All Tutorials

  • Wed Aug 4, 1:00 pm - 3:00 pm
    Nils Hasselmo Hall (NHH)

    The Basic Sciences Computing Laboratory has recently expanded its visualization capabilities. The new equipment acquired by the lab includes a 48-processor SGI Altix server, a 16-processor SGI Onyx4 system, and a 60"x48" VizEveryWhere visualization system.

    This tutorial will focus on the visualization features of Onyx4 and VizEveryWhere systems. We will describe how the system works, its capabilities, and how to get started utilizing this new resource.

  • Thu Jul 29, 1:00 pm - 3:00 am
    Walter Library

    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 Jul 28, 1:00 pm - 3:00 pm
    Cargill Building

    In today's post-genome era, scientists are trying to understand the millions of interrelations between proteins, small molecules, and phenotypes. BioPathways’ analysis tools, in conjunction with biological knowledge databases, provide a powerful computational solution to this problem.

    PathwayAssist is a piece of commercial pathway analysis software. It can help analyze the biological association networks of a given gene list. The database built-in with this system can be enriched by importing Public pathway databases or extracting text facts from pubmed.

    This tutorial will demonstrate the functionalities of this software.

  • Tue Jul 27, 1:00 pm - 3:00 pm
    Walter Library

    This tutorial will give an overview of the movie creation process in Final Cut Pro, starting from capture of digital video, editing and finally printing on your media. The tutorial will include a lecture and demonstration of how to prepare your clips for import, file formats and conversions, and setting up sequences.

    The tutorial will cover basic video editing skills such as putting scenes in order, creating transitions and cuts, and other kinds of editing to put together a project. Simple techniques of adding audio to make your presentations self-explanatory by audio clips and recording a voiceover will also be shown.

  • Thu Jul 22, 1:00 pm - 3:00 pm
    Walter Library

    Building a web interface for your database will expand the use of your database. A web-based database is more convenient for viewing and sharing data, especially in the field of bioinformatics. This tutorial will introduce how to build a web database using CGI/PERL and PHP in the Unix environment. It will cover the dynamic web page development using CGI or PHP, as well as how to connect databases such as Oracle and mySQL using DBI. SQL will also be introduced in the tutorial.

  • Wed Jul 21, 1:00 pm - 3:00 pm
    Walter Library

    LaTeX is a high-quality typesetting system, with features designed for the production of technical and scientific documentation. LaTeX has been largely used for the communication and publication of scientific documents.

    This tutorial will cover the basic commands and syntax of setting article layout, mathematical equations, lists, tables, figures and bibliographies. It will also introduce the flexible features of automatic numbering and cross referencing. A one hour hands-on component will follow the lecture to help the attendees practice the Latex commands and write an example of scientific article using LaTex.

  • Tue Jul 20, 1:00 pm - 3:00 pm
    Walter Library

    From the Web to PowerPoint presentations, animations and graphics are powerful collaboration and research tools. This tutorial will introduce some powerful tools for generating high-quality molecular images and animations for both the biologist and chemist. We will focus on the AMIRA program for producing and manipulating molecular pictures and various tools for generating animations from the created images.

  • 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.