highlights of the software include: a user-friendly interface, simultaneous prediction of hundreds of peptide modifications (~175) and non-tryptic cleavages, the ability to perform quantification at the protein iso-form level, and a sophisticated FDR (false discovery rate) analysis that includes protein- and peptide-level reports. The newest version of ProteinPilot™ also supports identification of peptides and proteins from data acquired on non-Applied Biosystems instruments after conversion of raw data into *.mgf file format.

    The tutorial will include an introduction to the software followed by iTRAQ® Data analysis workflow and FDR analysis overviews.

    This tutorial will be webcast. See for more information.

  • Tue Dec 1, 12:00 am - 12:00 am
    Walter Library

    Visual programming consists of creating a flow chart of operations that need to be performed. Since vtk and itk, programming libraries that perform image processing and visualization, are pipeline-based (i.e., output from one step is fed as input to the next stage), they naturally lend themselves to flow chart-based visual programming.

    MeVisLab is being developed by MeVis Research GmbH, Bremen, Germany, and works on Windows, Linux and MacOSX. The software is free for noncommercial use and supports various file formats like DICOM, jpeg, tiff, 3d Studio Max, STL, VRML, etc.

    In this talk, we will look at the basics of MeVisLab like modules, networks etc. We will supplement these definitions with some image processing and visualization examples. We will conclude with a hands-on session.

  • Tue Nov 24, 1:30 pm - 3:30 pm
    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
    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
    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
    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 for more information.

  • Thu Nov 12, 1:00 pm - 3:00 pm
    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
    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
    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.


    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


    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


    How To Share Your Analysis Project with Colleagues