All Tutorials

  • Thu Dec 6, 1:00 pm - 3:00 pm
    402
    Walter Library

    Analyst software is used to control Applied Biosystems/MDS SCIEX mass spectrometers and other devices, configure the devices attached to instrument workstations, turn instruments, optimize systems, acquire samples, perform qualitative analysis, perform quantitative analysis, and print reports. BioAnalyst software analyzes mass spectrometry data obtained from biological samples. You can perform mass reconstruction, sequence peptides, search databases, display sequence information, perform theoretical enzyme digests of protein sequences, and consult a data dictionary. This tutorial will cover how to use Analyst QS and BioAnalyst to view and analyze mass spectrometry data.


  • Tue Dec 4, 1:00 pm - 3:00 pm
    575
    Walter Library

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


  • Thu Nov 29, 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 will 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.


  • Tue Nov 27, 1:30 pm - 3:00 pm
    575
    Walter Library

    The CCP4 suite is a large collection of programs used in most of the computations involved in protein x-ray crystallography. The package includes the programs necessary to solve x-ray crystal structures and includes a convenient GUI interface to do most calculations.


    This tutorial will delve into the CCP4 package and cover some of the more advanced features that the introductory course did not cover, using both a lecture and an open discussion format.


    Please contact Can Ergenekan during the semester if there is a particular topic you would like discussed.


  • Thu Nov 15, 1:00 pm - 3:00 pm
    575
    Walter Library

    The Expressionist version Pro4.0 is a comprehensive microarray data analysis system. It provides many analysis methods. In this tutorial we will demonstrate some of these complicated methods including raw data inspection, N-Way ANOVA, volcano plot, Fisher's Exact test for annotation, profile shift analysis and periodogram, Ranking, Maximal Order Preserving set (MOPS), regression, Operon identification, and analysis workflow.


  • Tue Nov 13, 1:00 pm - 3:00 pm
    575
    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.


    This hands-on tutorial will introduce 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. We will practice these features using demo data.


  • Thu Nov 8, 1:00 pm - 3:00 pm
    575
    Walter Library

    Tecplot is a software package for 2D or 3D visualization of technical data obtained from analysis, experiments, and simulations. The objective of this tutorial is to teach users how to use Tecplot. This tutorial consists of three parts:


    1. A lecture describing the capabilities of Tecplot.

    2. An introduction to different graphing capabilities.

    3. A hands-on session focusing on the use of this tool for your practical applications.


  • Tue Nov 6, 1:00 pm - 3:00 pm
    402
    Walter Library

    The GCG Wisconsin Package is an integrated collection of tools for molecular biology. It includes more than 130 programs/applications for sequence analysis, database searching, DNA/RNA secondary structure, fragment assembly, gene identification, pattern analysis, and many others.


    This tutorial will cover: UNIX basic for using GCG, overview of GCG, how to get started, command line with GCG, and seqLab GUI interface for GCG.


  • Thu Nov 1, 10:00 am - 4:00 pm
    575
    Walter Library

    OpenMP is a parallel programming interface for shared-memory architectures and is available on the IBM Regatta, the Blade Center, the SGI Altix and Calhoun. This workshop will help users to use OpenMP programming more productively for high-performance computing by addressing the different aspects of OpenMP, such as parallel and worksharing constructs, data scope attribute clauses, and synchronization constructs. In addition, the new features in the OpenMP II standard will be covered. A hands-on practice will follow the lecture. Provided examples will enable users to insert OpenMP directives for different parallel tasks and data scope attribute clauses. Users are also encouraged to bring in their serial application codes. The User Support staff will help you parallelize the code with OpenMP.


  • Tue Oct 30, 1:30 pm - 3:00 pm
    402
    Walter Library

    CHARMM (Chemistry at HARvard Macromolecular Mechanics) is an academically and commercially distributed software for molecular dynamics (MD) simulations. It is used extensively to simulate the dynamic behavior of molecular and biomolecular systems as well as free energy calculations. This tutorial will cover the basic fundamental theory of MD simulation and how an MD simulation can be used to study the conformational dynamics of a biomolecular system. This tutorial will also show you how to write simple command files for doing a simple MD simulation and how to carry out a typical analysis in CHARMM.


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