All Tutorials

  • 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

  • Tue Nov 3, 1:00 pm - 3:00 pm
    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 for more information.

  • Thu Oct 29, 1:00 pm - 3:00 pm
    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
    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.

  • Wed Oct 28, 10:30 am - 12:00 pm
    Walter Library

    Computational modeling of proteins is a complex task, and there are many computational tools out there to answer many types of questions. The goal of this lecture is to give those not familiar with the tools of protein molecular mechanics an idea what tools are available in the field and what kind of questions they can help answer.

    This tutorial will touch on a wide array of computational techniques used to model protein structure, including Energy Minimizations, homology modeling, Monte Carlo simulations, and various types of Molecular Dynamic simulations, and will discuss what kind of information can be gathered from such techniques.

  • Tue Oct 27, 1:00 pm - 3:00 pm
    Walter Library

    EnSight is a post-processing package for scientific and engineering data. EnSight provides a set of tools to help with many types of analysis, visualization and communication. With EnSight you can create contours, isosurfaces, particle traces, vector arrows, elevated surfaces, profile plots and much more. Ensight also supports animation and VR.

    Dave Baumgartner, Senior Software Developer from CEI, makers of Ensight, will be presenting the Ensight tutorial. There will be an opportunity for you to speak directly with Dave about your research projects. If you would like to see a particular topic included in the tutorial or would like to schedule time to speak with Dave, contact Nancy Rowe at

  • Thu Oct 22, 1:00 pm - 3:00 pm
    Walter Library

    Understanding the regulatory mechanisms of gene expression is the major function of genomics. The Trans/Cis-regulatory elements are regions of DNA or RNA that regulate the expression of genes. Except the experimental discovery, many bioinformaticians have developed various algorithms for predicting transcriptional regulatory mechanisms from the sequence, gene expression and interaction data. MSI has several such tools and databases for Trans/Cis-regulatory element analysis.

    This tutorial will introduce tools for Trans/Cis-regulatory element analysis including Transfac, MEME, Hmmer, and Bioprospector, and will demonstrate their use using sample sequence data.