All Tutorials

  • Thu Jul 9, 1:00 pm - 3:00 pm
    575
    Walter Library

    GeneSpring is one of the most widely used microarray software programs for both one-channel and two-channel microarray data analysis. Besides the basic statistical methods, it shows strength in various normalizations, gene annotation and gene ontology analysis, and user-friendly visualizations.


    Using test data, we will demonstrate GeneSpring functions including genome installation, data loading, experiment creation, normalization, filtering, clustering, group comparisons, gene list Venn diagram, and gene ontology, class prediction tool, gene ontology, pathway, Scripts, etc.


  • Tue Jul 7, 1:00 pm - 3:00 pm
    585
    Walter Library

    MATLAB is one of the most practical software programs used for numerical calculations and system design. MATLAB applications, however, can run much more slowly than FORTRAN and C codes for the same kind of applications. MATLAB code debugging is also an unavoidable component of application development. This tutorial will teach users how to use MATLAB’s debugging and profiling tools in addition to the basic techniques to write efficient MATLAB codes.


    A hands-on practice will follow the lecture. We will provide examples to enable participants to use the debugging and profiling tools to write an efficient MATLAB code. You are also encouraged to bring in your application codes. The user support staff will help you debug your code and/or improve the code’s performance.


  • Tue Jun 30, 1:00 pm - 3:00 pm
    575
    Walter Library

    Trying to discover patterns in data? Looking for techniques for classification and prediction? In this hands-on tutorial, we show you how to accomplish these data mining tasks using Weka. Weka is a freely available software package for knowledge analysis and pattern discovery that contains tools for data pre-processing, classification, regression, clustering, association rules, and visualization.


    In this tutorial, we go through the basic steps involved in loading data into Weka, exploring and filtering data, and applying Weka data mining tools. The main focus is on techniques for classification, such as decision trees or neural nets, but we will also explore the other capabilities of Weka (clustering, association analysis, etc.) as time allows.


  • Thu Jun 25, 1:00 pm - 3:00 pm
    575
    Walter Library

    This is a hands-on workshop introducing relational databases and structural query language (SQL). Attendees will practice creating and querying databases in an Oracle environment. Topics include a brief overview of relational database design concepts and principals, and conceptual data models and constraints.


  • Tue Jun 23, 1:00 pm - 3:00 pm
    402 and 575
    Walter Library

    MATLAB is an integrated technical computing environment that combines numeric computation, graphics and visualization, and a high-level programming language. MATLAB includes hundreds of functions for data analysis and visualization, numeric and symbolic computation engineering, and scientific graphics modeling and simulation.


    This tutorial consists of two parts:


    1. A 90-minute lecture describing the use of computation and visualization functions and tools


    2. An optional one-hour, hands-on session focusing on the use of these functions for your application


  • Fri Jun 19, 9:30 am - 3:30 pm
    575
    Walter Library

    IPA is a web-based software application that enables you to analyze data derived from expression and SNP microarrays, proteomics experiments, and small-scale experiments that generate gene lists. It also enables you to search for targeted information on genes, proteins, chemicals, and drugs, as well as build your own biological models. With IPA, you can easily search the scientific literature for insights relevant to your experiment and quickly analyze your experimental data to identify key insights.


    This seminar is appropriate for scientists with or without experimental data. Topics covered will be of interest to therapeutic area researchers, biologists, clinicians, toxicologists and bioinformaticians alike.


  • Thu Jun 18, 10:00 am - 4:00 pm
    575
    Walter Library

    The Schrodinger software suite is a full-featured molecular modeling package designed to solve real world problems in pharmaceutical, biotechnology, and materials science research. One major advantage over other computational chemistry packages is that little to no text editing, scripting, or other manual preparation of files is necessary to get started with the suite. This introduction to molecular modeling will focus on developing input and setting up calculations with the front-end GUI Maestro, various molecular mechanics and dynamics calculations, and the technical aspects of docking, quantum mechanics, and QM/MM studies.


    The Tutorial is broken up into two parts: a morning lecture from 10:00 to 12:00 in 402 Walter to demonstrate the basic functionality of the Schrodinger suite and a hands-on afternoon workshop in 575 Walter where users will get a chance to set up different models and use some of Schrodinger’s tools.


    If you would like a certain topic discussed in detail as part of workshop, please indicate what you would like to discuss in the comments section when you register.


  • Tue Jun 16, 10:00 am - 4:00 pm
    575
    Walter Library

    This one-day workshop on MPI will help researchers write better and portable parallel codes for distributed-memory machines like Linux clusters, such as MSI’s 2,048-core Intel-based cluster (Calhoun), the 1,000-core AMD cluster (Blade), and the SGI Altix Itanium-based shared-memory system. It 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 is Small,” 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 Jun 11, 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.


  • Wed Jun 10, 1:00 pm - 3:00 pm
    125
    Walter Library

    The LMVL is a large-screen visualization system capable of immersive visualization with 3D stereo projection and motion tracking. The system can be run as a large desktop enabling users to easily view their data in 3D stereo with software they already use on their desktop systems. The system can also be used to display high-resolution images. The screen is 28 feet wide by 7.5 feet high and can display a resolution of 7680 x 2048 in high resolution.


    This tutorial will teach users how to access the system and how to use the system in both stereo mode and high-definition mode. We will cover the software programs currently being used in the lab, the control system, motion tracking, etc.


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