All Tutorials

  • Mon Jul 12, 1:00 pm - 3:00 pm
    402
    Walter Library

    GeneSpring is one of the most widely used microarray analysis software packages. Besides many analysis and statistic tools, it provides flexible normalization methods, and is powerful for both one-channel and two-channel data analysis. Gene annotation and gene ontology grouping is another strength of GeneSpring.


    This tutorial will demonstrate with test data how to use GeneSpring, including loading data, creating experiment, normalization, filtering, clustering, group comparisons, gene list Venn diagram, and gene ontology.


  • Thu Jul 8, 1:00 pm - 3:00 pm
    101
    Walter Library

    Microarrays are becoming very popular and important tools for understanding gene expression. Proper interpretation of the results requires a reasonable understanding of the statistics involved in analyzing the data.


    This tutorial is designed to give an explanation of the necessary statistical concepts for interpreting the results from microarray experiments. We will incorporate the most frequently used tools in GeneData Expressionist to demonstrate and aid in understanding the statistics behind the tools.


    In the first section we will cover topics like viewing and describing data, such as histograms and box plots. We will also cover some topics in the basics of hypothesis testing and analysis of variance.


  • Wed Jul 7, 1:00 pm - 3:00 pm
    402
    Walter Library

    The purpose of visualization is to analyze, understand and communicate information contained within computed data. There are various tools and techniques in computer graphics that enable raw data to be visualized in 2D-3D form.


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


  • Tue Jul 6, 1:00 pm - 3:00 pm
    585
    Walter Library

    Relational Database is a type of database management system (DBMS) that stores data in the form of related tables. It has been widely used in scientific research and industry. SQL is the standard language for accessing relational database management system.


    The topics which will be discussed in this tutorial:


    1) A brief overview of relational database design concepts and principals


    2) Conceptual data model, data, and constraints


    3) Introduction to Structural Query Language (SQL)


    4) A demonstration on how to create database and tables, input data, and retrieve or query data from database using Oracle database.


  • Thu Jul 1, 1:00 pm - 3:00 pm
    138
    Cargill Building

    Motifs are conserved regions in protein or nucleic acid sequences that are predictive for structures and functions of these sequences. There are a few motif analysis programs and databases publicly available. They are extensively used for individual sequence structural or functional analysis and genome sequence annotations.


    This tutorial will review all these motif programs and databases and demonstrate Pfam and InterProScan software.


  • Wed Jun 30, 1:00 pm - 3:00 pm
    402
    Walter Library

    Molecular modeling is a general term that covers a wide range of molecular graphics and computational chemistry techniques that is used to build, display, manipulate, simulate, and calculate molecular properties. InsightII is a graphic user interface that acts as a front end to many of these molecular modeling tools.


    This tutorial covers the basic biomolecular building and visualization features within InsightII, in addition to demonstrating its interface to some of its molecular modeling modules.


  • Tue Jun 29, 10:00 am - 4:00 pm
    585
    Walter Library

    This one day workshop will help researchers write better and portable parallel codes. 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.


    The workshop will combine lecture with hands-on practice. The lecture introduces basic principles and the hands-on portion focuses on the use of MPI principles via the selected examples. Programming will be done in FORTRAN or C, so any background in these two languages is helpful.


  • Mon Jun 28, 1:00 pm - 3:00 pm
    402
    Walter Library

    This tutorial is designed to help users run Gaussian calculations effectively on the Institute resources. The tutorial will include how to submit jobs, how to interpret some calculations, and how to visualize results.


  • Fri Jun 25, 1:00 pm - 3:00 pm
    402
    Walter Library

    Molecular modeling is a general term that covers a wide range of molecular graphics and computational techniques that are used to build, display, manipulate, simulate, and calculate molecular properties. Cerius2 and MaterialStudio are two graphic user interfaces that act as a front end to many of these molecular modeling tools.


    This tutorial covers the basic molecular crystals building and visualization features within these two interfaces, in addition to demonstrating some of their utility modules.


  • Thu Jun 24, 1:00 pm - 3:00 pm
    402
    Walter Library

    Statistics are very important to many scientific research projects. R and S-PLUS are powerful statistical computing environments available at the Supercomputing Institute. The S language and environment was developed in the 1980s by Bell Laboratories for data analysis. S was further developed into a commercial product called S-PLUS. R is a dialect of the S language.


    This tutorial will demonstrate how to read and manipulate data in the R and S-PLUS environments. In addition, attendees will learn how to perform basic statistical analysis and how to produce graphics with the software packages.


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