All Tutorials

  • Thu Jul 15, 10:00 am - 4:00 pm
    Walter Library

    OpenMP is a parallel programming interface for shared memory architectures and is available on the IBM Regatta, IBM SP, and the SGI Altix. This workshop will help users better use OpenMP programming in 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 also be covered.

    A hands-on practice will follow the lecture. Provided examples will enable the users to insert OpenMP directives for different parallel tasks and data scope attribute clauses. The users are also encouraged to bring in their serial application codes. The User Support Staff will help you parallelize the code with OpenMP.

  • Wed Jul 14, 1:00 pm - 3:00 pm
    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 to 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 carry out a typical analysis in CHARMM.

  • Tue Jul 13, 1:00 pm - 3:00 pm
    Walter Library

    Tecplot is a software package for 2-D or 3-D visualization of technical data, obtained from analysis, experiments, and simulations.

    The objective of this tutorial is to teach users how to use Tecplot, especially its advanced features. This tutorial consists of two parts:

    1. A lecture to describe the capabilities of Tecplot.

    2. A hands-on part focusing on the use of this tool for your practical applications.

    Users are encouraged to contact Seema( to format their data to make the workshop more effective. Data sets will be available to use if you want to learn Tecplot, but do not have a dataset ready.

  • Mon Jul 12, 1:00 pm - 3:00 pm
    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
    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
    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
    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
    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
    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
    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.