All Tutorials

  • Thu Jul 5, 1:00 pm - 3:00 pm
    575
    Walter Library

    Proteomics research includes the characterization of protein mixtures in order to understand complex biological systems and determine relationships between proteins, their function, and protein-protein interactions. Established methods for relative quantitation of proteins involve growth on an isotope-enriched medium or chemical or enzymatic modifications. Recently, an MS/MS-based quantitation method (iTRAQ) has been developed. This tutorial will cover an overview of iTRAQ technology and the software for iTRAQ data analysis, ProteinPilot. Sample iTRAQ data, analysis and how to work with the results for each of the searches available in ProteinPilot will be described.


  • Thu Jun 28, 1:00 pm - 4:00 pm
    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.


  • Tue Jun 26, 1:00 pm - 3:00 pm
    575
    Walter Library

    This hands-on workshop focuses on an introduction to relational databases and structural query language (SQL). Participants will have an opportunity to practice creating and querying databases in an Oracle environment. Topics will include a brief overview of relational database design concepts and principles, and conceptual data models and constraints.


  • Thu Jun 21, 1:00 pm - 3:00 pm
    585
    Walter Library

    Two-channel microarray shows special strength for small genomes such as bacteria microarray studies. There are several software packages for two-channel microarray image analysis. BlueFuse is a new program developed by Cambridge BlueGnome Ltd. It does automatic grid placement, quantification, spot confidence estimation, and multiple-image batch processing using Bayesian algorithms. It also comes with many normalization protocols based on different image conditions. BlueFuse also provides CGH (Comparative Genomic Hybridization) analysis for tiling arrays.


    In this tutorial we will walk through the image analysis of BlueFuse using demo data.


  • Wed Jun 20, 1:00 pm - 3:00 pm
    402
    Walter Library

    Gaussian is a program that can be used to calculate a variety of chemical properties and is primarily used for carrying out electronic structure calculations. This tutorial will give an overview of the program capabilities, a detailed description of how to run the program at the Institute, and tips on how to run jobs efficiently.


  • Tue Jun 19, 10:00 am - 5:00 pm
    585
    Walter Library

    Ingenuity Pathways Analysis (IPA) is a software tool/database to model, analyze and understand complex biological systems.


    This training will cover basic and advanced usage of IPA, including the advanced search and reporting features. Example use-cases will be used to highlight functionality. Special topics, Q&A and hands-on sessions will follow the formal presentation. Users are encouraged to bring their own datasets to upload and analyze during this portion of the workshop.


    10:00 am - 11:30 am Introduction to Ingenuity Pathways Analysis


    11:30 am - 12:30 pm Lunch break


    12:30 pm - 1:45 pm Beginning training hands-on session


    1:45 pm - 2:00 pm Break


    2:00 pm - 3:15 pm Intermediate training hands-on session


    3:15 pm - 3:30 pm Break


    3:30 pm - 5:00 pm Advanced training hands-on session


  • Thu Jun 14, 1:00 pm - 3:00 pm
    402
    Walter Library

    This tutorial will introduce hardware, software, database resources and user support for bioinformatics researchers at the Supercomputing Institute. The main focus will be on the more than 100 software tools covering sequence analysis, functional genomics, proteomics, and database development, etc.


  • Thu Jun 14, 10:00 am - 4:00 pm
    585
    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 the Institute's IBM Power4, the SGI Altix, and the Netfinity Cluster. 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 introduces basic principles, and the hands-on portion focuses 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 Alltoall.


    Programming will be done in Fortran and C, so any background in these two languages will be helpful.


  • Tue Jun 12, 1:00 pm - 3:00 pm
    402
    Walter Library

    Schrödinger, Inc. provides a wide range of computational chemistry and molecular modeling software packages that are used to build, display, manipulate, simulate, and calculate molecular properties. Maestro is the common graphic user-interface that acts as a front-end to many of these tools. This tutorial covers the basic biomolecular building and visualization features within Maestro. We will also demonstrate its interface with some of its molecular modeling and computational chemistry modules.


  • Thu Jun 7, 1:00 pm - 3:00 pm
    402
    Walter Library

    PERL is a scripting language that can make writing and maintaining scripts for various UNIX tasks considerably easier than using one of the many shell languages. For example, PERL is very useful for retrieving output from files of completed jobs for use in reports, input to subsequent jobs, and so forth. PERL scripts are often very portable, since PERL is supported on virtually all computer platforms. PERL scripts can be extremely simple or complicated and powerful.


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